diff --git a/Scripts/Heatmap_scripts/test_heatmaps_gap_thresh_and_min_bl.py b/Scripts/Heatmap_scripts/test_heatmaps_gap_thresh_and_min_bl.py
new file mode 100644
index 0000000000000000000000000000000000000000..14de00abeb1d895788a2e00e048a8f93fab9a8dc
--- /dev/null
+++ b/Scripts/Heatmap_scripts/test_heatmaps_gap_thresh_and_min_bl.py
@@ -0,0 +1,2912 @@
+import numpy as np
+import pandas as pd
+import re
+import warnings
+import sys
+import pickle
+import csv
+import seaborn as sns
+import matplotlib.pyplot as plt
+import time
+import os
+import wandb
+
+# os.environ["WANDB_NOTEBOOK_NAME"] = "wandb.ipynb"
+# os.environ["WANDB_SILENT"] = "true"
+# time_stamp = time.strftime("%m%d-%H%M")
+# # start a new wandb run to track this script
+# wandb.init(project="brassica_parameters_gt_mbl", name=str(time_stamp))
+
+# function for finding gaps in each columns
+def find_gaps(col, gap_threshold, m):
+ """
+ Finds the gaps in the each column of the matrix
+ col: column of the matrix
+ gap_threshold: threshold for the gap
+ m: number of rows in the matrix
+
+ returns: indices of the beginning and end of the gaps
+ """
+ # indices for ones in given column
+ indices_one = np.where(col == 1)[0]
+ # print(indices_one)
+ # calculate difference between consective indices
+ d = np.diff(indices_one)
+ # print(d)
+
+ # if the difference is bigger than the gap threshold then store them
+ initial_gaps = np.where(d > gap_threshold)[0]
+ # print(initial_gaps)
+ # number of gaps
+ r = len(initial_gaps)
+ # calculate gaps
+ gaps = np.zeros((r, 2))
+ # find the indices of beginning and end of gaps
+ gaps[:, 0] = indices_one[initial_gaps] + 1
+ gaps[:, 1] = indices_one[initial_gaps + 1] - 1
+ # fix the end of gap index for the last gap
+ if r > 0 and indices_one[-1] + 1 < m:
+ gaps = np.append(gaps, np.array([[indices_one[-1] + 1, m]]), axis=0)
+ return gaps
+
+#get the input file as an argument (collinear file)
+
+input_file = sys.argv[1]
+
+#convert the collinear file to a dataframe
+C_df_csv = pd.read_csv(input_file, sep = '\t', header=None)
+#make a copy of the dataframe
+C_df = C_df_csv.copy()
+C_df_with_head = pd.read_csv(input_file, sep = '\t')
+C_df_head = C_df_with_head.iloc[0:, 1:-3]
+#convert all the 'x' to 0 and all the other entries which are not equal to 'x' to 1 omitting first column and last three columns and first row
+# C_df_head = C_df_head.replace(r'^x$', 0, regex=True)
+# #convert all the other entries starts with a letter to 1
+# C_df_head = C_df_head.replace(r'^[a-zA-Z]', 1, regex=True)
+
+C_df_updated = C_df.iloc[1:, 1:-3]
+#convert all the 'x' to 0 and all the other entries which are not equal to 'x' to 1 omitting first column and last three columns and first row
+C_df_updated = C_df_updated.replace(r'^x$', 0, regex=True)
+#convert all the other entries starts with a letter to 1
+C_df_updated = C_df_updated.replace(r'^[a-zA-Z]', 1, regex=True)
+#set first row index starts from 0
+C_df_updated.index = C_df_updated.index - 1
+C_df_updated_copy = C_df.iloc[1:, 1:-3]
+C_df_updated_copy.columns = C_df.iloc[0,1:-3]
+C_df_updated_copy.index = C_df_updated_copy.index - 1
+GT = sys.argv[5]
+#get the number of subgenomes as a comand line argument
+n_subgenomes = int(sys.argv[4])
+
+# Split the dataframe based on the first letter of column names
+dfs = {}
+for column in C_df_head.columns:
+ print(column)
+ first_letter = column[0]
+ if first_letter not in dfs:
+ dfs[first_letter] = pd.DataFrame()
+ dfs[first_letter][column] = C_df_head[column]
+
+# Print the resulting dataframes
+for key, value in dfs.items():
+ if key == 'A':
+ continue
+ if key == 'S':
+ print(f"Dataframe with columns starting with '{key}':")
+ first_letter_get = key
+ print(first_letter_get)
+ print(value)
+ print()
+ #make C_df_new empty first
+ C_df_new = pd.DataFrame()
+ C_df_new = C_df_with_head.iloc[:, [0]].join(value).join(C_df_with_head.iloc[:, -3:])
+ value = value.replace(r'^x$', 0, regex=True)
+ #convert all the other entries starts with a letter to 1
+ value = value.replace(r'^[a-zA-Z]', 1, regex=True)
+ # Convert the dataframe to a numpy array
+ C = value.to_numpy()
+ print(C)
+ m, n = C.shape
+ print(m, n)
+ # print(m, n)
+
+
+ # gap_threshold is the threshold to determine if there is a gap or not
+ # min_block_length is the minimum length of the signal blocks
+
+ def gap_calculation(C, gap_threshold, min_block_length):
+ # get all gaps in all columns
+ gaps_cell = [find_gaps(C[:, i], gap_threshold, m) for i in range(n)]
+ break_point_indices = np.zeros(10000)
+ # for the first iteration, we only look at the best two columns
+ col_ind = np.argpartition(np.sum(C[:min_block_length, :], axis=0), -2)[-2:]
+ # print(col_ind)
+
+ if gaps_cell[col_ind[0]][0][0] <= gaps_cell[col_ind[1]][0][0]:
+ i = int(gaps_cell[col_ind[0]][0][0])
+ else:
+ i = int(gaps_cell[col_ind[1]][0][0])
+ # the first gap is our first breakpoint
+ break_point_indices[0] = i
+ # we have one break point, so count=1
+ count = 1
+ while i <= m - 1:
+ i = int(i)
+ col_ind = np.argpartition(
+ np.sum(C[i: min(m, i + min_block_length), :], axis=0), -3
+ )[-3:]
+ i_0 = gaps_cell[col_ind[0]][gaps_cell[col_ind[0]][:, 0] > i]
+ i_1 = gaps_cell[col_ind[1]][gaps_cell[col_ind[1]][:, 0] > i]
+ i_2 = gaps_cell[col_ind[2]][gaps_cell[col_ind[2]][:, 0] > i]
+ if len(i_0) == 0:
+ i_0 = [m]
+ if len(i_1) == 0:
+ i_1 = [m]
+ if len(i_2) == 0:
+ i_2 = [m]
+ i = min(np.min(i_0), np.min(i_1), np.min(i_2))
+ if abs(i - break_point_indices[count - 1]) > gap_threshold:
+ break_point_indices[count] = i
+ count += 1
+ break_point_indices = np.resize(break_point_indices, count)
+
+ if break_point_indices[-1]!= m-2 and break_point_indices[-1]!= m-1 and break_point_indices[-1]!= m:
+ break_point_indices = np.append(break_point_indices, m-2)
+ if break_point_indices[-1]== m-1 or break_point_indices[-1]== m:
+ break_point_indices = break_point_indices[:-1] + 1
+ if break_point_indices[-1]!= m-1 or break_point_indices[-1]!= m:
+ break_point_indices = break_point_indices + 1
+ return break_point_indices
+
+
+ def get_densities(C, break_point_indices, n , m):
+ # calculate densities of each block
+ b = len(break_point_indices) # number of breakpoints
+ densities = np.zeros((b, n)) # densities for each blocks
+ for i in range(b):
+ if i == 0: # for block one
+ densities[i, :] = (
+ np.sum(C[: int(break_point_indices[i]), :], axis=0)
+ / int(break_point_indices[i])
+ ).astype(float)
+ elif i == b: # for last block
+ densities[i, :] = (
+ np.sum(C[int(break_point_indices[i - 1]+1): m, :], axis=0)
+ / int(m - break_point_indices[i - 1]+1)
+ ).astype(float)
+ else: # for all else
+ densities[i, :] = (
+ np.sum(
+ C[int(break_point_indices[i - 1]+1): int(break_point_indices[i]), :],
+ axis=0,
+ )
+ / int(break_point_indices[i] - break_point_indices[i - 1]+1)
+ ).astype(float)
+ return densities
+
+ def create_excel_sheet(C_df, break_point_indices, densities):
+ # calculate row_end indices as in excel sheet
+ row_end = (break_point_indices[: len(break_point_indices)]
+ ).astype(int)
+ # row_end=np.append(row_end[:-1]+1)
+ # calculate row_start indices as in excel sheet
+ row_start = (
+ np.append(0, break_point_indices[: len(break_point_indices)-1] + 1)
+ ).astype(int)
+ # calculate number of genes
+ number_genes = (row_end - row_start+1).astype(int)
+
+ # read gene IDs from the given file
+ gene_id = C_df.iloc[:,0]
+ gene_id = gene_id.to_numpy()
+ # prepare data for gene_start and gene_end columns for excel sheet
+ gene_start = []
+ gene_end = []
+ b = len(break_point_indices)
+ for i in range(b):
+ gene_start.append(gene_id[row_start[i]])
+ gene_end.append(gene_id[row_end[i]])
+
+ E = pd.DataFrame()
+ # prepare data matrix for excel sheet
+ E = np.column_stack(
+ (np.arange(1, b + 1),
+ gene_start,
+ gene_end,
+ row_start,
+ row_end,
+ number_genes,
+ densities,
+ )
+ )
+
+ # Initialize the header list with the fixed column names
+ header = ["Block no.",
+ "Block_start",
+ "Block_end",
+ "Row start #",
+ "Row end #",
+ "# genes in block",
+ ]
+
+ # Extract the prefix letter from the column names using regex
+ prefixes = set((re.findall(r'^[A-Za-z]', col)[0], int(re.findall(r'\d+', col)[0])) for col in value.columns)
+ prefixes = sorted(set([f'N{suffix}' if suffix % 2 == 1 else f'N{suffix}.r' for _, suffix in prefixes]))
+
+ # Sort the columns by the letter prefix and the number following the letter
+ cols = sorted(value.columns, key=lambda col: (re.findall(r'^[A-Za-z]', col)[0], int(re.findall(r'\d+', col)[0])))
+
+ # Loop through the columns and update the header list
+ for i in range(0, len(cols), 2):
+ n = (i // 2) + 1
+ header.extend([f"N{n}", f"N{n}.r"])
+
+ # write matrix to excel sheet
+ df = pd.DataFrame(E, columns=header)
+ df.to_excel(f"{first_letter_get}_gene_matrix_output_Bra.xlsx",
+ sheet_name="Output", startrow = 0, startcol=0)
+
+
+
+ def get_subgenomes(filepath, num_subgenomes):
+ '''
+ This function takes the filepath of the excel sheet generated by the previous function and the number of subgenomes as input and returns a list of subgenomes
+
+ Parameters:
+ filepath (str): The filepath of the excel sheet generated by the previous function
+ num_subgenomes (int): The number of subgenomes
+
+ Returns:
+ subgenomes (list): A list of subgenomes
+ '''
+ # Read the generated break point output
+ df_temp = pd.read_excel(filepath, usecols="H:AA")
+
+ # Get the number of cells in each row where it doesn't contain a value equals to zero and store it as a value in the next column of df
+ df_temp["Non_zero"] = df_temp.iloc[:, :].apply(lambda x: x[x != 0].count(), axis=1)
+
+ # Iterate over each row and get the columnname with max and have it as a value in the next column of df disregarding the last column
+ df_temp["subgenome1"] = df_temp.iloc[:, :-1].apply(lambda x: x.sort_values(ascending=False).index[0], axis=1)
+
+ # Iterate over each row and get the second highest value's column name disregarding the last column of each row as the second highest value in the next column of df
+ df_temp["subgenome2"] = df_temp.iloc[:, :-2].apply(lambda x: x.sort_values(ascending=False).index[1], axis=1)
+
+ if num_subgenomes > 2:
+ for i in range(3, num_subgenomes+1):
+ # Iterate over each row and get the i-th highest value's column name disregarding the last (i-1) columns of each row as the i-th highest value in the next column of df
+ df_temp[f"subgenome{i}"] = df_temp.iloc[:, :-i].apply(lambda x: x.sort_values(ascending=False).index[i-1], axis=1)
+
+ return df_temp
+
+
+ # df_temp = get_subgenomes("gene_matrix_output_Bra.xlsx", n_subgenomes)
+
+ def assign_subgenomes(df_temp, file_path, num_subgenomes):
+ '''
+ Assigns the subgenomes to the blocks based on the gene density inside the blocks
+
+ Parameters
+ ----------
+ df_temp: pd.DataFrame
+ The dataframe with the gene density inside the blocks
+ file_path: str
+ The path of the file to be read
+ num_subgenomes: int
+ The number of subgenomes to be assigned to the blocks
+ Returns
+ -------
+ df: pd.DataFrame
+ The dataframe with the subgenomes assigned to the blocks
+ '''
+ # Columns with density lower than 0.1 inside a block has been removed
+ for col in df_temp.columns[:-4]:
+ for i in range(len(df_temp)):
+ if df_temp[col][i] < 0.1:
+ df_temp.at[i, col] = 0
+ warnings.filterwarnings("ignore")
+
+ # Remove last four columns
+ df = df_temp[df_temp.columns[:-4]]
+
+
+ # Assignment of the columns into subgenomes depending on gene density inside blocks
+ df.loc[:, "Non_zero"] = df.iloc[:, :].apply(
+ lambda x: x[x != 0].count(), axis=1)
+ for i in range(1, num_subgenomes+1):
+ df.loc[:, f"subgenome{i}"] = df.iloc[:, :-i].apply(
+ lambda x: x.sort_values(ascending=False).index[i-1], axis=1
+ )
+
+ # Read the generated break point output
+ df_new = pd.read_excel(file_path, usecols="A:G")
+ df = pd.concat([df_new.reset_index(drop=True), df], axis=1)
+
+ # Assignment of the columns into subgenomes depending on gene density inside blocks
+ for i in range(len(df)):
+ if i == 0 and df["Non_zero"][i] == num_subgenomes - 1:
+ if df["Non_zero"][i + 1] == num_subgenomes - 1:
+ df.at[i, f"subgenome{num_subgenomes}"] = df.at[i + 2, f"subgenome{num_subgenomes}"]
+ if df["Non_zero"][i + 1] > num_subgenomes - 1:
+ df.at[i, f"subgenome{num_subgenomes}"] = df.at[i + 1, f"subgenome{num_subgenomes}"]
+ elif df["Non_zero"][i] <= num_subgenomes - 1:
+ if df["Non_zero"][i] == num_subgenomes - 1:
+ if df.at[i, f"subgenome{n_subgenomes-1}"] != df.at[i-1, f"subgenome{n_subgenomes}"] and df.at[i, f"subgenome{n_subgenomes-2}"] != df.at[i-1, f"subgenome{n_subgenomes}"]:
+ df.at[i, f"subgenome{n_subgenomes}"] = df.at[i - 1, f"subgenome{n_subgenomes}"]
+ elif df.at[i, f"subgenome{n_subgenomes-1}"] == df.at[i-1, f"subgenome{n_subgenomes}"] and df.at[i, f"subgenome{n_subgenomes-2}"] != df.at[i-1, f"subgenome{n_subgenomes}"]:
+ if df.at[i-1, f"subgenome{n_subgenomes-1}"] != df.at[i, f"subgenome{n_subgenomes-2}"]:
+ df.at[i, f"subgenome{n_subgenomes-1}"] = df.at[i - 1, f"subgenome{n_subgenomes-1}"]
+ df.at[i, f"subgenome{n_subgenomes}"] = df.at[i - 1, f"subgenome{n_subgenomes}"]
+ elif df.at[i-1, f"subgenome{n_subgenomes-1}"] == df.at[i, f"subgenome{n_subgenomes-2}"]:
+ df.at[i, f"subgenome{n_subgenomes-1}"] = df.at[i - 1, f"subgenome{n_subgenomes-2}"]
+ df.at[i, f"subgenome{n_subgenomes}"] = df.at[i - 1, f"subgenome{n_subgenomes}"]
+
+ elif df.at[i, f"subgenome{n_subgenomes-2}"] == df.at[i-1, f"subgenome{n_subgenomes}"] and df.at[i, f"subgenome{n_subgenomes-1}"] != df.at[i-1, f"subgenome{n_subgenomes}"]:
+ if df.at[i-1, f"subgenome{n_subgenomes-2}"] != df.at[i, f"subgenome{n_subgenomes-1}"]:
+ df.at[i, f"subgenome{n_subgenomes-2}"] = df.at[i - 1, f"subgenome{n_subgenomes-2}"]
+ df.at[i, f"subgenome{n_subgenomes}"] = df.at[i - 1, f"subgenome{n_subgenomes}"]
+ elif df.at[i-1, f"subgenome{n_subgenomes-2}"] == df.at[i, f"subgenome{n_subgenomes-1}"]:
+ df.at[i, f"subgenome{n_subgenomes-2}"] = df.at[i - 1, f"subgenome{n_subgenomes-1}"]
+ df.at[i, f"subgenome{n_subgenomes}"] = df.at[i - 1, f"subgenome{n_subgenomes}"]
+
+ if df["Non_zero"][i] == num_subgenomes - 2:
+ if df.at[i, f"subgenome{n_subgenomes-2}"] != df.at[i-1, f"subgenome{n_subgenomes}"] and df.at[i, f"subgenome{n_subgenomes-2}"] != df.at[i-1, f"subgenome{n_subgenomes-1}"]:
+ df.at[i, f"subgenome{n_subgenomes-1}"] = df.at[i - 1, f"subgenome{n_subgenomes-1}"]
+ df.at[i, f"subgenome{n_subgenomes}"] = df.at[i - 1, f"subgenome{n_subgenomes}"]
+ elif df.at[i, f"subgenome{n_subgenomes-2}"] == df.at[i-1, f"subgenome{n_subgenomes}"]:
+ df.at[i, f"subgenome{n_subgenomes-2}"] = df.at[i - 1, f"subgenome{n_subgenomes-2}"]
+ df.at[i, f"subgenome{n_subgenomes-1}"] = df.at[i - 1, f"subgenome{n_subgenomes-1}"]
+ df.at[i, f"subgenome{n_subgenomes}"] = df.at[i - 1, f"subgenome{n_subgenomes}"]
+ elif df.at[i, f"subgenome{n_subgenomes-2}"] == df.at[i-1, f"subgenome{n_subgenomes-1}"]:
+ df.at[i, f"subgenome{n_subgenomes-2}"] = df.at[i - 1, f"subgenome{n_subgenomes-2}"]
+ df.at[i, f"subgenome{n_subgenomes-1}"] = df.at[i - 1, f"subgenome{n_subgenomes-1}"]
+ df.at[i, f"subgenome{n_subgenomes}"] = df.at[i - 1, f"subgenome{n_subgenomes}"]
+
+ if df["Non_zero"][i] == num_subgenomes - 3:
+ df.at[i, f"subgenome{n_subgenomes-2}"] = df.at[i - 1, f"subgenome{n_subgenomes-2}"]
+ df.at[i, f"subgenome{n_subgenomes-1}"] = df.at[i - 1, f"subgenome{n_subgenomes-1}"]
+ df.at[i, f"subgenome{n_subgenomes}"] = df.at[i - 1, f"subgenome{n_subgenomes}"]
+ return df
+
+ # df = assign_subgenomes(df_temp, "gene_matrix_output_Bra.xlsx", n_subgenomes)
+
+
+ # # Saving the file
+ # df.to_excel("subgenome_density_bra.xlsx")
+
+ #get another input file for groundtruth as a command line argument
+
+ # # Get the column names from df_subgenome_density that start with N followed by a number
+ # column_names = df.filter(regex=r'^N\d+').columns.tolist()
+
+ # # Replace the columns starting from the second column until the end of C_df_updated with the selected column names
+ # df_synteny = C_df_csv.iloc[1:,1:-3].rename(columns={C_df_csv.iloc[1:,1:-3].columns[i-1]: column_names[i-1] for i in range(1, len(column_names)+1)})
+ # #append the first column of C_df to the first column of df_synteny
+ # df_synteny.insert(0, "locus_id", C_df_csv.iloc[1:,0])
+ # #update first row index starting from 0
+ # df_synteny.index = df_synteny.index - 1
+
+ def subgenome_overlap(GT_file_path, df_subgenome_density_file_path, df_synteny, num_subgenomes, sub_no):
+ # Read the data
+ df_subgenome_density = pd.read_excel(df_subgenome_density_file_path)
+ # Create a list of subgenomes
+ subgenomes = [[] for _ in range(num_subgenomes)]
+ for i in range(len(df_subgenome_density["Row start #"])):
+ for j in range(df_subgenome_density["Row start #"].values[i], df_subgenome_density["Row end #"].values[i] + 1):
+ for k in range(num_subgenomes):
+ subgenomes[k].append(df_synteny[df_subgenome_density[f"subgenome{k+1}"].values[i]][j])
+
+ # Create a dataframe of subgenomes
+ df_subgenome = pd.DataFrame(subgenomes).transpose()
+ # Change the column names
+ df_subgenome.columns = [f"subgenome{i+1}" for i in range(num_subgenomes)]
+
+ # Load the dataframes
+ df_groundtruth = pd.read_excel(GT_file_path) # dataframe for groundtruth
+
+
+ # Check for exact matches of gene ids and 'x' between subgenome1 of both dataframes
+ exact_matches = 0
+ total_genes = 0
+ missing_genes = 0
+ missing_genes_list = []
+
+ for i, row_groundtruth in df_groundtruth.iterrows():
+ if i < len(df_groundtruth) - 1:
+ gene_id_groundtruth = row_groundtruth[f"{first_letter_get}_subgenome{sub_no+1}"]
+ if gene_id_groundtruth != "x":
+ total_genes += 1
+ if i < len(df_subgenome):
+ row_subgenome = df_subgenome.iloc[i]
+ gene_id_subgenome = row_subgenome[f"subgenome{sub_no+1}"]
+ if gene_id_groundtruth == gene_id_subgenome:
+ exact_matches += 1
+ else:
+ missing_genes += 1
+ missing_genes_list.append(gene_id_groundtruth)
+
+ # Calculate the overlap percentage for each subgenome
+ overlaps = exact_matches / total_genes
+ print(overlaps, sub_no+1)
+ return overlaps
+
+ #take gap_threshold and min_block_length which are numbers as arguments
+ gap_threshold = int(sys.argv[2])
+ min_block_length = int(sys.argv[3])
+
+ # break_point_indices = gap_calculation(C, gap_threshold, min_block_length)
+ # densities = get_densities(C, break_point_indices, n, m)
+ # create_excel_sheet(C_df_new, break_point_indices, densities)
+ # df_temp = get_subgenomes(f"{first_letter_get}_gene_matrix_output_Bra.xlsx", n_subgenomes)
+ # df = assign_subgenomes(df_temp, f"{first_letter}_gene_matrix_output_Bra.xlsx", n_subgenomes)
+ # df.to_excel(f"{first_letter_get}_subgenome_density_bra.xlsx")
+ # # Get the column names from df_subgenome_density that start with N followed by a number
+ # column_names = df.filter(regex=r'^N\d+').columns.tolist()
+
+ # # Replace the columns starting from the second column until the end of C_df_updated with the selected column names
+ # df_synteny = C_df_new.iloc[0:,1:-3].rename(columns={C_df_new.iloc[0:,1:-3].columns[i-1]: column_names[i-1] for i in range(1, len(column_names)+1)})
+ # #append the first column of C_df to the first column of df_synteny
+ # df_synteny.insert(0, "locus_id", C_df_new.iloc[0:,0])
+ # #update first row index starting from 0
+ # df_synteny.index = df_synteny.index - 1
+
+ #Input the file for chains generated in DagChainer as a command line argument
+ chains_file = sys.argv[6]
+ #Input the file for blastp generated in DagChainer as a command line argument
+ blastp_file = sys.argv[7]
+
+ def generate_heatmap(acc_matrix, subgenome_index, gap_threshold, min_block_length):
+ sub_acc_matrix = acc_matrix[subgenome_index]
+ sns.set(font_scale=1.2) # Increase the font scale to 1.2 or any desired value
+ plt.figure(figsize=(8, 10))
+ ax = sns.heatmap(sub_acc_matrix, cmap='YlGnBu', annot=True, fmt=".2f", cbar=False,
+ xticklabels=range(10, gap_threshold+1, 5), yticklabels=range(50, min_block_length+1, 10))
+ plt.title("Subgenome " + str(subgenome_index + 1) + " Accuracy Matrix")
+ plt.xlabel("Gap Threshold")
+ plt.ylabel("Minimum Block Length")
+ plt.savefig("subgenome_" + str(subgenome_index+1) + str(first_letter_get)+"_heatmap.png", dpi=300, bbox_inches='tight')
+
+
+
+ def get_breakpoints(C, C_df_new, gap_threshold, min_block_length, n_subgenomes, GT, n, m):
+ best_params = []
+ accuracies = []
+ for k in range(n_subgenomes):
+ row_k = []
+ for j in range(50, min_block_length+1, 10):
+ row_j = []
+ for i in range(10, gap_threshold+1, 5):
+ break_point_indices = gap_calculation(C, i, j)
+ densities = get_densities(C, break_point_indices, n, m)
+ create_excel_sheet(C_df_new, break_point_indices, densities)
+ df_temp = get_subgenomes(f"{first_letter_get}_gene_matrix_output_Bra.xlsx", n_subgenomes)
+ df = assign_subgenomes(df_temp, f"{first_letter_get}_gene_matrix_output_Bra.xlsx", n_subgenomes)
+ # Saving the file
+ df.to_excel(f"{first_letter_get}_subgenome_density_bra.xlsx")
+
+ df = pd.read_excel(f"{first_letter_get}_subgenome_density_bra.xlsx")
+ # Get the column names from df_subgenome_density that start with N followed by a number
+ column_names = df.filter(regex=r'^N\d+').columns.tolist()
+
+ df_synteny = pd.DataFrame()
+ # Replace the columns starting from the second column until the end of C_df_updated with the selected column names
+ df_synteny = C_df_new.iloc[0:,1:-3].rename(columns={C_df_new.iloc[0:,1:-3].columns[i-1]: column_names[i-1] for i in range(1, len(column_names)+1)})
+ #append the first column of C_df to the first column of df_synteny
+ df_synteny.insert(0, "locus_id", C_df_new.iloc[0:,0])
+ #update first row index starting from 0
+ # df_synteny.index = df_synteny.index - 1
+
+ acc = subgenome_overlap(GT, f"{first_letter_get}_subgenome_density_bra.xlsx", df_synteny, n_subgenomes, k)
+ print(acc)
+ # if k == 0:
+ # wandb.log({"acc_sub1": acc, "bl_sub1": j, "gt_sub1": i, "subgenome": k+1})
+ # elif k == 1:
+ # wandb.log({"acc_sub2": acc, "bl_sub2": j, "gt_sub2": i, "subgenome": k+1})
+ # elif k == 2:
+ # wandb.log({"acc_sub3": acc, "bl_sub3": j, "gt_sub3": i, "subgenome": k+1})
+ row_j.append(acc)
+ row_k.append(row_j)
+ accuracies.append(row_k)
+ print(accuracies)
+
+ # Generate heatmap for subgenome k
+ for l in range(n_subgenomes):
+ generate_heatmap(accuracies, l, gap_threshold, min_block_length)
+ print(accuracies)
+
+
+ # Get the highest accuracy value and its corresponding gap threshold and minimum block length values for subgenome k
+ max_acc = max([max(row) for row in accuracies[k]])
+ max_indices = [(i, j) for i, row in enumerate(accuracies[k]) for j, val in enumerate(row) if val == max_acc]
+ best_params.append((k, max_acc, max_indices))
+
+ return best_params
+
+
+ # df = pd.read_excel("subgenome_density_bra.xlsx")
+ # # Get the column names from df_subgenome_density that start with N followed by a number
+ # column_names = df.filter(regex=r'^N\d+').columns.tolist()
+
+ # # Replace the columns starting from the second column until the end of C_df_updated with the selected column names
+ # df_synteny = C_df_csv.iloc[1:,1:-3].rename(columns={C_df_csv.iloc[1:,1:-3].columns[i-1]: column_names[i-1] for i in range(1, len(column_names)+1)})
+ # #append the first column of C_df to the first column of df_synteny
+ # df_synteny.insert(0, "locus_id", C_df_csv.iloc[1:,0])
+ # #update first row index starting from 0
+ # df_synteny.index = df_synteny.index - 1
+ max_parameters = get_breakpoints(C, C_df_new, gap_threshold, min_block_length, n_subgenomes, GT, n , m)
+ print(max_parameters)
+
+#call the function to get breakpoints
+# break_point_indices = get_breakpoints(C, gap_threshold, min_block_length)
+
+
+# def get_blocks(df_subgenome_density, df_synteny, num_blocks, num_subgenomes):
+# '''
+# This function takes in the subgenome density dataframe, the synteny dataframe, the number of blocks and the number of subgenomes
+# and returns a dictionary with the blocks as the keys and the subgenomes as the values
+
+# Parameters
+# ----------
+# df_subgenome_density: pandas dataframe
+# The dataframe containing the subgenome density information
+# df_synteny: pandas dataframe
+# The dataframe containing the synteny information
+# num_blocks: int
+# The number of blocks
+# num_subgenomes: int
+# The number of subgenomes
+
+# Returns
+# -------
+# blocks: dictionary
+# The dictionary containing the blocks as the keys and the subgenomes as the values
+# '''
+# # store the blocks in a dictionary with the block number as the key
+# blocks = {}
+# for i in range(num_blocks):
+# blocks[i] = {}
+# for j in range(num_subgenomes):
+# subgenome_col = "subgenome" + str(j+1)
+# block_key = str(i) + "_" + df_subgenome_density[subgenome_col].values[i]
+# start_row = df_subgenome_density.loc[i, "Row start #"]
+# end_row = df_subgenome_density.loc[i, "Row end #"]
+# block_val = df_synteny.loc[start_row:end_row, df_subgenome_density.loc[i, subgenome_col]]
+# genes = df_synteny.loc[start_row:end_row, 'gene_id'].tolist()
+# block_val_dict = {}
+# for k in range(len(genes)):
+# sub_key = genes[k]
+# block_val_dict[sub_key] = block_val.iloc[k]
+# blocks[i][block_key] = block_val_dict
+# return blocks
+
+
+
+
+# def create_chains_dict(df_chains):
+# """
+# Creates a dictionary with keys as the zeroth column in df_chains and values as the list of values belonging to the same
+# keys in the fourth column values in df_chains.
+
+# Args:
+# df_chains: pandas dataframe containing four columns
+
+# Returns:
+# chains: dictionary with keys as the zeroth column in df_chains and values as the list of values belonging to the same
+# keys in the fourth column values in df_chains.
+# """
+# chains = {}
+# for i in range(len(df_chains[0])):
+# chains[df_chains[0][i]] = []
+# for i in range(len(df_chains[0])):
+# chains[df_chains[0][i]].append(df_chains[2][i])
+# return chains
+
+# def calculate_density(blocks_dict, num_blocks):
+# """
+# Calculates the density of each block in each subgenome.
+
+# Parameters:
+# blocks_dict (dict): A dictionary containing all the blocks and their genes for each subgenome.
+# num_blocks (int): The total number of blocks.
+
+# Returns:
+# dict: A dictionary containing the density of each block for each subgenome.
+# """
+# density_dict = {}
+# for i in range(num_blocks):
+# density_dict[i] = {}
+# for j in range(len(blocks_dict[i])):
+# subgenome_blocks = list(blocks_dict[i].values())[j]
+# num_genes = len([gene for gene in subgenome_blocks.values() if gene != "x"])
+# block_size = len(subgenome_blocks)
+# density_dict[i][list(blocks_dict[i].keys())[j]] = (
+# num_genes / block_size if block_size > 0 else 0
+# )
+# return density_dict
+
+# def calculate_pid(blocks, df, num_blocks, pickle_file):
+# '''
+# Calculates the PID of each block in each subgenome.
+
+# Parameters:
+# blocks (dict): A dictionary containing all the blocks and their genes for each subgenome.
+# df (pandas dataframe): A dataframe containing the PID values for each gene pair.
+# num_blocks (int): The total number of blocks.
+# pickle_file (str): The path to the pickle file containing the PID values for each gene pair.
+
+# Returns:
+# dict: A dictionary containing the PID of each block for each subgenome.
+# '''
+# # #Remove dot and number after dot in gene_id_AT
+# # df["gene_id_AT"] = [re.sub(r"\.\d+", "", gene_id) for gene_id in df["gene_id_AT"]]
+
+# # # Initialize the dictionary "pid"
+# # pid = {}
+# # for i in range(num_blocks):
+# # pid[i] = {}
+# # for j in range(len(blocks[i])):
+# # key = list(blocks[i].keys())[j]
+# # block = blocks[i][key]
+# # pid_values = []
+# # for sub_key in block.keys():
+# # if sub_key in df["gene_id_AT"].tolist():
+# # val = block[sub_key]
+# # # Create a dictionary to store gene_id as keys and PID as values
+# # gene_id_to_pid = dict(zip(zip(df["gene_id_Brassica"], df["gene_id_AT"]), df["PID"]))
+# # if val!="x":
+# # brassica_id = df.loc[(df["gene_id_AT"] == sub_key) & (df["gene_id_Brassica"] == val), "gene_id_Brassica"].values
+# # pid_val = gene_id_to_pid.get((brassica_id[0], sub_key), "x") if len(brassica_id) > 0 and val != "x" else "x"
+# # else:
+# # pid_val = "x"
+# # pid_values.append(pid_val)
+# # pid[i][key] = pid_values
+# # #save in pickle file
+# # with open(pickle_file, "wb") as f:
+# # pickle.dump(pid, f)
+
+# #load from pickle file
+# with open(pickle_file, "rb") as f:
+# pid = pickle.load(f)
+# return pid
+
+# def calculate_avg_pid(num_blocks, blocks, pid):
+# avg_pid = {}
+# for i in range(num_blocks):
+# avg_pid[i] = {}
+# for j in range(len(blocks[i])):
+# avg_pid[i][list(blocks[i].keys())[j]] = 0
+# if len([x for x in pid[i][list(blocks[i].keys())[j]] if x != "x"]) != 0:
+# avg_pid[i][list(blocks[i].keys())[j]] = (
+# sum([x for x in pid[i][list(blocks[i].keys())[j]] if x != "x"])
+# / len([x for x in pid[i][list(blocks[i].keys())[j]]])
+# ) / 100
+# return avg_pid
+
+
+# def process_files_weight_cal(chains_file, blastp_file, df_subgenome_density_file_path, df_subgenomes_file_path, synteny_file, pickle_file):
+# '''
+# Processes the files and returns the required dataframes.
+
+# Parameters:
+# chains_file (str): Path to the chains file.
+# blastp_file (str): Path to the blastp file.
+# df_subgenome_density_file_path (str): Path to the subgenome density file.
+# synteny_file (str): Path to the synteny file.
+# pickle_file (str): Path to the pickle file.
+
+# Returns:
+# blocks_dict: A dictionary containing all the blocks and their genes for each subgenome.
+# density_dict: A dictionary containing the density of each block for each subgenome.
+# chains_dict: A dictionary containing the chains of each block for each subgenome.
+# pid_dict: A dictionary containing the PID of each block for each subgenome.
+# avg_pid_dict: A dictionary containing the average PID of each block for each subgenome.
+# '''
+
+# # read the blastp file
+# blastp = pd.read_csv(blastp_file, sep="\t", header=None)
+# df_blastp = blastp.iloc[:, 0:3]
+# #have column names for the blastp file as gene_id_Brassica, gene_id_AT, PID
+# df_blastp.columns = ["gene_id_Brassica", "gene_id_AT", "PID"]
+
+# # read the chains file
+# df_chains = pd.read_csv(chains_file, sep="\t", header=None)
+
+# # get the column names from df_subgenome_density that start with N followed by a number
+# df_subgenome = pd.read_excel(df_subgenome_density_file_path)
+# column_names = ['gene_id'] + df_subgenome.filter(regex=r'^N\d+').columns.tolist()
+# df_subgenome_density = pd.read_excel(df_subgenomes_file_path)
+
+# df_synteny = synteny_file.rename(columns={synteny_file.columns[i]: column_names[i] if i > 0 else "gene_id" for i in range(len(column_names))})
+
+# # Start the index from 0
+# df_synteny.index = df_synteny.index - 1
+
+# # number of blocks
+# num_blocks = len(df_subgenome_density)
+# print("===========================================")
+# print(f"Number of blocks: {num_blocks}")
+# print("===========================================")
+
+
+
+
+# blocks= get_blocks(df_subgenome_density, df_synteny, num_blocks, n_subgenomes)
+# density = calculate_density(blocks, num_blocks)
+# chains_dict = create_chains_dict(df_chains)
+# pid = calculate_pid(blocks, df_blastp, num_blocks, pickle_file)
+# avg_pid = calculate_avg_pid(num_blocks, blocks, pid)
+
+# return (blocks, density, chains_dict, pid, avg_pid)
+
+# graph_input = process_files_weight_cal(chains_file, blastp_file, "subgenome_density_bra.xlsx", "subgenome_density_bra.xlsx", C_df_csv.iloc[1:,:-3], "pid_genes_removed_blastn.pickle")
+
+# def create_block_graph(blocks, density, chains, avg_pid, num_subgenomes):
+# '''
+# Creates a graph of blocks.
+
+# Parameters:
+# blocks (dict): A dictionary containing all the blocks and their genes for each subgenome.
+# density (dict): A dictionary containing the density of each block for each subgenome.
+# chains (dict): A dictionary containing the chains of each block for each subgenome.
+# avg_pid (dict): A dictionary containing the average PID of each block for each subgenome.
+# num_subgenomes (int): Number of subgenomes.
+
+# Returns:
+# graph (dict): A dictionary containing the graph of blocks.
+# '''
+
+# graph = {}
+# num_blocks = len(blocks)
+# for i in range(num_blocks - 1):
+# for k in range(num_subgenomes):
+# graph[list(blocks[i].keys())[k]] = {}
+# for s in range(num_subgenomes):
+# graph[list(blocks[i + 1].keys())[s]] = {}
+# for j in range(len(chains)):
+# for l in range(num_subgenomes):
+# for m in range(num_subgenomes):
+# if (
+# list(blocks[i].keys())[l].split("_")[1]
+# == list(blocks[i + 1].keys())[m].split("_")[1]
+# or list(blocks[i].keys())[l].split("_")[1].split(".")[0]
+# == list(blocks[i + 1].keys())[l].split("_")[1].split(".")[0]
+# ):
+# graph[list(blocks[i].keys())[l]][
+# list(blocks[i + 1].keys())[m]
+# ] = (
+# list(density[i].values())[l]
+# - (
+# list(density[i].values())[l]
+# - list(density[i + 1].values())[m]
+# )
+# ) + (
+# list(avg_pid[i].values())[l]
+# - (
+# list(avg_pid[i].values())[l]
+# - list(avg_pid[i + 1].values())[m]
+# )
+# )
+# new_list = (
+# list(blocks[i][list(blocks[i].keys())[l]].values())
+# + list(blocks[i + 1][list(blocks[i + 1].keys())[m]].values())
+# )
+# new_list = list(filter(lambda a: a != "x", new_list))
+# # concatenate the two blocks
+
+# if (
+# list(blocks[i].keys())[l].split("_")[1].split(".")[0]
+# == list(chains.keys())[j].split("_")[0]
+# or list(blocks[i].keys())[l].split("_")[1]
+# == list(chains.keys())[j].split("_")[0]
+# ):
+# if (
+# len(set(new_list) & set(
+# chains[list(chains.keys())[j]]))
+# / float(
+# len(set(new_list) | set(
+# chains[list(chains.keys())[j]]))
+# )
+# * 100
+# > 20
+# ):
+# graph[list(blocks[i].keys())[l]][
+# list(blocks[i + 1].keys())[m]
+# ] = 2
+# elif len(graph[list(blocks[i].keys())[l]]) != num_subgenomes:
+# graph[list(blocks[i].keys())[l]][
+# list(blocks[i + 1].keys())[m]
+# ] = (
+# list(density[i].values())[l]
+# - (
+# list(density[i].values())[l]
+# - list(density[i + 1].values())[m]
+# )
+# ) + (
+# list(avg_pid[i].values())[l]
+# - (
+# list(avg_pid[i].values())[l]
+# - list(avg_pid[i + 1].values())[m]
+# )
+# )
+
+# elif (
+# list(blocks[i].keys())[l].split("_")[1]
+# == list(blocks[i + 1].keys())[m].split("_")[1].split(".")[0]
+# or list(blocks[i + 1].keys())[l].split("_")[1]
+# == list(blocks[i].keys())[m].split("_")[1].split(".")[0]
+# ):
+# graph[list(blocks[i].keys())[l]][
+# list(blocks[i + 1].keys())[m]
+# ] = (
+# list(density[i].values())[l]
+# - (
+# list(density[i].values())[l]
+# - list(density[i + 1].values())[m]
+# )
+# ) + (
+# list(avg_pid[i].values())[l]
+# - (
+# list(avg_pid[i].values())[l]
+# - list(avg_pid[i + 1].values())[m]
+# )
+# )
+# else:
+# graph[list(blocks[i].keys())[l]][list(blocks[i + 1].keys())[m]] = (
+# list(density[i].values())[l]
+# - (
+# list(density[i].values())[l]
+# - list(density[i + 1].values())[m]
+# )
+# ) + (
+# list(avg_pid[i].values())[l]
+# - (
+# list(avg_pid[i].values())[l]
+# - list(avg_pid[i + 1].values())[m]
+# )
+# )
+
+# return graph
+
+
+# # function for finding gaps in each columns
+
+# def add_edge_weights(blocks, graph, weight, num_blocks):
+# '''
+# This function adds edge weights to the graph
+
+# Parameters
+# ----------
+# blocks : list
+# list of blocks
+# graph : dict
+# graph of blocks
+# weight : int
+# weight of the edge
+
+# Returns
+# -------
+# graph : dict
+# graph of blocks with edge weights
+# '''
+# for i in range(num_blocks - 1):
+# for node in blocks[i].keys():
+# max_value = -1
+# max_next_node = None
+# for next_node in blocks[i + 1].keys():
+# if (
+# node.split("_")[1] == next_node.split("_")[1]
+# or node.split("_")[1] == next_node.split("_")[1].split(".")[0]
+# or next_node.split("_")[1] == node.split("_")[1].split(".")[0]
+# ):
+# if graph[node][next_node] > max_value:
+# max_value = graph[node][next_node]
+# max_next_node = next_node
+# if max_next_node is not None:
+# current_edge_value = max_value
+# new_edge_value = current_edge_value + weight
+# graph[node][max_next_node] = new_edge_value
+
+# return graph
+
+
+# def get_nodes(start_node, end_node, num_blocks, graph):
+# '''
+# This function returns the nodes between the start and end node
+
+# Parameters
+# ----------
+# start_node : str
+# start node
+# end_node : str
+# end node
+# num_blocks : int
+# number of blocks
+# graph : dict
+# graph of blocks
+
+# Returns
+# -------
+# nodes_sub : list
+# list of nodes between the start and end node
+# '''
+# nodes_sub = []
+# for i in range(num_blocks - 1):
+# while start_node != end_node:
+# nodes_sub.append(start_node)
+# start_node = list(list(graph.values())[list(graph.keys()).index(start_node)])[
+# list(
+# list(graph.values())[
+# list(graph.keys()).index(start_node)].values()
+# ).index(
+# max(
+# list(
+# list(graph.values())[
+# list(graph.keys()).index(start_node)
+# ].values()
+# )
+# )
+# )
+# ]
+# break
+# nodes_sub.append(end_node)
+# return nodes_sub
+
+
+# def remove_nodes_from_graph(nodes_sub, graph, blocks):
+# '''
+# This function removes the nodes from the graph
+
+# Parameters
+# ----------
+# nodes_sub : list
+# list of nodes between the start and end node
+# graph : dict
+# graph of blocks
+# blocks : list
+# list of blocks
+
+# Returns
+# -------
+# graph : dict
+# graph of blocks with nodes removed
+# blocks : list
+# list of blocks with nodes removed
+# '''
+# for i in range(len(nodes_sub)):
+# graph.pop(nodes_sub[i], None)
+# for j in range(len(graph)):
+# graph[list(graph.keys())[j]].pop(nodes_sub[i], None)
+# # remove blocks in blocks[] matching the nodes in nodes[]
+# for i in range(len(nodes_sub)):
+# for j in range(len(blocks)):
+# blocks[j].pop(nodes_sub[i], None)
+# return graph, blocks
+
+
+# def update_graph_edges(num_blocks, blocks, graph, weight):
+# '''
+# This function updates the graph edges
+
+# Parameters
+# ----------
+# num_blocks : int
+# number of blocks
+# blocks : list
+# list of blocks
+# graph : dict
+# graph of blocks
+# weight : int
+# weight of the edge
+
+# Returns
+# -------
+# graph : dict
+# graph of blocks with updated edges
+# '''
+# for i in range(num_blocks - 1):
+# for node in blocks[i].keys():
+# max_value = -1
+# max_next_node = None
+# for next_node in blocks[i + 1].keys():
+# if (
+# node.split("_")[1] == next_node.split("_")[1]
+# or node.split("_")[1] == next_node.split("_")[1].split(".")[0]
+# or next_node.split("_")[1] == node.split("_")[1].split(".")[0]
+# ):
+# if graph[node][next_node] > max_value:
+# max_value = graph[node][next_node]
+# max_next_node = next_node
+# if max_next_node is not None:
+# current_edge_value = max_value
+# new_edge_value = current_edge_value - weight
+# graph[node][max_next_node] = new_edge_value
+# return graph
+
+# def node_traverse_most_weighted_path(n_subgenomes, subgenome_density_file_path, nodes, W1, W2):
+# '''
+# This function traverses the graph to find the most weighted path
+
+# Parameters
+# ----------
+# n_subgenomes : int
+# number of subgenomes
+
+# Returns
+# -------
+# nodes_df : pandas dataframe
+# dataframe with the nodes_sub lists as columns
+# '''
+# # Get input from command line
+# weight_1 = float(W1)
+# weight_2 = float(W2)
+
+# # Get input from files
+# subgenome_density = pd.read_excel(subgenome_density_file_path)
+# # Create graph with edge weights and get nodes for first subgenome
+# graph = add_edge_weights(graph_input[0], create_block_graph(graph_input[0], graph_input[1], graph_input[2], graph_input[4], n_subgenomes), weight_1, len(graph_input[0]))
+# #get the first value in subgenome1 column (first row) in subgenome_density file as start node
+# start_node = f"0_{subgenome_density.iloc[0]['subgenome1']}"
+# #get the last value in subgenome1 column (last row) in subgenome_density file as end node
+# end_node = f"{len(subgenome_density)-1}_{subgenome_density.iloc[-1]['subgenome1']}"
+# nodes_sub1 = get_nodes(start_node, end_node, len(graph_input[0]), graph)
+
+# # Remove nodes from graph and get nodes for remaining subgenomes
+# blocks = graph_input[0]
+# nodes_df = pd.DataFrame({"nodes_sub1": nodes_sub1}) # Define the nodes_df variable here
+# for i in range(n_subgenomes - 1):
+# graph, blocks = remove_nodes_from_graph(nodes_sub1, graph, blocks)
+# graph = update_graph_edges(len(blocks), blocks, graph, weight_2)
+# start_node = f"0_{subgenome_density.iloc[0][f'subgenome{i+2}']}"
+# end_node = f"{len(subgenome_density)-1}_{subgenome_density.iloc[-1][f'subgenome{i+2}']}"
+# nodes_sub = get_nodes(start_node, end_node, len(blocks), graph)
+# nodes_sub_name = f"nodes_sub{i+2}"
+# nodes_df[nodes_sub_name] = nodes_sub
+# remove_nodes_from_graph(nodes_sub, graph, blocks)
+
+# # rename the columns as subgenomes
+# nodes_df.columns = [f"subgenome{i}" for i in range(1, n_subgenomes+1)]
+
+# #Append Row start # and Row end # columns from subgenome_density_bra as first two columns of the dataframe
+# nodes_df.insert(0, "Row start #", subgenome_density["Row start #"])
+# nodes_df.insert(1, "Row end #", subgenome_density["Row end #"])
+
+# #remove everything before _ in the nodes_df subgenome columns
+# for i in range(1, n_subgenomes+1):
+# column_name = f"subgenome{i}"
+# nodes_df[column_name] = nodes_df[column_name].str.split("_", n=1, expand=True)[1]
+
+# nodes_df.to_excel(nodes, index=False)
+
+# return nodes_df
+
+
+# node_traverse_most_weighted_path(n_subgenomes, "subgenome_density_bra.xlsx", "nodes.xlsx", sys.argv[8], sys.argv[9])
+# print("===========================================")
+# print("Accuracy of subgenome assignment(Weighted_Graph_Approach(Main_BP)):")
+# print("===========================================")
+# subgenome_overlap(GT, "nodes.xlsx", df_synteny, 3)
+
+
+
+# def find_small_gaps(col, gap_threshold, m, row_start):
+# """
+# Finds the gaps in the each column of the matrix
+# col: column of the matrix
+# gap_threshold: threshold for the gap
+# m: number of rows in the matrix
+
+# returns: indices of the beginning and end of the gaps
+# """
+# # indices for ones in given column
+# indices_one = np.where(col == 1)[0]
+
+# # calculate difference between consective indices
+# d = np.diff(indices_one)
+
+# # if the difference is bigger than the gap threshold then store them
+# initial_gaps = np.where(d > gap_threshold)[0]
+
+# # number of gaps
+# r = len(initial_gaps)
+
+# # calculate gaps
+# gaps = np.zeros((r, 2))
+
+# # find the indices of beginning and end of gaps
+# gaps[:, 0] = indices_one[initial_gaps] + 1 + row_start
+# gaps[:, 1] = indices_one[initial_gaps + 1] - 1 + row_start
+
+# # add row_start as the 1st column and indices_one[initial_gaps[0]] + 1 + row_start-1 as the second column for the first entry in gaps[]
+# if r == 1:
+# gaps[0, 0] = row_start
+# gaps[0, 1] = (indices_one[initial_gaps[0]] + 1 + row_start) - 2
+# if r > 1:
+# # add without replacing the first entry
+# gaps = np.insert(gaps, 0, np.array(
+# [[row_start, gaps[0, 0] - 2]]), axis=0)
+# gaps = np.insert(gaps, 1, np.array(
+# [[gaps[1, 0] - 1, gaps[1, 0] - 1]]), axis=0)
+
+# # fix the end of gap index for the last gap
+# if r > 0 and indices_one[-1] + 1 < m:
+# gaps = np.append(
+# gaps,
+# np.array([[indices_one[-1] + 1 + row_start, m + row_start - 1]]),
+# axis=0,
+# )
+# if r > 0 and indices_one[-1] + 1 == m:
+# gaps = np.append(
+# gaps, np.array([[m + row_start - 1, m + row_start - 1]]), axis=0
+# )
+
+# return gaps
+
+# def get_gaps(breakpoints_file, sub_density_file, C, num_subgenomes, gap_threshold=1):
+# '''
+# Returns the gaps in the blocks
+
+# breakpoints_file: file containing the main breakpoints
+# sub_density_file: file containing the subgenome density and chromosome blocks
+# num_subgenomes: number of subgenomes
+# gap_threshold: threshold for the gap
+
+# returns: list of gaps
+
+# '''
+# breakpoints_main = pd.read_excel(breakpoints_file, usecols="H:AA")
+# sub_density = pd.read_excel(sub_density_file)
+# gaps = []
+
+# for i in range(len(breakpoints_main)):
+# for j in range(len(breakpoints_main.columns)):
+# if breakpoints_main.iloc[i, j] < 0.1 and breakpoints_main.iloc[i, j] != 0:
+# # subgenome_names = [sub_density[f"subgenome{k+1}"][i].split(".")[0] for k in range(num_subgenomes)]
+# # subgenome_combinations = [[subgenome_names[k], subgenome_names[l]] for k in range(num_subgenomes-1) for l in range(k+1, num_subgenomes)]
+# if (
+# (
+# sub_density["subgenome1"][i].split(".")[0]
+# != sub_density["subgenome2"][i]
+# )
+# and (
+# sub_density["subgenome1"][i].split(".")[0]
+# != sub_density["subgenome3"][i]
+# )
+# and (
+# sub_density["subgenome3"][i].split(".")[0]
+# != sub_density["subgenome2"][i]
+# )
+# and (
+# sub_density["subgenome2"][i].split(".")[0]
+# != sub_density["subgenome1"][i]
+# )
+# and (
+# sub_density["subgenome3"][i].split(".")[0]
+# != sub_density["subgenome1"][i]
+# )
+# and (
+# sub_density["subgenome2"][i].split(".")[0]
+# != sub_density["subgenome3"][i]
+# )
+# ):
+
+# # print("Block no.:", i+1, "Row no.:", sub_density['Row start #'][i], "Subgenome:", breakpoints_main.columns [j], "Density:", breakpoints_main.iloc[i,j])
+# # gap_threshold is the threshold to determine if there is a gap or not
+# # min_block_length is the minimum length of the signal blocks
+# gap_threshold = 1
+# # min_block_length = 10
+# # get all gaps in all columns
+# gaps_cell = [
+# find_small_gaps(
+# C[
+# sub_density["Row start #"][i]: sub_density["Row end #"][i]
+# + 1,
+# j,
+# ],
+# gap_threshold,
+# sub_density["# genes in block"][i],
+# sub_density["Row start #"][i],
+# )
+# ]
+# if len(gaps_cell[0]) != 0:
+# gaps.append((gaps_cell, i, j))
+# return gaps
+
+# def merge_gaps(gaps):
+# '''
+# Merges gaps that are adjacent to each other.
+
+# Parameters
+# ----------
+# gaps : list
+# A list of tuples, where each tuple contains a list of arrays, the row number of the gap, and the column number of the gap.
+
+# Returns
+# -------
+# merged_gaps : list
+# A list of tuples, where each tuple contains a list of arrays, the row number of the gap, and the column number of the gap.
+
+# '''
+# merged_gaps = []
+# i = 0
+# while i < len(gaps) - 1:
+# if gaps[i][1] == gaps[i + 1][1]:
+# merged_row = []
+# j = 0
+# k = 0
+# while j < len(gaps[i][0][0]) and k < len(gaps[i + 1][0][0]):
+# if j == 0 and k == 0:
+# if gaps[i][0][0][0][1] > gaps[i + 1][0][0][0][1]:
+# merged_row.append(np.array(gaps[i + 1][0][0][k]))
+# k += 1
+
+# elif gaps[i][0][0][0][1] < gaps[i + 1][0][0][0][1]:
+# merged_row.append(np.array(gaps[i][0][0][j]))
+# j += 1
+
+# elif gaps[i][0][0][0][1] == gaps[i + 1][0][0][0][1]:
+# merged_row.append(np.array(gaps[i][0][0][j]))
+# j += 1
+# k += 1
+
+# elif (
+# j > 0
+# and gaps[i + 1][0][0][k][0] == gaps[i][0][0][j][1] + 1
+# and k > 0
+# ):
+# merged_row.append(np.array(gaps[i + 1][0][0][k]))
+# k += 1
+# elif (
+# j > 0
+# and k > 0
+# and gaps[i + 1][0][0][k][0] != gaps[i][0][0][j][1] + 1
+# and gaps[i + 1][0][0][k][0] < gaps[i][0][0][j][0]
+# and gaps[i + 1][0][0][k][1] < gaps[i][0][0][j][1]
+# ):
+# merged_row.append(np.array(gaps[i + 1][0][0][k]))
+# k += 1
+# else:
+# merged_row.append(np.array(gaps[i][0][0][j]))
+# j += 1
+
+# while j < len(gaps[i][0][0]):
+# merged_row.append(np.array(gaps[i][0][0][j]))
+# j += 1
+# while k < len(gaps[i + 1][0][0]):
+# merged_row.append(np.array(gaps[i + 1][0][0][k]))
+# k += 1
+# merged_gaps.append(([np.array(merged_row)], gaps[i][1]))
+# i += 3
+# elif (
+# gaps[i][1] == gaps[i + 1][1]
+# and gaps[i][1] != gaps[i + 2][1]
+# and gaps[i][1] != gaps[i - 1][1]
+# ):
+# merged_row = []
+# j = 0
+# k = 0
+# while j < len(gaps[i][0][0]) and k < len(gaps[i + 1][0][0]):
+# if j == 0 and k == 0:
+# if gaps[i][0][0][0][1] > gaps[i + 1][0][0][0][1]:
+# merged_row.append(np.array(gaps[i + 1][0][0][k]))
+# k += 1
+
+# elif gaps[i][0][0][0][1] < gaps[i + 1][0][0][0][1]:
+# merged_row.append(np.array(gaps[i][0][0][j]))
+# j += 1
+
+# elif gaps[i][0][0][0][1] == gaps[i + 1][0][0][0][1]:
+# merged_row.append(np.array(gaps[i][0][0][j]))
+# j += 1
+# k += 1
+
+# elif (
+# j > 0
+# and gaps[i + 1][0][0][k][0] == gaps[i][0][0][j][1] + 1
+# and k > 0
+# ):
+# merged_row.append(np.array(gaps[i + 1][0][0][k]))
+# k += 1
+# elif (
+# j > 0
+# and k > 0
+# and gaps[i + 1][0][0][k][0] != gaps[i][0][0][j][1] + 1
+# and gaps[i + 1][0][0][k][0] < gaps[i][0][0][j][0]
+# and gaps[i + 1][0][0][k][1] < gaps[i][0][0][j][1]
+# ):
+# merged_row.append(np.array(gaps[i + 1][0][0][k]))
+# k += 1
+# else:
+# merged_row.append(np.array(gaps[i][0][0][j]))
+# j += 1
+
+# while j < len(gaps[i][0][0]):
+# merged_row.append(np.array(gaps[i][0][0][j]))
+# j += 1
+# while k < len(gaps[i + 1][0][0]):
+# merged_row.append(np.array(gaps[i + 1][0][0][k]))
+# k += 1
+# merged_gaps.append(
+# ([np.array(merged_row)], gaps[i][1], gaps[i][2]))
+# i += 2
+# else:
+# merged_gaps.append(gaps[i])
+# i += 1
+# if i == len(gaps) - 1:
+# merged_gaps.append(gaps[i])
+# return merged_gaps
+
+
+
+# def sort_gaps(gaps):
+# '''
+# Sort the gaps in each row of the gap list
+
+# Parameters
+# ----------
+# gaps : list
+# A list of tuples. Each tuple contains a list of arrays and a string.
+# The list of arrays contains the gaps in each row of the gene matrix.
+# The string is the name of the chromosome.
+
+# Returns
+# -------
+# sorted_gaps : list
+# A list of tuples. Each tuple contains a list of arrays and a string.
+# The list of arrays contains the gaps in each row of the gene matrix.
+# The string is the name of the chromosome.
+# The gaps in each row are sorted by the start position of the gap.
+# '''
+# sorted_gaps = []
+# for gap in gaps:
+# sorted_gap = []
+# for row in gap[0]:
+# sorted_gap.append(row[row[:, 0].argsort()])
+# sorted_gaps.append((sorted_gap, gap[1]))
+# return sorted_gaps
+
+# def find_small_breakpoints(gaps, sub_density):
+# '''
+# Find the breakpoints that are smaller than the minimum gap size.
+
+# Parameters
+# ----------
+# gaps : list
+# A list of tuples. Each tuple contains a list of arrays and a string.
+# The list of arrays contains the gaps in each row of the gene matrix.
+# The string is the name of the chromosome.
+
+# Returns
+# -------
+# small_breakpoints : dict
+# A dictionary of dictionaries. The keys are the index of the gap
+# and the index of the row in the gap. The values are dictionaries
+# containing the start and end positions of the breakpoint and the
+# main breakpoint.
+# '''
+# sub_density = pd.read_excel(sub_density)
+# small_breakpoints = {}
+# for i in range(len(gaps)):
+# for j in range(len(gaps[i][0][0])):
+# if len(gaps[i][0][0]) == 2:
+# rowstart = gaps[i][0][0][j][0]
+# row_end = gaps[i][0][0][j][1]
+# if j == 0:
+# max_bp = sub_density["subgenome1"][gaps[i][1]]
+# small_breakpoints[i, j] = {
+# "Row start #": rowstart,
+# "Row end #": row_end,
+# "main_bp": gaps[i][1],
+# }
+
+# if j == 1 and rowstart > gaps[i][0][0][0][1] + 1:
+# rowstart = gaps[i][0][0][j - 1][1] + 1
+# row_end = gaps[i][0][0][j][0] - 1
+
+# small_breakpoints[i, j] = {
+# "Row start #": rowstart,
+# "Row end #": row_end,
+# "main_bp": gaps[i][1],
+# }
+
+# if j == len(gaps[i][0][0]) - 1:
+# rowstart = gaps[i][0][0][j][0]
+# row_end = gaps[i][0][0][j][1]
+# small_breakpoints[i, j + 1] = {
+# "Row start #": rowstart,
+# "Row end #": row_end,
+# "main_bp": gaps[i][1],
+# }
+
+# if len(gaps[i][0][0]) > 2:
+# rowstart = gaps[i][0][0][j][0]
+# row_end = gaps[i][0][0][j][1]
+# if j == 0:
+# small_breakpoints[i, j] = {
+# "Row start #": rowstart,
+# "Row end #": row_end,
+# "main_bp": gaps[i][1],
+# }
+# if j == 1 and rowstart == gaps[i][0][0][0][1] + 1:
+# rowstart = gaps[i][0][0][j][1]
+# row_end = gaps[i][0][0][j][0]
+# small_breakpoints[i, j] = {
+# "Row start #": rowstart,
+# "Row end #": row_end,
+# "main_bp": gaps[i][1],
+# }
+
+# if (j <= (len(gaps[i][0][0]) - 1)) and (j >= 1):
+# if gaps[i][0][0][j][0] > gaps[i][0][0][j - 1][1] + 1:
+# rowstart = gaps[i][0][0][j - 1][1] + 1
+# row_end = gaps[i][0][0][j][0] - 1
+# small_breakpoints[i, j] = {
+# "Row start #": rowstart,
+# "Row end #": row_end,
+# "main_bp": gaps[i][1],
+# }
+
+# rowstart = gaps[i][0][0][j][0]
+# row_end = gaps[i][0][0][j][1]
+# small_breakpoints[i, j, 0] = {
+# "Row start #": rowstart,
+# "Row end #": row_end,
+# "main_bp": gaps[i][1],
+# }
+
+# return small_breakpoints
+
+
+# def update_small_breakpoints(small_breakpoints):
+# '''
+# Update the small breakpoints.
+
+# Parameters
+# ----------
+# small_breakpoints : dict
+# A dictionary of dictionaries. The keys are the index of the gap
+# and the index of the row in the gap. The values are dictionaries
+# containing the start and end positions of the breakpoint and the
+# main breakpoint.
+
+# Returns
+# -------
+# small_breakpoints_new : dict
+# A dictionary of dictionaries. The keys are the index of the gap
+# and the index of the row in the gap. The values are dictionaries
+# containing the start and end positions of the breakpoint and the
+# main breakpoint.
+# '''
+# small_breakpoints = {
+# i: small_breakpoints[key] for i, key in enumerate(small_breakpoints)
+# }
+# small_breakpoints
+# # Check if the row start and row end numbers are like row start number = from the previous row end number + 1 and row end number = from the next row start number - 1, if not, update the row start and row end numbers.
+# small_breakpoints_new = small_breakpoints.copy()
+# for i in range(len(small_breakpoints) - 1):
+# if i == 0:
+# small_breakpoints_new[i] = small_breakpoints[i]
+# if i == len(small_breakpoints) - 1:
+# small_breakpoints_new[i] = small_breakpoints[i]
+# if i > 0 and i < len(small_breakpoints) - 1:
+# # if small_breakpoints[i]['Row end #'] == small_breakpoints[i+1]['Row end #'] and small_breakpoints[i]['Row start #'] == small_breakpoints[i+1]['Row start #']:
+# # continue
+# if (
+# small_breakpoints[i]["Row end #"]
+# != small_breakpoints[i + 1]["Row start #"] - 1
+# ):
+# # Check whether you can find this row end number in any of the row end numbers coming in upcoming rows.
+# if (
+# small_breakpoints[i]["Row start #"]
+# != small_breakpoints[i + 1]["Row start #"]
+# and small_breakpoints[i]["Row end #"]
+# != small_breakpoints[i + 1]["Row end #"]
+# ):
+# row_end_list = []
+# for s in range(i + 1, len(small_breakpoints)):
+# row_end_list.append(small_breakpoints[s]["Row end #"])
+# if small_breakpoints[i]["Row end #"] in row_end_list:
+# # If you can find this row end number in any of the row end numbers coming in upcoming rows, then update the current row's end number.
+# small_breakpoints_new[i] = {
+# "Row start #": small_breakpoints[i]["Row start #"],
+# "Row end #": small_breakpoints[i + 1]["Row start #"] - 1,
+# "main_bp": small_breakpoints[i]["main_bp"],
+# }
+
+# elif (
+# small_breakpoints[i]["Row end #"] not in row_end_list
+# and small_breakpoints[i]["Row end #"]
+# > small_breakpoints[i + 1]["Row start #"]
+# ):
+# small_breakpoints_new[i] = {
+# "Row start #": small_breakpoints[i]["Row start #"],
+# "Row end #": small_breakpoints[i + 1]["Row start #"] - 1,
+# "main_bp": small_breakpoints[i]["main_bp"],
+# }
+# # If you can't find this row end number in any of the row end numbers coming in upcoming rows, then add it where row end number < row end number of next row but row end number > row end number of the row of focus and row start number of next row < row end number.
+# for j in range(i + 1, len(small_breakpoints) - 1):
+# if (
+# small_breakpoints[i]["Row end #"]
+# < small_breakpoints[j + 1]["Row start #"]
+# and small_breakpoints[i]["Row end #"]
+# > small_breakpoints[j]["Row start #"]
+# ):
+# # Add this row end number and row start number of next row as a new row.
+# new_row = {
+# "Row start #": small_breakpoints[j]["Row start #"],
+# "Row end #": small_breakpoints[i]["Row end #"],
+# "main_bp": small_breakpoints[i]["main_bp"],
+# }
+# small_breakpoints_new[i + 1, j] = new_row
+
+# if (
+# small_breakpoints[i]["Row start #"]
+# == small_breakpoints[i + 1]["Row start #"]
+# and small_breakpoints[i]["Row end #"]
+# != small_breakpoints[i + 1]["Row end #"]
+# and small_breakpoints[i]["Row end #"]
+# <= small_breakpoints[i + 1]["Row end #"]
+# ):
+# small_breakpoints_new[i] = small_breakpoints[i]
+# small_breakpoints_new[i + 1] = {
+# "Row start #": small_breakpoints[i]["Row end #"] + 1,
+# "Row end #": small_breakpoints[i + 1]["Row end #"],
+# "main_bp": small_breakpoints[i + 1]["main_bp"],
+# }
+# else:
+# continue
+
+# if (
+# small_breakpoints[i]["Row end #"]
+# == small_breakpoints[i + 1]["Row start #"] - 1
+# ):
+# if i < len(small_breakpoints) - 2:
+# if (
+# small_breakpoints[i + 1]["Row start #"]
+# == small_breakpoints[i + 2]["Row start #"]
+# and small_breakpoints[i + 1]["Row end #"]
+# > small_breakpoints[i + 2]["Row start #"]
+# ):
+# small_breakpoints_new[i] = small_breakpoints[i]
+# small_breakpoints_new[i + 1] = small_breakpoints[i + 2]
+
+# small_breakpoints = {
+# i: small_breakpoints_new[key] for i, key in enumerate(small_breakpoints_new)
+# }
+
+# return small_breakpoints
+
+# def merge_main_small_breakpoints(small_breakpoints_new, sub_density_file):
+# '''
+# This function merges the main breakpoints and small breakpoints.
+
+# Parameters
+# ----------
+# small_breakpoints_new : dict
+# Dictionary of small breakpoints.
+# sub_density_file : str
+# Path to the sub density file.
+
+# Returns
+# -------
+# small_breakpoints_copy : dict
+# Dictionary of merged breakpoints.
+# '''
+# sub_density = pd.read_excel(sub_density_file)
+# small_breakpoints = {
+# i: small_breakpoints_new[key] for i, key in enumerate(small_breakpoints_new)
+# }
+
+# sub_density = (
+# sub_density.copy()
+# ) # make a copy to avoid modifying the original DataFrame
+# small_breakpoints_copy = {} # make a copy to avoid modifying the original dictionary
+
+# for i in range(len(small_breakpoints) - 1):
+# if i == 0:
+# small_breakpoints_copy[i] = small_breakpoints[i]
+# if i == len(small_breakpoints) - 1:
+# small_breakpoints_copy[i] = small_breakpoints[i]
+# for j in range(len(sub_density)):
+# if i > 0 and i < len(small_breakpoints) - 1:
+# if (
+# small_breakpoints[i - 1]["Row end #"] + 1
+# == small_breakpoints[i]["Row start #"]
+# ):
+# small_breakpoints_copy[i] = small_breakpoints[i]
+# if (
+# small_breakpoints[i - 1]["Row end #"] + 1
+# != small_breakpoints[i]["Row start #"]
+# and small_breakpoints[i - 1]["Row start #"]
+# == sub_density["Row start #"][j]
+# ):
+# small_breakpoints_copy[i] = small_breakpoints[i]
+
+# elif (
+# small_breakpoints[i - 1]["Row end #"] + 1
+# != small_breakpoints[i]["Row start #"]
+# and small_breakpoints[i - 1]["Row end #"] + 1
+# == sub_density["Row start #"][j]
+# ):
+# small_breakpoints_copy[i] = {
+# "Row start #": sub_density["Row start #"][j],
+# "Row end #": sub_density["Row end #"][j],
+# "main_bp": j,
+# }
+# for k in range(j, small_breakpoints[i]["main_bp"]):
+# if (
+# sub_density["Row end #"][k] + 1
+# == small_breakpoints[i]["Row start #"]
+# ):
+# small_breakpoints_copy[i, k] = small_breakpoints[i]
+# break
+# elif (
+# sub_density["Row end #"][k] + 1
+# != small_breakpoints[i]["Row start #"]
+# ):
+# if (
+# sub_density["Row end #"][k] + 1
+# == sub_density["Row start #"][k + 1]
+# ):
+# small_breakpoints_copy[i, k] = {
+# "Row start #": sub_density["Row start #"][k + 1],
+# "Row end #": sub_density["Row end #"][k + 1],
+# "main_bp": k + 1,
+# }
+# small_breakpoints_copy = {
+# i: small_breakpoints_copy[key] for i, key in enumerate(small_breakpoints_copy)
+# }
+# small_breakpoints = small_breakpoints_copy
+
+# return small_breakpoints
+
+# def modify_small_breakpoints(small_breakpoints):
+# '''
+# This function modifies the small breakpoints.
+
+# Parameters
+# ----------
+# small_breakpoints : dict
+# Dictionary of small breakpoints.
+
+# Returns
+# -------
+# small_breakpoints : dict
+# Dictionary of modified small breakpoints.
+# '''
+# # update row start of current row start # == row end of previous row end # +1 in small_breakpoints
+# for i in range(len(small_breakpoints) - 1):
+# if i == 0:
+# small_breakpoints[i]["Row start #"] = small_breakpoints[i]["Row start #"]
+# elif i > 0 and i < len(small_breakpoints) - 1:
+# small_breakpoints[i]["Row start #"] = small_breakpoints[i -
+# 1]["Row end #"] + 1
+# else:
+# small_breakpoints[i]["Row start #"] = small_breakpoints[i]["Row start #"]
+
+# return small_breakpoints
+
+# def remove_invalid_entries(small_breakpoints):
+# '''
+# This function removes invalid entries from the small breakpoints.
+
+# Parameters
+# ----------
+# small_breakpoints : dict
+# Dictionary of small breakpoints.
+
+# Returns
+# -------
+# small_breakpoints_new : dict
+# Dictionary of small breakpoints with invalid entries removed.
+# '''
+# # remove entries from small_breakpoints that have ['Row end #'] < ['Row start #']
+# small_breakpoints_new = {}
+# for i in range(len(small_breakpoints)):
+# if small_breakpoints[i]["Row end #"] >= small_breakpoints[i]["Row start #"]:
+# small_breakpoints_new[i] = small_breakpoints[i]
+# # rename keys in small_breakpoints_new
+# small_breakpoints_new = {
+# i: small_breakpoints_new[key] for i, key in enumerate(small_breakpoints_new)
+# }
+# small_breakpoints = small_breakpoints_new
+# return small_breakpoints
+
+
+
+# small_BP = remove_invalid_entries(modify_small_breakpoints(merge_main_small_breakpoints(update_small_breakpoints(find_small_breakpoints(sort_gaps(merge_gaps(merge_gaps(get_gaps( "gene_matrix_output_Bra.xlsx", "subgenome_density_bra.xlsx", C, n_subgenomes,1)))), "subgenome_density_bra.xlsx")), "subgenome_density_bra.xlsx")))
+# # print(small_BP)
+
+# def update_df_synteny(C_df,synteny_file, df_subgenome_density_file_path):
+# '''
+# This function updates the df_synteny dataframe.
+
+# Parameters
+# ----------
+# df_synteny : dataframe
+# Dataframe of synteny.
+
+# Returns
+# -------
+# df_synteny : dataframe
+# Dataframe of synteny with chromosome names where the gene belongs.
+# '''
+# # Read the data
+# df_subgenome_density = pd.read_excel(df_subgenome_density_file_path)
+
+# # Get the column names from df_subgenome_density that start with N followed by a number
+# column_names = df_subgenome_density.filter(regex=r'^N\d+').columns.tolist()
+
+# # Replace the columns starting from the second column until the end of C_df_updated with the selected column names
+# df_synteny = synteny_file.rename(columns={synteny_file.columns[i-1]: column_names[i-1] for i in range(1, len(column_names)+1)})
+
+# # Start the index from 0
+# df_synteny.index = df_synteny.index - 1
+# for i in range(len(df_synteny)):
+# for j in range(len(df_synteny.columns)):
+# if df_synteny.iloc[i, j] == 1:
+# df_synteny.iloc[i, j] = df_synteny.columns[j]
+# #append the first column of the C_df to the df_synteny as first column
+# df_synteny.insert(0, "Gene_id", C_df.iloc[1:, 0])
+
+# df_synteny.to_excel("modified_synteny_chromosome_names.xlsx")
+
+# return df_synteny
+
+# update_df_synteny(C_df, C_df_updated, "subgenome_density_bra.xlsx")
+
+# def check_gaps(final_gaps_df):
+# for i in range(len(final_gaps_df) - 2):
+# if (final_gaps_df.iloc[i]["Row end #"] + 1 != final_gaps_df.iloc[i + 1]["Row start #"]):
+# # print("error1", i)
+# if (final_gaps_df.iloc[i-1]["Row end #"] + 1 == final_gaps_df.iloc[i + 1]["Row start #"]):
+# final_gaps_df.drop(i, inplace=True)
+# final_gaps_df.reset_index(drop=True, inplace=True)
+# else:
+# final_gaps_df.iloc[i, final_gaps_df.columns.get_loc("Row end #")] = final_gaps_df.iloc[i + 1]["Row start #"] - 1
+# if final_gaps_df.iloc[i]["Row end #"] < final_gaps_df.iloc[i]["Row start #"]:
+# print("error2", i)
+# return final_gaps_df
+
+
+# def subgenome_assignment_all_BP(sub_density, main_breakpoints, small_breakpoints):
+# sub_density = pd.read_excel(sub_density)
+# synteny_df = pd.read_excel(main_breakpoints, usecols="C:V")
+# # print(synteny_df)
+# final_gaps_df = pd.DataFrame(columns=["Row start #", "Row end #"])
+# sub1 = sub2 = sub3 = 0
+# for i in range(len(small_breakpoints)):
+# sub1_found = False
+# sub2_found = False
+# sub3_found = False
+
+# # final_gaps_df = final_gaps_df.append({'Row start #': small_breakpoints [i]['Row start #'], 'Row end #': small_breakpoints [i]['Row end #'], 'Subgenome1': sub_density['subgenome1'][small_breakpoints[i]['main_bp']], 'Subgenome2': sub_density['subgenome2'][small_breakpoints[i]['main_bp']], 'Subgenome3': sub_density['subgenome3'][small_breakpoints[i]['main_bp']]}, ignore_index=True)
+# # break out of outer loop as well
+# # break
+# if small_breakpoints[i]["Row start #"] != small_breakpoints[i]["Row end #"]:
+# gaps_list_sub1 = []
+# gaps_list_sub2 = []
+# gaps_list_sub3 = []
+
+# for l in range(
+# int(small_breakpoints[i]["Row start #"]),
+# int(small_breakpoints[i]["Row end #"] + 1),
+# ):
+# if (
+# synteny_df.iloc[l][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome1"]
+# ]
+# != 0
+# and synteny_df.iloc[l][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome1"]
+# ]
+# == sub_density.iloc[small_breakpoints[i]["main_bp"]]["subgenome1"]
+# ):
+# gaps_list_sub1.append(
+# synteny_df.iloc[l][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome1"]
+# ]
+# )
+# if (
+# synteny_df.iloc[l][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome2"]
+# ]
+# != 0
+# and synteny_df.iloc[l][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome2"]
+# ]
+# == sub_density.iloc[small_breakpoints[i]["main_bp"]]["subgenome2"]
+# ):
+# gaps_list_sub2.append(
+# synteny_df.iloc[l][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome2"]
+# ]
+# )
+# if (
+# synteny_df.iloc[l][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome3"]
+# ]
+# != 0
+# and synteny_df.iloc[l][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome3"]
+# ]
+# == sub_density.iloc[small_breakpoints[i]["main_bp"]]["subgenome3"]
+# ):
+# gaps_list_sub3.append(
+# synteny_df.iloc[l][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome3"]
+# ]
+# )
+
+# if len(gaps_list_sub1) > 0:
+# sub1_found = False
+# if (
+# sub1_found == False
+# and gaps_list_sub1[0]
+# == sub_density["subgenome1"][small_breakpoints[i]["main_bp"]]
+# ):
+# sub1 = sub_density["subgenome1"][small_breakpoints[i]["main_bp"]]
+# # sub2=sub_density['subgenome2'][small_breakpoints[i]['main_bp']]
+# # sub3=sub_density['subgenome3'][small_breakpoints[i]['main_bp']]
+# if sub2_found == False and sub3_found == False:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2_found == False and sub3_found == True:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2_found == True and sub3_found == False:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# # if sub2_found and sub3_found:
+# # break
+# # break
+
+# if len(gaps_list_sub1) == 0:
+# sub1_found = False
+# for l in range(
+# int(small_breakpoints[i]["Row start #"]),
+# int(small_breakpoints[i]["Row end #"] + 1),
+# ):
+# for b in range(len(synteny_df.columns)):
+# if (
+# sub1_found == False
+# and synteny_df.iloc[l][b] != 0
+# and synteny_df.iloc[l][b].split(".")[0]
+# == sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# ):
+# if sub2_found == False and sub3_found == False:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1 = synteny_df.iloc[l][b]
+# sub1_found = True
+
+# if sub2_found == False and sub3_found == True:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub3 != synteny_df.iloc[l][b]:
+# sub1 = synteny_df.iloc[l][b]
+# sub1_found = True
+# else:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# if sub2_found == True and sub3_found == False:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2 != synteny_df.iloc[l][b]:
+# sub1 = synteny_df.iloc[l][b]
+# sub1_found = True
+# else:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# if sub2_found == True and sub3_found == True:
+# if (
+# sub2 != synteny_df.iloc[l][b]
+# and sub3 != synteny_df.iloc[l][b]
+# ):
+# sub1 = synteny_df.iloc[l][b]
+# sub1_found = True
+# else:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# # if sub2_found and sub3_found:
+# # break
+# # break
+# for b in range(len(synteny_df.columns)):
+# if (
+# sub1_found == False
+# and synteny_df.iloc[l][b] != 0
+# and synteny_df.iloc[l][b].split(".")[0]
+# != sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# and synteny_df.iloc[l][b].split(".")[0]
+# != sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# and synteny_df.iloc[l][b].split(".")[0]
+# != sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# ):
+
+# if sub2_found == False and sub3_found == False:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1 = synteny_df.iloc[l][b]
+# sub1_found = True
+# if sub2_found == False and sub3_found == True:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub3 != synteny_df.iloc[l][b]:
+# sub1 = synteny_df.iloc[l][b]
+# sub1_found = True
+# else:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# if sub2_found == True and sub3_found == False:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2 != synteny_df.iloc[l][b]:
+# sub1 = synteny_df.iloc[l][b]
+# sub1_found = True
+# else:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# if sub2_found == True and sub3_found == True:
+# if (
+# sub2 != synteny_df.iloc[l][b]
+# and sub3 != synteny_df.iloc[l][b]
+# ):
+# sub1 = synteny_df.iloc[l][b]
+# sub1_found = True
+# else:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# # if sub2_found and sub3_found:
+# # break
+# # sub2=sub_density['subgenome2'][small_breakpoints[i]['main_bp']]
+# # sub3=sub_density['subgenome3'][small_breakpoints[i]['main_bp']]
+# # break
+
+# if len(gaps_list_sub2) > 0:
+# sub2_found = False
+# if (
+# sub2_found == False
+# and gaps_list_sub2[0]
+# == sub_density["subgenome2"][small_breakpoints[i]["main_bp"]]
+# ):
+# # sub1=sub_density['subgenome1'][small_breakpoints[i]['main_bp']]
+# sub2 = sub_density["subgenome2"][small_breakpoints[i]["main_bp"]]
+# # sub3=sub_density['subgenome3'][small_breakpoints[i]['main_bp']]
+# if sub1_found == False and sub3_found == False:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub1_found == False and sub3_found == True:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub1_found == True and sub3_found == False:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+# # if sub1_found and sub3_found:
+# # break
+# # break
+
+# elif len(gaps_list_sub2) == 0:
+# sub2_found = False
+# for l in range(
+# int(small_breakpoints[i]["Row start #"]),
+# int(small_breakpoints[i]["Row end #"] + 1),
+# ):
+# for b in range(len(synteny_df.columns)):
+# if (
+# sub2_found == False
+# and synteny_df.iloc[l][b] != 0
+# and synteny_df.iloc[l][b].split(".")[0]
+# == sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# ):
+# # sub1=sub_density['subgenome1'][small_breakpoints[i]['main_bp']]
+
+# # if sub1_found and sub3_found:
+# # break
+# if sub1_found == False and sub3_found == False:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2 = synteny_df.iloc[l][b]
+# sub2_found = True
+
+# if sub1_found == False and sub3_found == True:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub3 != synteny_df.iloc[l][b]:
+# sub2 = synteny_df.iloc[l][b]
+# sub2_found = True
+# else:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+
+# if sub1_found == True and sub3_found == False:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub1 != synteny_df.iloc[l][b]:
+# sub2 = synteny_df.iloc[l][b]
+# sub2_found = True
+# else:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+# if sub1_found == True and sub3_found == True:
+# if (
+# sub1 != synteny_df.iloc[l][b]
+# and sub3 != synteny_df.iloc[l][b]
+# ):
+# sub2 = synteny_df.iloc[l][b]
+# sub2_found = True
+# else:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+
+# # sub3=sub_density['subgenome3'][small_breakpoints[i]['main_bp']]
+# # break
+# for b in range(len(synteny_df.columns)):
+# if (
+# sub2_found == False
+# and synteny_df.iloc[l][b] != 0
+# and synteny_df.iloc[l][b].split(".")[0]
+# != sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# and synteny_df.iloc[l][b].split(".")[0]
+# != sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# and synteny_df.iloc[l][b].split(".")[0]
+# != sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# ):
+# # sub1=sub_density['subgenome1'][small_breakpoints[i]['main_bp']]
+# # sub3=sub_density['subgenome3'][small_breakpoints[i]['main_bp']]
+# if sub1_found == False and sub3_found == False:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2 = synteny_df.iloc[l][b]
+# sub2_found = True
+# if sub1_found == False and sub3_found == True:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub3 != synteny_df.iloc[l][b]:
+# sub2 = synteny_df.iloc[l][b]
+# sub2_found = True
+# else:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+# if sub1_found == True and sub3_found == False:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub1 != synteny_df.iloc[l][b]:
+# sub2 = synteny_df.iloc[l][b]
+# sub2_found = True
+# else:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+# if sub1_found == True and sub3_found == True:
+# if (
+# sub1 != synteny_df.iloc[l][b]
+# and sub3 != synteny_df.iloc[l][b]
+# ):
+# sub2 = synteny_df.iloc[l][b]
+# sub2_found = True
+# else:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+# # if sub1_found and sub3_found:
+# # break
+# # break
+
+# if len(gaps_list_sub3) > 0:
+# sub3_found = False
+# if (
+# sub3_found == False
+# and gaps_list_sub3[0]
+# == sub_density["subgenome3"][small_breakpoints[i]["main_bp"]]
+# ):
+# # sub1=sub_density['subgenome1'][small_breakpoints[i]['main_bp']]
+# # sub2=sub_density['subgenome2'][small_breakpoints[i]['main_bp']]
+# sub3 = sub_density["subgenome3"][small_breakpoints[i]["main_bp"]]
+# if sub2_found == False and sub1_found == False:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2_found == False and sub1_found == True:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2_found == True and sub1_found == False:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# # if sub1_found and sub2_found:
+# # break
+# # break
+
+# if len(gaps_list_sub3) == 0:
+# sub3_found = False
+# for l in range(
+# int(small_breakpoints[i]["Row start #"]),
+# int(small_breakpoints[i]["Row end #"] + 1),
+# ):
+# for b in range(len(synteny_df.columns)):
+# if (
+# sub3_found == False
+# and synteny_df.iloc[l][b] != 0
+# and synteny_df.iloc[l][b].split(".")[0]
+# == sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# ):
+# # sub1=sub_density['subgenome1'][small_breakpoints[i]['main_bp']]
+# # sub2=sub_density['subgenome2'][small_breakpoints[i]['main_bp']]
+# if sub2_found == False and sub1_found == False:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = synteny_df.iloc[l][b]
+# sub3_found = True
+# if sub2_found == False and sub1_found == True:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub1 != synteny_df.iloc[l][b]:
+# sub3 = synteny_df.iloc[l][b]
+# sub3_found = True
+# else:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# if sub2_found == True and sub1_found == False:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2 != synteny_df.iloc[l][b]:
+# sub3 = synteny_df.iloc[l][b]
+# sub3_found = True
+# else:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# if sub2_found == True and sub1_found == True:
+# if (
+# sub1 != synteny_df.iloc[l][b]
+# and sub2 != synteny_df.iloc[l][b]
+# ):
+# sub3 = synteny_df.iloc[l][b]
+# sub3_found = True
+# else:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# # if sub1_found and sub2_found:
+# # break
+# # break
+# for b in range(len(synteny_df.columns)):
+# if (
+# sub3_found == False
+# and synteny_df.iloc[l][b] != 0
+# and synteny_df.iloc[l][b].split(".")[0]
+# != sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# and synteny_df.iloc[l][b].split(".")[0]
+# != sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# and synteny_df.iloc[l][b].split(".")[0]
+# != sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# ):
+# # sub1=sub_density['subgenome1'][small_breakpoints[i]['main_bp']]
+# # sub2=sub_density['subgenome2'][small_breakpoints[i]['main_bp']]
+
+# if sub2_found == False and sub1_found == False:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = synteny_df.iloc[l][b]
+# sub3_found = True
+# if sub2_found == False and sub1_found == True:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub1 != synteny_df.iloc[l][b]:
+# sub3 = synteny_df.iloc[l][b]
+# sub3_found = True
+# else:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# if sub2_found == True and sub1_found == False:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2 != synteny_df.iloc[l][b]:
+# sub3 = synteny_df.iloc[l][b]
+# sub3_found = True
+# else:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# if sub2_found == True and sub1_found == True:
+# if (
+# sub1 != synteny_df.iloc[l][b]
+# and sub2 != synteny_df.iloc[l][b]
+# ):
+# sub3 = synteny_df.iloc[l][b]
+# sub3_found = True
+# else:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# # if sub1_found and sub2_found:
+# # break
+# # break
+# if small_breakpoints[i]["Row start #"] == small_breakpoints[i]["Row end #"]:
+# gaps_list_sub1 = []
+# gaps_list_sub2 = []
+# gaps_list_sub3 = []
+
+# if (
+# synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome1"]
+# ]
+# != 0
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome1"]
+# ]
+# == sub_density.iloc[small_breakpoints[i]["main_bp"]]["subgenome1"]
+# ):
+# gaps_list_sub1.append(
+# synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome1"]
+# ]
+# )
+# if (
+# synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome2"]
+# ]
+# != 0
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome2"]
+# ]
+# == sub_density.iloc[small_breakpoints[i]["main_bp"]]["subgenome2"]
+# ):
+# gaps_list_sub2.append(
+# synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome2"]
+# ]
+# )
+# if (
+# synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome3"]
+# ]
+# != 0
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome3"]
+# ]
+# == sub_density.iloc[small_breakpoints[i]["main_bp"]]["subgenome3"]
+# ):
+# gaps_list_sub3.append(
+# synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][
+# sub_density.iloc[small_breakpoints[i]
+# ["main_bp"]]["subgenome3"]
+# ]
+# )
+
+# if len(gaps_list_sub1) > 0:
+# sub1_found = False
+# if (
+# sub1_found == False
+# and gaps_list_sub1[0]
+# == sub_density["subgenome1"][small_breakpoints[i]["main_bp"]]
+# ):
+# sub1 = sub_density["subgenome1"][small_breakpoints[i]["main_bp"]]
+# # sub2=sub_density['subgenome2'][small_breakpoints[i]['main_bp']]
+# # sub3=sub_density['subgenome3'][small_breakpoints[i]['main_bp']]
+# if sub2_found == False and sub3_found == False:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2_found == False and sub3_found == True:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2_found == True and sub3_found == False:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# # if sub2_found and sub3_found:
+# # break
+# # break
+
+# if len(gaps_list_sub1) == 0:
+# sub1_found = False
+
+# for b in range(len(synteny_df.columns)):
+# if (
+# sub1_found == False
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b] != 0
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b].split(".")[0]
+# == sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# ):
+# if sub2_found == False and sub3_found == False:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub1_found = True
+
+# if sub2_found == False and sub3_found == True:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub3 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]:
+# sub1 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub1_found = True
+# else:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# if sub2_found == True and sub3_found == False:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]:
+# sub1 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub1_found = True
+# else:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# if sub2_found == True and sub3_found == True:
+# if (
+# sub2 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# and sub3 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# ):
+# sub1 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub1_found = True
+# else:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# # if sub2_found and sub3_found:
+# # break
+# # break
+# for b in range(len(synteny_df.columns)):
+# if (
+# sub1_found == False
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b] != 0
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b].split(".")[0]
+# != sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b].split(".")[0]
+# != sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b].split(".")[0]
+# != sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# ):
+
+# if sub2_found == False and sub3_found == False:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub1_found = True
+# if sub2_found == False and sub3_found == True:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub3 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]:
+# sub1 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub1_found = True
+# else:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# if sub2_found == True and sub3_found == False:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]:
+# sub1 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub1_found = True
+# else:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# if sub2_found == True and sub3_found == True:
+# if (
+# sub2 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# and sub3 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# ):
+# sub1 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub1_found = True
+# else:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1_found = True
+# # if sub2_found and sub3_found:
+# # break
+# # sub2=sub_density['subgenome2'][small_breakpoints[i]['main_bp']]
+# # sub3=sub_density['subgenome3'][small_breakpoints[i]['main_bp']]
+# # break
+
+# if len(gaps_list_sub2) > 0:
+# sub2_found = False
+# if (
+# sub2_found == False
+# and gaps_list_sub2[0]
+# == sub_density["subgenome2"][small_breakpoints[i]["main_bp"]]
+# ):
+# # sub1=sub_density['subgenome1'][small_breakpoints[i]['main_bp']]
+# sub2 = sub_density["subgenome2"][small_breakpoints[i]["main_bp"]]
+# # sub3=sub_density['subgenome3'][small_breakpoints[i]['main_bp']]
+# if sub1_found == False and sub3_found == False:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub1_found == False and sub3_found == True:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub1_found == True and sub3_found == False:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+# # if sub1_found and sub3_found:
+# # break
+# # break
+
+# elif len(gaps_list_sub2) == 0:
+# sub2_found = False
+
+# for b in range(len(synteny_df.columns)):
+# if (
+# sub2_found == False
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b] != 0
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b].split(".")[0]
+# == sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# ):
+# # sub1=sub_density['subgenome1'][small_breakpoints[i]['main_bp']]
+
+# # if sub1_found and sub3_found:
+# # break
+# if sub1_found == False and sub3_found == False:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub2_found = True
+
+# if sub1_found == False and sub3_found == True:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub3 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]:
+# sub2 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub2_found = True
+# else:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+
+# if sub1_found == True and sub3_found == False:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub1 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]:
+# sub2 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub2_found = True
+# else:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+# if sub1_found == True and sub3_found == True:
+# if (
+# sub1 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# and sub3 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# ):
+# sub2 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub2_found = True
+# else:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+
+# # sub3=sub_density['subgenome3'][small_breakpoints[i]['main_bp']]
+# # break
+# for b in range(len(synteny_df.columns)):
+# if (
+# sub2_found == False
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b] != 0
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b].split(".")[0]
+# != sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b].split(".")[0]
+# != sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b].split(".")[0]
+# != sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# ):
+# # sub1=sub_density['subgenome1'][small_breakpoints[i]['main_bp']]
+# # sub3=sub_density['subgenome3'][small_breakpoints[i]['main_bp']]
+# if sub1_found == False and sub3_found == False:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2 = synteny_df.iloc[l][b]
+# sub2_found = True
+# if sub1_found == False and sub3_found == True:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub3 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]:
+# sub2 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub2_found = True
+# else:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+# if sub1_found == True and sub3_found == False:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub1 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]:
+# sub2 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub2_found = True
+# else:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+# if sub1_found == True and sub3_found == True:
+# if (
+# sub1 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# and sub3 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# ):
+# sub2 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub2_found = True
+# else:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub2_found = True
+# # if sub1_found and sub3_found:
+# # break
+# # break
+
+# if len(gaps_list_sub3) > 0:
+# sub3_found = False
+# if (
+# sub3_found == False
+# and gaps_list_sub3[0]
+# == sub_density["subgenome3"][small_breakpoints[i]["main_bp"]]
+# ):
+# # sub1=sub_density['subgenome1'][small_breakpoints[i]['main_bp']]
+# # sub2=sub_density['subgenome2'][small_breakpoints[i]['main_bp']]
+# sub3 = sub_density["subgenome3"][small_breakpoints[i]["main_bp"]]
+# if sub2_found == False and sub1_found == False:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2_found == False and sub1_found == True:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2_found == True and sub1_found == False:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# # if sub1_found and sub2_found:
+# # break
+# # break
+
+# if len(gaps_list_sub3) == 0:
+# sub3_found = False
+# for b in range(len(synteny_df.columns)):
+# if (
+# sub3_found == False
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b] != 0
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b].split(".")[0]
+# == sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# ):
+# # sub1=sub_density['subgenome1'][small_breakpoints[i]['main_bp']]
+# # sub2=sub_density['subgenome2'][small_breakpoints[i]['main_bp']]
+# if sub2_found == False and sub1_found == False:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub3_found = True
+# if sub2_found == False and sub1_found == True:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub1 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]:
+# sub3 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub3_found = True
+# else:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# if sub2_found == True and sub1_found == False:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]:
+# sub3 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub3_found = True
+# else:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# if sub2_found == True and sub1_found == True:
+# if (
+# sub1 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# and sub2 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# ):
+# sub3 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub3_found = True
+# else:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# # if sub1_found and sub2_found:
+# # break
+# # break
+# for b in range(len(synteny_df.columns)):
+# if (
+# sub3_found == False
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b] != 0
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b].split(".")[0]
+# != sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b].split(".")[0]
+# != sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# and synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b].split(".")[0]
+# != sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ].split(".")[0]
+# ):
+# # sub1=sub_density['subgenome1'][small_breakpoints[i]['main_bp']]
+# # sub2=sub_density['subgenome2'][small_breakpoints[i]['main_bp']]
+
+# if sub2_found == False and sub1_found == False:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub3_found = True
+# if sub2_found == False and sub1_found == True:
+# sub2 = sub_density["subgenome2"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub1 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]:
+# sub3 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub3_found = True
+# else:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# if sub2_found == True and sub1_found == False:
+# sub1 = sub_density["subgenome1"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# if sub2 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]:
+# sub3 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub3_found = True
+# else:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# if sub2_found == True and sub1_found == True:
+# if (
+# sub1 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# and sub2 != synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# ):
+# sub3 = synteny_df.iloc[int(small_breakpoints[i]["Row start #"])][b]
+# sub3_found = True
+# else:
+# sub3 = sub_density["subgenome3"][
+# small_breakpoints[i]["main_bp"]
+# ]
+# sub3_found = True
+# # if sub1_found and sub2_found:
+# # break
+# # break
+# final_gaps_df = final_gaps_df.append(
+# {
+# "Row start #": small_breakpoints[i]["Row start #"],
+# "Row end #": small_breakpoints[i]["Row end #"],
+# "subgenome1": sub1,
+# "subgenome2": sub2,
+# "subgenome3": sub3,
+# },
+# ignore_index=True,
+# )
+
+# # break
+# #save the final dataframe to excel
+# final_gaps_df = check_gaps(final_gaps_df)
+# final_gaps_df.to_excel("final_gaps_df.xlsx")
+# print("=========================================")
+# print("Number of small + main blocks:" , len(final_gaps_df))
+# print("=========================================")
+
+# return final_gaps_df
+
+# final_BP = subgenome_assignment_all_BP("nodes.xlsx", "modified_synteny_chromosome_names.xlsx", small_BP)
+# # print(final_BP)
+
+# print("===========================================")
+# print("Accuracy of subgenome assignment(Main BP + Small BP):")
+# print("===========================================")
+# subgenome_overlap(GT, "final_gaps_df.xlsx", df_synteny, 3)
+