fixed minor typos

module1_2/README.md

+
+# raccroche-v2
+
+This repository contains the code for Module 1 and 2 of the RACCROCHE pipeline.
+
+
+## Overview
+Given the phylogenetic relationships of several extant species, the reconstruction of their ancestral genomes at the gene and chromosome level is made difficult by the cycles of whole genome doubling followed by fractionation in plant lineages. Fractionation scrambles the gene adjacencies that enable existing reconstruction methods. We propose an alternative approach that postpones the selection of gene adjacencies for reconstructing small ancestral segments and instead accumulates a very large number of syntenically validated candidate adjacencies to produce long ancestral contigs through maximum weight matching. Likewise, we do not construct chromosomes by successively piecing together contigs into larger segments, but instead count all contig co-occurrences on the input genomes and cluster these, so that chromosomal assemblies of contigs all emerge naturally ordered at each ancestral node of the phylogeny. These strategies result in substantially more complete reconstructions than existing methods. We deploy a number of quality measures: contig lengths, continuity of contig structure on successive ancestors, coverage of the reconstruction on the input genomes, and rearrangement implications of the chromosomal structures obtained. The reconstructed ancestors can be functionally annotated and are visualized by painting the ancestral projections on the descendant genomes, and by highlighting syntenic ancestor-descendant relationships. Our methods can be applied to genomes drawn from a broad range of clades or orders.
+
+### Module 1: construct gene families and list candidate adjacencies
+- Step 1: Pre-process gene families
+- Step 2: List generalized adjacencies
+- Step 3: List candidate adjacencies
+
+### Module 2: construct ancestral contigs through Maximum Weight Matching
+- Step 4: Construct contigs through Maximum Weight Matching
+## Run Locally
+
+Clone the project
+
+```bash
+  git clone https://git.cs.usask.ca/nma904/module1_2.git
+```
+
+Go to the project directory
+
+```bash
+  cd module1_2
+```
+
+Add input data to the inputData folder
+
+Edit config.yaml to desired specifications
+
+### Run Modules Through Command Line
+
+Run the module1_main.py file
+```bash
+  python module1_main.py --config path_to_config_file
+```
+
+### Run Modules Using Module1_2.ipynb
+
+Run each cell block in the Jupyter Notebook.
+
+
+
+
+
+## Authors
+
+- [Qiaoji Xu](https://github.com/Qiaojilim)
+- [Lingling Jin](https://github.com/jin-repo/RACCROCHE)
+- Chunfang Zheng
+- James H. Leeben-Mack
+- David Sankoff
+- [Alex Liu](https://github.com/alexl0806)
+
+## Emails
+- limqiaojixu@gmail.com
+- lingling.jin@cs.usask.ca
+
+
+## License
+
+[BSD](https://en.wikipedia.org/wiki/BSD_licenses/)
+
+
+## Citations
+
+If you use the raccroche pipline for ancestral contigs reconstruction, please cite:
+[RACCROCHE: ancestral flowering plantchromosomes and gene ordersbased on generalized adjacenciesand chromosomal gene co-occurrences](https://link.springer.com/chapter/10.1007/978-3-030-79290-9_9)

module1_2/inputData/project-monocots/phyloTree.txt

 #treenode_number	window_size	genome_number	gf_number
 # Tree in Newick Format:
-(((51364, 54711), 51051), ((25734, 33018), 33908))
-#(((Spirodela_51364, Acorus_54711), Dioscorea_51051), ((Ananas_25734, Elaeis_33018), Asparagus_33908))
+#(((51364, 54711), 51051), ((25734, 33018), 33908))
+(((Spirodela_51364, Acorus_54711), Dioscorea_51051), ((Ananas_25734, Elaeis_33018), Asparagus_33908))
 #51364	54711	25734,33018,33908,51051
 #51051	51364,54711	25734,33018,33908
 #33908	25734,33018	51051,51364,54711

module1_2/src/module1_main.py

@@ -128,7 +128,7 @@ def main():
 
         # Performing Maximum Weight Matching
         print("Starting Maximum Weight Matching")
-        # maxWeightMatching(mwm_input, outfile_mwmout)
+        maxWeightMatching(mwm_input, outfile_mwmout)
         # print("Maximum Weight Matching DONE")
 
         # Constructing Ancestral Contigs