module1_2/inputData/project-legumes8/karyotype/karyotype_64734_Quillaja.txt

 chr	size
-1	19561049
-2	20977047
-3	37318896
-4	34047100
-5	21375137
-6	28584509
-7	26440503
-8	28358298
-9	26458845
-10	21706344
-11	21697428
-12	21470783
-13	18106809
-14	20802709
\ No newline at end of file
+quisa.S10.gnm1.Chr01	19561049
+quisa.S10.gnm1.Chr02	20977047
+quisa.S10.gnm1.Chr03	37318896
+quisa.S10.gnm1.Chr04	34047100
+quisa.S10.gnm1.Chr05	21375137
+quisa.S10.gnm1.Chr06	28584509
+quisa.S10.gnm1.Chr07	26440503
+quisa.S10.gnm1.Chr08	28358298
+quisa.S10.gnm1.Chr09	26458845
+quisa.S10.gnm1.Chr10	21706344
+quisa.S10.gnm1.Chr11	21697428
+quisa.S10.gnm1.Chr12	21470783
+quisa.S10.gnm1.Chr13	18106809
+quisa.S10.gnm1.Chr14	20802709
\ No newline at end of file

module1_2/inputData/project-legumes8/karyotype/karyotype_64742_Cercis.txt

 chr	size
-1	57468748
-2	51272464
-3	49996358
-4	48286772
-5	45669363
-6	45655421
-7	41929180
\ No newline at end of file
+cerca.ISC453364.gnm3.Chr01	57468748
+cerca.ISC453364.gnm3.Chr02	51272464
+cerca.ISC453364.gnm3.Chr03	49996358
+cerca.ISC453364.gnm3.Chr04	48286772
+cerca.ISC453364.gnm3.Chr05	45669363
+cerca.ISC453364.gnm3.Chr06	45655421
+cerca.ISC453364.gnm3.Chr07	41929180
\ No newline at end of file

module1_2/inputData/project-legumes8/karyotype/karyotype_64767_Sindora.txt

 chr	size
-1	136071090
-2	116487353
-3	109186524
-4	91914064
-5	88658134
-6	84872623
-7	83373435
-8	81990953
-9	76993406
-10	75912673
-11	75144154
-12	71117942
\ No newline at end of file
+singl.CAF01.gnm1.Chr01	136071090
+singl.CAF01.gnm1.Chr02	116487353
+singl.CAF01.gnm1.Chr03	109186524
+singl.CAF01.gnm1.Chr04	91914064
+singl.CAF01.gnm1.Chr05	88658134
+singl.CAF01.gnm1.Chr06	84872623
+singl.CAF01.gnm1.Chr07	83373435
+singl.CAF01.gnm1.Chr08	81990953
+singl.CAF01.gnm1.Chr09	76993406
+singl.CAF01.gnm1.Chr10	75912673
+singl.CAF01.gnm1.Chr11	75144154
+singl.CAF01.gnm1.Chr12	71117942
\ No newline at end of file

module1_2/inputData/project-legumes8/karyotype/karyotype_64768_Senna.txt

 chr	size
-1	32816166
-2	42009719
-3	37860065
-4	30689712
-5	52777034
-6	46512068
-7	30975534
-8	49705205
-9	35860388
-10	41499577
-11	30871617
-12	29799933
-13	41270226
\ No newline at end of file
+sento.Myeongyun.gnm1.Chr01	32816166
+sento.Myeongyun.gnm1.Chr02	42009719
+sento.Myeongyun.gnm1.Chr03	37860065
+sento.Myeongyun.gnm1.Chr04	30689712
+sento.Myeongyun.gnm1.Chr05	52777034
+sento.Myeongyun.gnm1.Chr06	46512068
+sento.Myeongyun.gnm1.Chr07	30975534
+sento.Myeongyun.gnm1.Chr08	49705205
+sento.Myeongyun.gnm1.Chr09	35860388
+sento.Myeongyun.gnm1.Chr10	41499577
+sento.Myeongyun.gnm1.Chr11	30871617
+sento.Myeongyun.gnm1.Chr12	29799933
+sento.Myeongyun.gnm1.Chr13	41270226
\ No newline at end of file

module1_2/inputData/project-legumes8/karyotype/karyotype_64962_Prunus.txt

 chr	size
-1	47851208
-2	30405870
-3	27368013
-4	25843236
-5	18496696
-6	30767194
-7	22388614
-8	22573980
\ No newline at end of file
+prupe.Lovell.gnm2.Pp01	47851208
+prupe.Lovell.gnm2.Pp02	30405870
+prupe.Lovell.gnm2.Pp03	27368013
+prupe.Lovell.gnm2.Pp04	25843236
+prupe.Lovell.gnm2.Pp05	18496696
+prupe.Lovell.gnm2.Pp06	30767194
+prupe.Lovell.gnm2.Pp07	22388614
+prupe.Lovell.gnm2.Pp08	22573980
\ No newline at end of file

module1_2/inputData/project-legumes8/karyotype/karyotype_64963_Phaseolus.txt

 chr	size
-1	51433939
-2	49670989
-3	53438756
-4	48048378
-5	40923498
-6	31236378
-7	40041001
-8	63048260
-9	38250102
-10	44302882
-11	53580169
\ No newline at end of file
+phavu.G19833.gnm2.Chr01	51433939
+phavu.G19833.gnm2.Chr02	49670989
+phavu.G19833.gnm2.Chr03	53438756
+phavu.G19833.gnm2.Chr04	48048378
+phavu.G19833.gnm2.Chr05	40923498
+phavu.G19833.gnm2.Chr06	31236378
+phavu.G19833.gnm2.Chr07	40041001
+phavu.G19833.gnm2.Chr08	63048260
+phavu.G19833.gnm2.Chr09	38250102
+phavu.G19833.gnm2.Chr10	44302882
+phavu.G19833.gnm2.Chr11	53580169
\ No newline at end of file

module1_2/inputData/project-legumes8/karyotype/karyotype_64964_Medicago.txt

 chr	size
-1	52991155
-2	45729672
-3	55515152
-4	56582383
-5	43630510
-6	35275713
-7	49172423
-8	45569985
\ No newline at end of file
+medtr.A17_HM341.gnm4.chr1	52991155
+medtr.A17_HM341.gnm4.chr2	45729672
+medtr.A17_HM341.gnm4.chr3	55515152
+medtr.A17_HM341.gnm4.chr4	56582383
+medtr.A17_HM341.gnm4.chr5	43630510
+medtr.A17_HM341.gnm4.chr6	35275713
+medtr.A17_HM341.gnm4.chr7	49172423
+medtr.A17_HM341.gnm4.chr8	45569985
\ No newline at end of file

module1_2/inputData/project-legumes8/karyotype/karyotype_64965_Vitis.txt

 chr	size
-1	23037639
-2	18779844
-3	19341862
-4	23867706
-5	25021643
-6	21508407
-7	21026613
-8	22385789
-9	23006712
-10	18140952
-11	19818926
-12	22702307
-13	24396255
-14	30274277
-15	20304914
-16	22053297
-17	17126926
-18	29360087
-19	24021853
\ No newline at end of file
+vitvi.PN40024.gnm2.chr1	23037639
+vitvi.PN40024.gnm2.chr2	18779844
+vitvi.PN40024.gnm2.chr3	19341862
+vitvi.PN40024.gnm2.chr4	23867706
+vitvi.PN40024.gnm2.chr5	25021643
+vitvi.PN40024.gnm2.chr6	21508407
+vitvi.PN40024.gnm2.chr7	21026613
+vitvi.PN40024.gnm2.chr8	22385789
+vitvi.PN40024.gnm2.chr9	23006712
+vitvi.PN40024.gnm2.chr10	18140952
+vitvi.PN40024.gnm2.chr11	19818926
+vitvi.PN40024.gnm2.chr12	22702307
+vitvi.PN40024.gnm2.chr13	24396255
+vitvi.PN40024.gnm2.chr14	30274277
+vitvi.PN40024.gnm2.chr15	20304914
+vitvi.PN40024.gnm2.chr16	22053297
+vitvi.PN40024.gnm2.chr17	17126926
+vitvi.PN40024.gnm2.chr18	29360087
+vitvi.PN40024.gnm2.chr19	24021853
\ No newline at end of file

module1_2/inputData/project-monocots/config.yaml

 # project name
-project_name: "project-monocots"
+project_name: "project-buxus"
 
 # input : path to genome information file
 input_file:
@@ -52,21 +52,21 @@ gf3: 1
 K: 7
 
 ## set thresholds
-ctgLen: 1   ## minimum length in each contig
-nctg: 250    ## only include first nctg contigs
+#ctgLen: 1   ## minimum length in each contig
+#nctg: 250    ## only include first nctg contigs
 
 ## threshold of distance (1MB) between two genes in the same contig on the same chromosome
 ## if the distance between two genes is smaller than the threshold, merge them into one block
-DIS.threshold: 1000000
+#DIS.threshold: 1000000
 
 ## threshold to visualize the gene/block (150 kb)
 ## if a block is less than this length, do not show it --> keep the plot clean
-blockLEN.threshold: 150000
+#blockLEN.threshold: 150000
 
 
 ## threshold for coocurrence analysis
 ## only count blocks that are longer than 15KB
-lenBLK.threshold: 15000
+#lenBLK.threshold: 15000
 
 
 

module1_2/inputData/project-monocots/karyotype/karyotype_25734_Ananas.txt

+chr	size
+LG01	24880688
+LG02	17334668
+LG03	16781886
+LG04	15584765
+LG05	15024279
+LG06	14747297
+LG07	14728688
+LG08	13970067
+LG09	13841557
+LG10	13112115
+LG11	13096665
+LG12	12612916
+LG13	11759267
+LG14	11705491
+LG15	11365478
+LG16	11174208
+LG17	11156084
+LG18	10911977
+LG19	10815949
+LG20	10792357
+LG21	10645290
+LG22	10398566
+LG23	7979763
+LG24	7684463
+LG25	3739203

module1_2/inputData/project-monocots/karyotype/karyotype_33018_Elaeis.txt

+chr	size
+REF_ELAGV01 	68435666
+REF_ELAGV02 	65558141
+REF_ELAGV03 	60060032
+REF_ELAGV04 	57251647
+REF_ELAGV05 	51955539
+REF_ELAGV06 	44357769
+REF_ELAGV07 	43454766
+REF_ELAGV08 	40195399
+REF_ELAGV09 	38056896
+REF_ELAGV10 	31890735
+REF_ELAGV11	30068910
+REF_ELAGV12	28800575
+REF_ELAGV13	27817470
+REF_ELAGV14	24379743
+REF_ELAGV15	24314465
+REF_ELAGV16	21371083

module1_2/inputData/project-monocots/karyotype/karyotype_33908_Asparagus.txt

+chr	size
+AsparagusV1_01	132393784
+AsparagusV1_02	84732013
+AsparagusV1_03	113259003
+AsparagusV1_04	146560859
+AsparagusV1_05	131469567
+AsparagusV1_06	78779235
+AsparagusV1_07	151357931
+AsparagusV1_08	131339754
+AsparagusV1_09	68543460
+AsparagusV1_10	73452336

module1_2/inputData/project-monocots/karyotype/karyotype_51051_Dioscorea.txt

+chr	size
+1	31431123
+2	33969142
+3	19547260
+4	27749968
+5	32871075
+6	32866201
+7	18053115
+8	28021425
+9	23324680
+10	17904088
+11	17195437
+12	25272979
+13	29719729
+14	15713101
+15	10474557
+16	23371965
+17	20585887
+18	22795539
+19	9927364
+20	10677198
+21	5203141

module1_2/inputData/project-monocots/karyotype/karyotype_51364_Spirodela.txt

+chr	size
+1	11560055
+2	8180930
+3	8870115
+4	9537711
+5	7072156
+6	8333076
+7	7949387
+8	8482602
+9	7754086
+10	7963964
+11	6749155	
+12	5993893
+13	6317482
+14	5575328
+15	4557367
+16	5820572
+17	4601490
+18	5315945
+19	3959434
+20	3997407

module1_2/inputData/project-monocots/karyotype/karyotype_54711_Acorus.txt

+chr	size
1	37743429
2	34360390
3	33772675
4	31994915
5	31167455
6	30970160
7	30771956
8	28400560
9	28235908
10	25518903
11	25169648
12	24790462
\ No newline at end of file

module1_2/src/Genome.py

@@ -81,7 +81,7 @@ class Genome:
                     f.write(chromosome + " ")
 
                     for gene in genes:
-                        f.write("%s " % genes)
+                        f.write("%s " % gene)
 
                     f.write("\n")