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- Removed the option to add metadata file (was not used anyway).
- Added the column 'Ref_genome' to the genome-specific final tables.
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@inbalpaz
inbalpaz authored and ipaz committed Sep 17, 2024
1 parent 1396d36 commit f2ca65d
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10 changes: 4 additions & 6 deletions README.md
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Expand Up @@ -95,9 +95,10 @@ python syntracker.py -out SynTracker_output/ -mode continue_all_genomes

```
python syntracker.py [-h] [-target target_directory_path] [-ref ref_directory_path]
[-out output_directory_path] [-metadata metadata_file]
[-mode 'new'/'continue'] [-cores number_of_cores] [-length region_length]
[--identity blast_identity] [--coverage blast_coverage] [--no_seed] [--avg_all]
[-out output_directory_path] [-mode 'new'/'continue']
[-cores number_of_cores] [-length region_length]
[--identity blast_identity] [--coverage blast_coverage]
[--no_seed] [--avg_all]
options:
-h, --help show this help message and exit
Expand All @@ -114,9 +115,6 @@ options:
already exists, it will be written over). When running in 'continue' mode, it is mandatory to provide the
path to the output directory of the run that is requested to be continued.
-metadata [metadata_file]
Path to a metadata file (optional). The file should be in CSV format and must include the sample ID.
-mode ['new'/'continue'/'continue_all_genomes']
The running mode: 'new' or 'continue' (default='new').
Start a new run or continue a previous run that has been terminated.
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134 changes: 67 additions & 67 deletions ...ple/E_coli_K-12_MG1655/final_output/E_coli_K-12_MG1655_avg_synteny_scores_100_regions.csv
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@@ -1,67 +1,67 @@
"Sample1","Sample2","Average_score","Compared_regions"
"ASM15512v1","ASM17195v1",0.970648281428632,100
"ASM15512v1","ASM2222v1",0.988920473138213,100
"ASM15512v1","ASM2516v1",0.978161328114248,100
"ASM15512v1","ASM666v1",0.975919136509695,100
"ASM15512v1","ASM886v1",0.985969167141804,100
"ASM15512v1","SRR10358485",0.806606914055079,100
"ASM15512v1","SRR10358486",0.807554933726527,100
"ASM15512v1","SRR10358487",0.776992389080627,100
"ASM15512v1","SRR10358488",0.818761499330412,100
"ASM15512v1","SRR10358489",0.84828596552558,100
"ASM15512v1","SRR10358491",0.814646741863062,100
"ASM17195v1","ASM2222v1",0.977094788525141,100
"ASM17195v1","ASM2516v1",0.965861654202739,100
"ASM17195v1","ASM666v1",0.971794204271571,100
"ASM17195v1","ASM886v1",0.97320828188072,100
"ASM17195v1","SRR10358485",0.83970920223097,100
"ASM17195v1","SRR10358486",0.842590019998246,100
"ASM17195v1","SRR10358487",0.813437959316661,100
"ASM17195v1","SRR10358488",0.809190154517898,100
"ASM17195v1","SRR10358489",0.819414075361978,100
"ASM17195v1","SRR10358491",0.799825275598122,100
"ASM2222v1","ASM2516v1",0.95197145416797,100
"ASM2222v1","ASM666v1",0.976048179173752,100
"ASM2222v1","ASM886v1",0.982857831518548,100
"ASM2222v1","SRR10358485",0.849367550382765,100
"ASM2222v1","SRR10358486",0.818296201737254,100
"ASM2222v1","SRR10358487",0.810906971060583,100
"ASM2222v1","SRR10358488",0.809238171153902,100
"ASM2222v1","SRR10358489",0.812160366755979,100
"ASM2222v1","SRR10358491",0.772850694481534,100
"ASM2516v1","ASM666v1",0.95347335249931,100
"ASM2516v1","ASM886v1",0.966119914282165,100
"ASM2516v1","SRR10358485",0.824138327942118,100
"ASM2516v1","SRR10358486",0.829807851894671,100
"ASM2516v1","SRR10358487",0.839520917950797,100
"ASM2516v1","SRR10358488",0.828379920427366,100
"ASM2516v1","SRR10358489",0.823770423799818,100
"ASM2516v1","SRR10358491",0.811384862924429,100
"ASM666v1","ASM886v1",0.959783005108187,100
"ASM666v1","SRR10358485",0.822929730197346,100
"ASM666v1","SRR10358486",0.815491119244996,100
"ASM666v1","SRR10358487",0.811613676609769,100
"ASM666v1","SRR10358488",0.841996793098517,100
"ASM666v1","SRR10358489",0.804308101764587,100
"ASM666v1","SRR10358491",0.831049501558925,100
"ASM886v1","SRR10358485",0.822163703852751,100
"ASM886v1","SRR10358486",0.838208363590133,100
"ASM886v1","SRR10358487",0.823862732968799,100
"ASM886v1","SRR10358488",0.801401216357652,100
"ASM886v1","SRR10358489",0.814795983505432,100
"ASM886v1","SRR10358491",0.812509979152218,100
"SRR10358485","SRR10358486",0.995145248714589,100
"SRR10358485","SRR10358487",0.984163548953185,100
"SRR10358485","SRR10358488",0.985269693184982,100
"SRR10358485","SRR10358489",0.996826331523995,100
"SRR10358485","SRR10358491",0.983610251241487,100
"SRR10358486","SRR10358487",1,100
"SRR10358486","SRR10358488",0.999984363487408,100
"SRR10358486","SRR10358489",0.99698970004336,100
"SRR10358486","SRR10358491",0.990855054153899,100
"SRR10358487","SRR10358488",0.999968709043022,100
"SRR10358487","SRR10358489",0.996966189133505,100
"SRR10358487","SRR10358491",0.999940860601824,100
"SRR10358488","SRR10358489",0.999985231641811,100
"SRR10358488","SRR10358491",0.999935645690511,100
"SRR10358489","SRR10358491",0.990793595300691,100
"Ref_genome","Sample1","Sample2","Average_score","Compared_regions"
"E_coli_K-12_MG1655","ASM15512v1","ASM17195v1",0.970648281428632,100
"E_coli_K-12_MG1655","ASM15512v1","ASM2222v1",0.988920473138213,100
"E_coli_K-12_MG1655","ASM15512v1","ASM2516v1",0.978161328114248,100
"E_coli_K-12_MG1655","ASM15512v1","ASM666v1",0.975919136509695,100
"E_coli_K-12_MG1655","ASM15512v1","ASM886v1",0.985969167141804,100
"E_coli_K-12_MG1655","ASM15512v1","SRR10358485",0.806606914055079,100
"E_coli_K-12_MG1655","ASM15512v1","SRR10358486",0.807554933726527,100
"E_coli_K-12_MG1655","ASM15512v1","SRR10358487",0.776992389080627,100
"E_coli_K-12_MG1655","ASM15512v1","SRR10358488",0.818761499330412,100
"E_coli_K-12_MG1655","ASM15512v1","SRR10358489",0.84828596552558,100
"E_coli_K-12_MG1655","ASM15512v1","SRR10358491",0.814646741863062,100
"E_coli_K-12_MG1655","ASM17195v1","ASM2222v1",0.977094788525141,100
"E_coli_K-12_MG1655","ASM17195v1","ASM2516v1",0.965861654202739,100
"E_coli_K-12_MG1655","ASM17195v1","ASM666v1",0.971794204271571,100
"E_coli_K-12_MG1655","ASM17195v1","ASM886v1",0.97320828188072,100
"E_coli_K-12_MG1655","ASM17195v1","SRR10358485",0.83970920223097,100
"E_coli_K-12_MG1655","ASM17195v1","SRR10358486",0.842590019998246,100
"E_coli_K-12_MG1655","ASM17195v1","SRR10358487",0.813437959316661,100
"E_coli_K-12_MG1655","ASM17195v1","SRR10358488",0.809190154517898,100
"E_coli_K-12_MG1655","ASM17195v1","SRR10358489",0.819414075361978,100
"E_coli_K-12_MG1655","ASM17195v1","SRR10358491",0.799825275598122,100
"E_coli_K-12_MG1655","ASM2222v1","ASM2516v1",0.95197145416797,100
"E_coli_K-12_MG1655","ASM2222v1","ASM666v1",0.976048179173752,100
"E_coli_K-12_MG1655","ASM2222v1","ASM886v1",0.982857831518548,100
"E_coli_K-12_MG1655","ASM2222v1","SRR10358485",0.849367550382765,100
"E_coli_K-12_MG1655","ASM2222v1","SRR10358486",0.818296201737254,100
"E_coli_K-12_MG1655","ASM2222v1","SRR10358487",0.810906971060583,100
"E_coli_K-12_MG1655","ASM2222v1","SRR10358488",0.809238171153902,100
"E_coli_K-12_MG1655","ASM2222v1","SRR10358489",0.812160366755979,100
"E_coli_K-12_MG1655","ASM2222v1","SRR10358491",0.772850694481534,100
"E_coli_K-12_MG1655","ASM2516v1","ASM666v1",0.95347335249931,100
"E_coli_K-12_MG1655","ASM2516v1","ASM886v1",0.966119914282165,100
"E_coli_K-12_MG1655","ASM2516v1","SRR10358485",0.824138327942118,100
"E_coli_K-12_MG1655","ASM2516v1","SRR10358486",0.829807851894671,100
"E_coli_K-12_MG1655","ASM2516v1","SRR10358487",0.839520917950797,100
"E_coli_K-12_MG1655","ASM2516v1","SRR10358488",0.828379920427366,100
"E_coli_K-12_MG1655","ASM2516v1","SRR10358489",0.823770423799818,100
"E_coli_K-12_MG1655","ASM2516v1","SRR10358491",0.811384862924429,100
"E_coli_K-12_MG1655","ASM666v1","ASM886v1",0.959783005108187,100
"E_coli_K-12_MG1655","ASM666v1","SRR10358485",0.822929730197346,100
"E_coli_K-12_MG1655","ASM666v1","SRR10358486",0.815491119244996,100
"E_coli_K-12_MG1655","ASM666v1","SRR10358487",0.811613676609769,100
"E_coli_K-12_MG1655","ASM666v1","SRR10358488",0.841996793098517,100
"E_coli_K-12_MG1655","ASM666v1","SRR10358489",0.804308101764587,100
"E_coli_K-12_MG1655","ASM666v1","SRR10358491",0.831049501558925,100
"E_coli_K-12_MG1655","ASM886v1","SRR10358485",0.822163703852751,100
"E_coli_K-12_MG1655","ASM886v1","SRR10358486",0.838208363590133,100
"E_coli_K-12_MG1655","ASM886v1","SRR10358487",0.823862732968799,100
"E_coli_K-12_MG1655","ASM886v1","SRR10358488",0.801401216357652,100
"E_coli_K-12_MG1655","ASM886v1","SRR10358489",0.814795983505432,100
"E_coli_K-12_MG1655","ASM886v1","SRR10358491",0.812509979152218,100
"E_coli_K-12_MG1655","SRR10358485","SRR10358486",0.995145248714589,100
"E_coli_K-12_MG1655","SRR10358485","SRR10358487",0.984163548953185,100
"E_coli_K-12_MG1655","SRR10358485","SRR10358488",0.985269693184982,100
"E_coli_K-12_MG1655","SRR10358485","SRR10358489",0.996826331523995,100
"E_coli_K-12_MG1655","SRR10358485","SRR10358491",0.983610251241487,100
"E_coli_K-12_MG1655","SRR10358486","SRR10358487",1,100
"E_coli_K-12_MG1655","SRR10358486","SRR10358488",0.999984363487408,100
"E_coli_K-12_MG1655","SRR10358486","SRR10358489",0.99698970004336,100
"E_coli_K-12_MG1655","SRR10358486","SRR10358491",0.990855054153899,100
"E_coli_K-12_MG1655","SRR10358487","SRR10358488",0.999968709043022,100
"E_coli_K-12_MG1655","SRR10358487","SRR10358489",0.996966189133505,100
"E_coli_K-12_MG1655","SRR10358487","SRR10358491",0.999940860601824,100
"E_coli_K-12_MG1655","SRR10358488","SRR10358489",0.999985231641811,100
"E_coli_K-12_MG1655","SRR10358488","SRR10358491",0.999935645690511,100
"E_coli_K-12_MG1655","SRR10358489","SRR10358491",0.990793595300691,100
134 changes: 67 additions & 67 deletions ...ple/E_coli_K-12_MG1655/final_output/E_coli_K-12_MG1655_avg_synteny_scores_200_regions.csv
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"Sample1","Sample2","Average_score","Compared_regions"
"ASM15512v1","ASM17195v1",0.974409823863967,200
"ASM15512v1","ASM2222v1",0.981137402165184,200
"ASM15512v1","ASM2516v1",0.967012514024994,200
"ASM15512v1","ASM666v1",0.972798012230779,200
"ASM15512v1","ASM886v1",0.979324195196183,200
"ASM15512v1","SRR10358485",0.816289796857911,200
"ASM15512v1","SRR10358486",0.807551089338847,200
"ASM15512v1","SRR10358487",0.808374220396527,200
"ASM15512v1","SRR10358488",0.83252211495731,200
"ASM15512v1","SRR10358489",0.830606853690981,200
"ASM15512v1","SRR10358491",0.808821529363191,200
"ASM17195v1","ASM2222v1",0.996922949680762,200
"ASM17195v1","ASM2516v1",0.957076254207283,200
"ASM17195v1","ASM666v1",0.967453178980589,200
"ASM17195v1","ASM886v1",0.991383794520002,200
"ASM17195v1","SRR10358485",0.834702122913191,200
"ASM17195v1","SRR10358486",0.813760485001912,200
"ASM17195v1","SRR10358487",0.79020256332172,200
"ASM17195v1","SRR10358488",0.800587220741443,200
"ASM17195v1","SRR10358489",0.815859500718599,200
"ASM17195v1","SRR10358491",0.821658046303846,200
"ASM2222v1","ASM2516v1",0.953127597865068,200
"ASM2222v1","ASM666v1",0.9615273108388,200
"ASM2222v1","ASM886v1",0.980643790116671,200
"ASM2222v1","SRR10358485",0.830164021174577,200
"ASM2222v1","SRR10358486",0.802021298328764,200
"ASM2222v1","SRR10358487",0.814082377829062,200
"ASM2222v1","SRR10358488",0.835988090153356,200
"ASM2222v1","SRR10358489",0.81809359403815,200
"ASM2222v1","SRR10358491",0.799109902187953,200
"ASM2516v1","ASM666v1",0.953961864073628,200
"ASM2516v1","ASM886v1",0.955035161347835,200
"ASM2516v1","SRR10358485",0.825771096709453,200
"ASM2516v1","SRR10358486",0.806576986326347,200
"ASM2516v1","SRR10358487",0.829868973511724,200
"ASM2516v1","SRR10358488",0.843130277732955,200
"ASM2516v1","SRR10358489",0.800363801652888,200
"ASM2516v1","SRR10358491",0.824541420684774,200
"ASM666v1","ASM886v1",0.975429168926038,200
"ASM666v1","SRR10358485",0.804043179344708,200
"ASM666v1","SRR10358486",0.821982628202101,200
"ASM666v1","SRR10358487",0.827958024698618,200
"ASM666v1","SRR10358488",0.808333066747167,200
"ASM666v1","SRR10358489",0.814243806488314,200
"ASM666v1","SRR10358491",0.828004253468836,200
"ASM886v1","SRR10358485",0.828502284405886,200
"ASM886v1","SRR10358486",0.825907982560536,200
"ASM886v1","SRR10358487",0.808706104723354,200
"ASM886v1","SRR10358488",0.81706381016285,200
"ASM886v1","SRR10358489",0.813836394966262,200
"ASM886v1","SRR10358491",0.807676025261368,200
"SRR10358485","SRR10358486",0.992674861589901,200
"SRR10358485","SRR10358487",0.996817380769312,200
"SRR10358485","SRR10358488",0.995910005885932,200
"SRR10358485","SRR10358489",0.995298651646181,200
"SRR10358485","SRR10358491",0.986876526299551,200
"SRR10358486","SRR10358487",0.999993042673324,200
"SRR10358486","SRR10358488",0.99758133501363,200
"SRR10358486","SRR10358489",0.999969498080782,200
"SRR10358486","SRR10358491",0.990751346416484,200
"SRR10358487","SRR10358488",0.996079241037144,200
"SRR10358487","SRR10358489",0.998487458357087,200
"SRR10358487","SRR10358491",0.993381465072069,200
"SRR10358488","SRR10358489",0.996959661175289,200
"SRR10358488","SRR10358491",0.995919587919752,200
"SRR10358489","SRR10358491",0.994464521500433,200
"Ref_genome","Sample1","Sample2","Average_score","Compared_regions"
"E_coli_K-12_MG1655","ASM15512v1","ASM17195v1",0.974409823863967,200
"E_coli_K-12_MG1655","ASM15512v1","ASM2222v1",0.981137402165184,200
"E_coli_K-12_MG1655","ASM15512v1","ASM2516v1",0.967012514024994,200
"E_coli_K-12_MG1655","ASM15512v1","ASM666v1",0.972798012230779,200
"E_coli_K-12_MG1655","ASM15512v1","ASM886v1",0.979324195196183,200
"E_coli_K-12_MG1655","ASM15512v1","SRR10358485",0.816289796857911,200
"E_coli_K-12_MG1655","ASM15512v1","SRR10358486",0.807551089338847,200
"E_coli_K-12_MG1655","ASM15512v1","SRR10358487",0.808374220396527,200
"E_coli_K-12_MG1655","ASM15512v1","SRR10358488",0.83252211495731,200
"E_coli_K-12_MG1655","ASM15512v1","SRR10358489",0.830606853690981,200
"E_coli_K-12_MG1655","ASM15512v1","SRR10358491",0.808821529363191,200
"E_coli_K-12_MG1655","ASM17195v1","ASM2222v1",0.996922949680762,200
"E_coli_K-12_MG1655","ASM17195v1","ASM2516v1",0.957076254207283,200
"E_coli_K-12_MG1655","ASM17195v1","ASM666v1",0.967453178980589,200
"E_coli_K-12_MG1655","ASM17195v1","ASM886v1",0.991383794520002,200
"E_coli_K-12_MG1655","ASM17195v1","SRR10358485",0.834702122913191,200
"E_coli_K-12_MG1655","ASM17195v1","SRR10358486",0.813760485001912,200
"E_coli_K-12_MG1655","ASM17195v1","SRR10358487",0.79020256332172,200
"E_coli_K-12_MG1655","ASM17195v1","SRR10358488",0.800587220741443,200
"E_coli_K-12_MG1655","ASM17195v1","SRR10358489",0.815859500718599,200
"E_coli_K-12_MG1655","ASM17195v1","SRR10358491",0.821658046303846,200
"E_coli_K-12_MG1655","ASM2222v1","ASM2516v1",0.953127597865068,200
"E_coli_K-12_MG1655","ASM2222v1","ASM666v1",0.9615273108388,200
"E_coli_K-12_MG1655","ASM2222v1","ASM886v1",0.980643790116671,200
"E_coli_K-12_MG1655","ASM2222v1","SRR10358485",0.830164021174577,200
"E_coli_K-12_MG1655","ASM2222v1","SRR10358486",0.802021298328764,200
"E_coli_K-12_MG1655","ASM2222v1","SRR10358487",0.814082377829062,200
"E_coli_K-12_MG1655","ASM2222v1","SRR10358488",0.835988090153356,200
"E_coli_K-12_MG1655","ASM2222v1","SRR10358489",0.81809359403815,200
"E_coli_K-12_MG1655","ASM2222v1","SRR10358491",0.799109902187953,200
"E_coli_K-12_MG1655","ASM2516v1","ASM666v1",0.953961864073628,200
"E_coli_K-12_MG1655","ASM2516v1","ASM886v1",0.955035161347835,200
"E_coli_K-12_MG1655","ASM2516v1","SRR10358485",0.825771096709453,200
"E_coli_K-12_MG1655","ASM2516v1","SRR10358486",0.806576986326347,200
"E_coli_K-12_MG1655","ASM2516v1","SRR10358487",0.829868973511724,200
"E_coli_K-12_MG1655","ASM2516v1","SRR10358488",0.843130277732955,200
"E_coli_K-12_MG1655","ASM2516v1","SRR10358489",0.800363801652888,200
"E_coli_K-12_MG1655","ASM2516v1","SRR10358491",0.824541420684774,200
"E_coli_K-12_MG1655","ASM666v1","ASM886v1",0.975429168926038,200
"E_coli_K-12_MG1655","ASM666v1","SRR10358485",0.804043179344708,200
"E_coli_K-12_MG1655","ASM666v1","SRR10358486",0.821982628202101,200
"E_coli_K-12_MG1655","ASM666v1","SRR10358487",0.827958024698618,200
"E_coli_K-12_MG1655","ASM666v1","SRR10358488",0.808333066747167,200
"E_coli_K-12_MG1655","ASM666v1","SRR10358489",0.814243806488314,200
"E_coli_K-12_MG1655","ASM666v1","SRR10358491",0.828004253468836,200
"E_coli_K-12_MG1655","ASM886v1","SRR10358485",0.828502284405886,200
"E_coli_K-12_MG1655","ASM886v1","SRR10358486",0.825907982560536,200
"E_coli_K-12_MG1655","ASM886v1","SRR10358487",0.808706104723354,200
"E_coli_K-12_MG1655","ASM886v1","SRR10358488",0.81706381016285,200
"E_coli_K-12_MG1655","ASM886v1","SRR10358489",0.813836394966262,200
"E_coli_K-12_MG1655","ASM886v1","SRR10358491",0.807676025261368,200
"E_coli_K-12_MG1655","SRR10358485","SRR10358486",0.992674861589901,200
"E_coli_K-12_MG1655","SRR10358485","SRR10358487",0.996817380769312,200
"E_coli_K-12_MG1655","SRR10358485","SRR10358488",0.995910005885932,200
"E_coli_K-12_MG1655","SRR10358485","SRR10358489",0.995298651646181,200
"E_coli_K-12_MG1655","SRR10358485","SRR10358491",0.986876526299551,200
"E_coli_K-12_MG1655","SRR10358486","SRR10358487",0.999993042673324,200
"E_coli_K-12_MG1655","SRR10358486","SRR10358488",0.99758133501363,200
"E_coli_K-12_MG1655","SRR10358486","SRR10358489",0.999969498080782,200
"E_coli_K-12_MG1655","SRR10358486","SRR10358491",0.990751346416484,200
"E_coli_K-12_MG1655","SRR10358487","SRR10358488",0.996079241037144,200
"E_coli_K-12_MG1655","SRR10358487","SRR10358489",0.998487458357087,200
"E_coli_K-12_MG1655","SRR10358487","SRR10358491",0.993381465072069,200
"E_coli_K-12_MG1655","SRR10358488","SRR10358489",0.996959661175289,200
"E_coli_K-12_MG1655","SRR10358488","SRR10358491",0.995919587919752,200
"E_coli_K-12_MG1655","SRR10358489","SRR10358491",0.994464521500433,200
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