Support cleaner output naming in dot_plot_v2.py and lolliplot.py

dot_plot/dot_plot_v2.py

@@ -2188,7 +2188,7 @@ def main():
     ############################### SUMMARY ###############################
 
     # Write summary output file
-    with open('log.txt', 'w') as out:
+    with open(f'log_{args.clinvar_class_type}.txt', 'w') as out:
         summary, summary_df = generate_summary(data = dataframe,
                                                d_cutoff = args.demask_threshold,
                                                r_cutoff = args.revel_threshold,
@@ -2232,7 +2232,7 @@ def main():
 ################################# AM CSV #################################
     filtered_am = filter_vep_summary(summary_df, classification_df, args.AMx, args.adf)
 
-    filtered_am.to_csv('mechanistic_indicators_out.csv', index=True)
+    filtered_am.to_csv(f'mechanistic_indicators_out_{args.clinvar_class_type}.csv', index=True)
 
 if __name__ == '__main__':
     main()

dot_plot/examples_v2/ensemble_mode/log.txt → dot_plot/examples_v2/ensemble_mode/log_aggregated.txt

@@ -39,10 +39,10 @@ Summary of the effects.
  - 133 variants are potentially damaging in terms of removing the function related to a phosphorylation. [cabsflex] See csv file for details.
  - 591 variants are predicted with damaging long range effects on pocket site(s). [md] See csv file for details.
  - Variants with multiple effects:
--- F113E, F113A, P190R, V197P, Y234D, F113S, V197D, Y234Q, Y220P, V218G, R249P, A138P, V197R, Y205N, P190F, V197N, Y234N, Y234T, P151R, Y220C, F270Q, I232S, Y236D, Y220D, F113T, F270G, Y205K, Y236H, Q165P, Y234C, Y234S, H193R, F270P, R158P, F113D, Y236G, C275R, F270D, Y236R, P151H, Y205S, Y236K, F270K, Y236C, Y205G, M160P, Y220G, Y205R, Y205T, Y234G, Y205D, V203D, Y205Q, F270N, I232G, Y236S, F270A, F113P, Y236P, H168P, Q136P, Y234R, Y220S, Y205E, Y103P, F270C, F113Q, F113R, V197G, F113N, Y236N, V197W, F270E, F270T, Y236T, Y234P, Y205A, V197Y, F270S, F113C, E198P, Y220A, Y220T, V216S, Y205P, I232D, V216P, Y234K, P151K, F113V, V197S, Y107G, R110P, I232A, F113K, H179P, R196P, V203K, V216G, I232R, Y205V, V173G, I232P, M237P, H193P, I195R, V197K, V203P, P190H, V218P, P151F, Y236E, F270R, Y234E, Y220N, C275K, V203G, Y205C, F113G, V197H, V216D, Y220E, Y236Q, Y234A, Y236A, Y205I -> [stability, long_range]
--- Y220S, Y220C, Y220P, R249P, Y220G, Y220A, Y220E, Y220T, T155P, T155G, Y220D, Y220N -> [stability, ptm]
--- Y220M, Y220S, R249N, R249Q, R249M, R249L, R249W, R249C, Y220I, R249G, Y220P, R249P, R249Y, R249A, R249S, R249F, R249H, Y220N, R249T, Y220C, Y220Q, R249I, Y220G, Y220E, Y220A, Y220T, Y220K, R249E, Y220D, Y220R, Y220H, R249V, R249D, Y220V, Y220L -> [long_range, ptm]
--- Y220S, Y220C, Y220P, R249P, Y220G, Y220E, Y220A, Y220T, Y220D, Y220N -> [stability, long_range, ptm]
+-- Y236Q, Y220T, V197N, V216S, Y236S, Y205K, Y205P, V197G, Y234D, Q136P, H193P, F270C, I232A, F113A, Y236D, V203G, Y234G, R249P, E198P, Y234P, F113D, V197W, V203K, Y205S, Y234C, F270K, F113V, Y205E, F270R, V216P, P190R, M237P, Y205I, F270G, P151F, Y236T, I232D, H193R, Y236G, Y220S, Y236C, Y205T, P190H, V203D, F113Q, Y220C, Y234E, Y236N, Y205D, Y236P, I232R, F113P, Y220G, Y236R, V197D, V173G, Y205Q, V197K, V216G, Q165P, Y205N, Y220E, I232P, Y205R, Y220P, Y220A, Y234R, F113T, Y234A, Y236K, V197H, F113S, M160P, Y103P, Y220N, Y236E, V216D, Y205A, F113C, C275R, F270E, V197R, F270T, V197Y, Y205V, Y234S, P151H, R158P, Y205C, A138P, Y236H, Y205G, F270P, P151K, Y236A, R196P, F270N, V218G, F113N, C275K, I195R, I232G, Y234N, Y234Q, F270A, F270S, I232S, V218P, H168P, Y234K, F113G, Y234T, R110P, V197P, F113R, Y107G, F113E, P190F, P151R, F270D, Y220D, H179P, F113K, F270Q, V203P, V197S -> [stability, long_range]
+-- Y220P, T155G, Y220A, Y220G, Y220C, Y220N, Y220E, Y220S, Y220T, Y220D, R249P, T155P -> [stability, ptm]
+-- Y220P, Y220A, Y220L, R249A, Y220I, R249T, Y220S, Y220K, R249Q, Y220T, Y220M, R249G, Y220C, Y220N, R249E, R249L, R249P, Y220H, Y220G, R249V, R249D, R249I, R249H, Y220D, R249M, R249C, Y220V, R249Y, R249N, Y220E, R249F, Y220Q, R249S, R249W, Y220R -> [long_range, ptm]
+-- Y220P, Y220A, Y220G, Y220C, Y220N, Y220E, Y220S, Y220T, Y220D, R249P -> [stability, long_range, ptm]
 - We aggregated all the variants that have at least one of the MAVISp modules with a predicted damaging effect (except for PTM.function) and retained only the ones with a REVEL score higher than 0.5 for a total of 287 variants which could be of interest for further investigation:
 -- ['P98H', 'P98L', 'P98S', 'S99F', 'S99P', 'Y103C', 'Y103H', 'G105C', 'G105D', 'G105R', 'G105V', 'S106R', 'Y107C', 'Y107D', 'Y107H', 'Y107S', 'G108V', 'F109C', 'F109I', 'F109S', 'F109V', 'R110G', 'R110H', 'R110L', 'R110P', 'R110S', 'L111P', 'L111Q', 'L111R', 'F113C', 'F113L', 'F113S', 'C124F', 'C124R', 'C124Y', 'T125A', 'T125K', 'T125P', 'T125R', 'Y126D', 'Y126N', 'Y126S', 'S127F', 'S127P', 'S127Y', 'N131I', 'M133K', 'M133R', 'F134C', 'F134S', 'C135R', 'C135W', 'C135Y', 'Q136E', 'Q136H', 'Q136K', 'Q136L', 'Q136P', 'Q136R', 'A138D', 'A138P', 'A138T', 'A138V', 'C141R', 'C141W', 'C141Y', 'V143E', 'V143G', 'L145P', 'L145R', 'V147F', 'S149P', 'P151A', 'P151H', 'P151L', 'P151R', 'P151S', 'G154V', 'T155I', 'T155N', 'T155P', 'R156P', 'V157D', 'V157G', 'R158C', 'R158G', 'R158H', 'R158L', 'R158P', 'R158S', 'M160K', 'M160R', 'M160T', 'M160V', 'A161D', 'Y163D', 'Y163S', 'Q165E', 'Q165P', 'H168D', 'H168L', 'H168N', 'H168P', 'H168Q', 'H168R', 'H168Y', 'V173A', 'V173E', 'V173G', 'R175C', 'R175G', 'R175H', 'R175L', 'R175P', 'R175S', 'C176F', 'H179D', 'H179L', 'H179N', 'H179P', 'H179Q', 'H179R', 'H179Y', 'R181P', 'S183L', 'S185R', 'D186E', 'D186G', 'D186H', 'D186V', 'G187V', 'A189G', 'P190A', 'P190H', 'P190L', 'P190R', 'P190S', 'Q192H', 'Q192K', 'Q192L', 'Q192R', 'H193D', 'H193L', 'H193N', 'H193P', 'H193Q', 'H193R', 'H193Y', 'L194F', 'L194H', 'L194R', 'I195F', 'I195S', 'R196G', 'R196L', 'R196P', 'R196Q', 'V197A', 'V197E', 'V197G', 'V197L', 'V197M', 'E198D', 'E198G', 'E198K', 'E198Q', 'G199V', 'N200I', 'N200S', 'N200Y', 'V203A', 'V203E', 'V203L', 'V203M', 'Y205C', 'Y205D', 'Y205H', 'Y205N', 'Y205S', 'T211A', 'T211I', 'T211N', 'T211P', 'R213P', 'S215C', 'S215G', 'S215I', 'S215N', 'S215T', 'V216A', 'V216E', 'V216G', 'V217G', 'V218A', 'V218G', 'Y220C', 'Y220D', 'Y220H', 'Y220N', 'Y220S', 'P222L', 'P222Q', 'G226V', 'S227P', 'I232F', 'I232N', 'I232S', 'I232T', 'Y234C', 'Y234D', 'Y234H', 'Y234N', 'Y234S', 'Y236C', 'Y236D', 'Y236H', 'Y236N', 'Y236S', 'M237K', 'M237R', 'M237T', 'M237V', 'C238F', 'C238R', 'C238W', 'C238Y', 'G244C', 'G244V', 'G245R', 'M246K', 'M246R', 'R248P', 'R249G', 'R249K', 'R249M', 'R249S', 'R249T', 'R249W', 'I251N', 'I251S', 'L252P', 'T253P', 'I254F', 'I254N', 'I254S', 'I255N', 'I255S', 'I255T', 'T256P', 'L257P', 'L257Q', 'L257R', 'D259Y', 'G262V', 'L265P', 'G266E', 'G266R', 'G266V', 'R267P', 'F270C', 'F270I', 'F270L', 'F270S', 'F270V', 'V272A', 'V272E', 'V272G', 'V274D', 'V274F', 'V274G', 'C275F', 'C275G', 'C275R', 'C275S', 'C275W', 'C275Y', 'P278H', 'P278L', 'P278R', 'P278S', 'G279E', 'G279R', 'G279V', 'G279W', 'R282P', 'T284I', 'T284P']
 - We aggregated all the variants that have at least one of the MAVISp modules with a predicted damaging effect (except for PTM.function) and retained only the ones with a Demask delta fitness >= 0.25 or <= -0.25 for a total of 906 variants which could be of interest for further investigation:

dot_plot/examples_v2/ensemble_mode_foldetta/log.txt → dot_plot/examples_v2/ensemble_mode_foldetta/log_aggregated.txt

@@ -55,10 +55,10 @@ Summary of the effects.
  - 133 variants are potentially damaging in terms of removing the function related to a phosphorylation. [cabsflex] See csv file for details.
  - 591 variants are predicted with damaging long range effects on pocket site(s). [md] See csv file for details.
  - Variants with multiple effects:
--- Y236R, Y205E, Y107D, V216D, R196Y, R158P, I232F, P190R, F113N, C275H, P222K, Y234C, A138P, F113Q, V203F, Y205Q, R175H, V173G, Y103P, N200W, R158G, V173S, Y236C, F270V, Y236A, V218D, I232W, P222H, M160P, Y220G, H193P, Y236D, Y236P, I232N, C275R, P222R, Y205S, V216G, Y205A, C275F, V197N, Y205K, H179R, F113P, P222Y, V197Y, R249P, F270N, Y220S, Y236S, E198P, V197W, P151S, H193R, I232S, V197D, I232Y, H179F, F270C, V197K, Y205G, V197G, Y205H, V203G, Y205P, F113G, H179Y, F113I, V216N, Y234D, M237P, I232A, Y220A, F270H, F113S, V197F, I232H, Y236K, V203W, C275Y, I195F, H179P, F113W, N200Y, R196P, Y205C, Y236G, Y234S, V203R, V203Y, Y107E, H193W, Y205T, Y234G, Y236Q, R158H, Y236E, I195R, C275W, R110P, I195Y, V203M, Y205N, P222W, Y234A, V197P, Y205D, Y234P, F113V, P190H, P151W, F270D, P151Y, V218P, Y107T, F113T, Y234N, Y107S, V203P, Y234T, F270P, I232E, F270Q, V197H, V203D, Y220P, Q136P, Y205R, Y220C, Y234R, H193Y, I232D, P151F, F113D, V173D, Y205I, Y107G, V197A, V216S, F270E, Y220T, F270S, P151G, Y107P, Y234K, F270R, I195W, V197S, P98R, P151K, P190W, P222F, V218G, F270G, Q165P, R158Y, Y236T, P151R, V197R, V203K, Y236N, Y234Q, I232P, F113E, H179W, Y234E, V216P, F113A, Y220E, Y220N, V203H, C275K, F113K, I232G, F113C, F270A, R196H, F270T, H168P, F113R, I232R, Y236H, P151H, Y220D, Y220K, P190F, F270K, Y205V -> [stability, long_range]
--- S149P, Y220G, Y220P, T211P, T155G, T284P, R249P, Y220E, Y220D, Y220K, Y220N, Y220A, Y220S, Y220C, T155P, Y220T -> [stability, ptm]
--- Y220H, R249W, R249Y, R249P, R249L, Y220S, Y220T, Y220M, Y220K, R249H, Y220R, R249S, R249E, R249M, R249D, Y220V, R249Q, Y220I, Y220E, Y220Q, R249N, R249F, Y220A, Y220N, R249T, Y220G, R249C, R249I, Y220L, R249A, R249V, R249G, Y220D, Y220P, Y220C -> [long_range, ptm]
--- Y220G, Y220P, R249P, Y220E, Y220D, Y220K, Y220N, Y220A, Y220S, Y220C, Y220T -> [stability, long_range, ptm]
+-- R158H, V218D, I232D, Y234C, F270K, F270N, I195W, H179F, V203K, Y205G, Y220T, I232W, F270A, F113P, V216D, Y107T, R158P, R196Y, Y236P, P151F, I232H, V218P, P151W, Y234R, Y205H, F270V, V203M, H179P, V203F, C275W, E198P, Y205D, F113N, Y107P, I232G, H168P, Y234G, R196P, C275R, V216N, Y107G, V173G, V197H, Y205C, P151K, F270T, Y234S, I195Y, Y205I, C275K, V203D, F270D, F113K, F113R, Y236H, N200Y, Y205V, Y107S, P222W, H193W, Y234A, R175H, H179R, M237P, P190H, V197A, Y236C, F113A, Y220S, F113G, Y234Q, I232R, R110P, F113E, V197Y, F113I, Y205E, F113Q, Q165P, Y236Q, H179Y, V197G, Y107E, R196H, F270C, F270H, P222F, I232A, V203P, F270E, F270S, V197F, V197D, Y234K, R249P, V203Y, V216S, F113W, H193Y, R158G, I232N, Y220C, P222H, P151Y, V173D, P151R, Y205A, I232P, Y220K, Y205R, Y236E, P151H, Y205S, Y236S, V197S, Y205Q, F270R, V203W, N200W, H193P, Y205P, P222Y, F270Q, Y103P, I232E, V173S, Y236D, C275Y, C275H, F113V, V197R, Y236A, Y234T, Y205T, Y236R, P190R, V197W, P222R, Y236K, Y220E, Y220N, Y234N, P151G, P222K, Y236G, Q136P, Y234E, H193R, V203R, Y220A, Y234D, P98R, F113T, V203H, M160P, V197N, I232Y, Y205N, Y220D, V203G, F113D, V218G, P190F, A138P, Y234P, Y236N, P190W, P151S, I232F, Y205K, H179W, Y107D, V197P, Y220P, C275F, V216G, V197K, I195F, Y220G, Y236T, F113C, F270G, V216P, I232S, F270P, I195R, F113S, R158Y -> [stability, long_range]
+-- Y220K, Y220P, Y220A, R249P, S149P, Y220E, T155P, Y220N, Y220S, T211P, Y220G, Y220C, Y220D, T284P, Y220T, T155G -> [stability, ptm]
+-- Y220I, R249T, R249P, Y220M, R249V, Y220E, Y220N, R249G, Y220Q, Y220C, R249L, R249S, R249F, Y220V, Y220T, Y220K, R249Q, Y220A, R249C, Y220D, Y220L, R249I, R249D, R249H, Y220S, R249M, R249A, R249Y, R249W, Y220H, Y220P, Y220G, R249N, R249E, Y220R -> [long_range, ptm]
+-- Y220K, Y220P, Y220A, R249P, Y220E, Y220N, Y220S, Y220G, Y220C, Y220D, Y220T -> [stability, long_range, ptm]
 - We aggregated all the variants that have at least one of the MAVISp modules with a predicted damaging effect (except for PTM.function) and retained only the ones with a REVEL score higher than 0.5 for a total of 350 variants which could be of interest for further investigation:
 -- ['S94P', 'S96P', 'P98H', 'P98L', 'P98S', 'S99F', 'S99P', 'Y103C', 'Y103H', 'G105C', 'G105D', 'G105R', 'G105S', 'G105V', 'S106R', 'Y107C', 'Y107D', 'Y107H', 'Y107S', 'G108C', 'G108D', 'G108S', 'G108V', 'F109C', 'F109I', 'F109S', 'F109V', 'R110G', 'R110H', 'R110L', 'R110P', 'R110S', 'L111P', 'L111Q', 'L111R', 'F113C', 'F113L', 'F113S', 'C124F', 'C124R', 'C124Y', 'T125A', 'T125K', 'T125P', 'T125R', 'Y126C', 'Y126D', 'Y126N', 'Y126S', 'S127F', 'S127P', 'S127Y', 'L130P', 'N131I', 'M133K', 'M133R', 'M133T', 'F134C', 'F134S', 'C135F', 'C135R', 'C135W', 'C135Y', 'Q136E', 'Q136H', 'Q136K', 'Q136L', 'Q136P', 'Q136R', 'A138D', 'A138P', 'A138T', 'A138V', 'C141F', 'C141G', 'C141R', 'C141W', 'C141Y', 'P142H', 'V143A', 'V143E', 'V143G', 'Q144P', 'L145P', 'L145Q', 'L145R', 'V147D', 'V147F', 'V147G', 'S149P', 'P151A', 'P151H', 'P151L', 'P151R', 'P151S', 'G154V', 'T155I', 'T155N', 'T155P', 'R156P', 'V157A', 'V157D', 'V157F', 'V157G', 'R158C', 'R158G', 'R158H', 'R158L', 'R158P', 'R158S', 'A159D', 'A159P', 'M160K', 'M160R', 'M160T', 'M160V', 'A161D', 'I162F', 'Y163C', 'Y163D', 'Y163N', 'Y163S', 'Q165E', 'Q165P', 'H168D', 'H168L', 'H168N', 'H168P', 'H168Q', 'H168R', 'H168Y', 'V172F', 'V173A', 'V173E', 'V173G', 'V173M', 'R175C', 'R175G', 'R175H', 'R175L', 'R175P', 'R175S', 'C176F', 'C176R', 'C176W', 'C176Y', 'H178P', 'H179D', 'H179L', 'H179N', 'H179P', 'H179Q', 'H179R', 'H179Y', 'R181P', 'S183L', 'S185R', 'D186E', 'D186G', 'D186H', 'D186V', 'G187V', 'A189G', 'A189P', 'P190A', 'P190H', 'P190L', 'P190R', 'P190S', 'P191H', 'Q192H', 'Q192K', 'Q192L', 'Q192R', 'H193D', 'H193L', 'H193N', 'H193P', 'H193Q', 'H193R', 'H193Y', 'L194F', 'L194H', 'L194P', 'L194R', 'I195F', 'I195N', 'I195S', 'R196G', 'R196L', 'R196P', 'R196Q', 'V197A', 'V197E', 'V197G', 'V197L', 'V197M', 'E198D', 'E198G', 'E198K', 'E198Q', 'G199V', 'N200I', 'N200S', 'N200Y', 'V203A', 'V203E', 'V203L', 'V203M', 'Y205C', 'Y205D', 'Y205H', 'Y205N', 'Y205S', 'D208G', 'D208Y', 'T211A', 'T211I', 'T211N', 'T211P', 'R213P', 'S215C', 'S215G', 'S215I', 'S215N', 'S215T', 'V216A', 'V216E', 'V216G', 'V216M', 'V217G', 'V218A', 'V218E', 'V218G', 'Y220C', 'Y220D', 'Y220H', 'Y220N', 'Y220S', 'P222L', 'P222Q', 'P223H', 'P223R', 'G226V', 'S227P', 'C229W', 'T230P', 'I232F', 'I232N', 'I232S', 'I232T', 'H233P', 'Y234C', 'Y234D', 'Y234H', 'Y234N', 'Y234S', 'Y236C', 'Y236D', 'Y236H', 'Y236N', 'Y236S', 'M237K', 'M237R', 'M237T', 'M237V', 'C238F', 'C238R', 'C238W', 'C238Y', 'S241P', 'C242F', 'C242R', 'C242W', 'C242Y', 'G244C', 'G244V', 'G245C', 'G245D', 'G245R', 'G245S', 'G245V', 'M246K', 'M246R', 'N247I', 'R248P', 'R249G', 'R249K', 'R249M', 'R249S', 'R249T', 'R249W', 'I251F', 'I251N', 'I251S', 'I251T', 'L252H', 'L252P', 'T253P', 'I254F', 'I254N', 'I254S', 'I255N', 'I255S', 'I255T', 'T256P', 'L257P', 'L257Q', 'L257R', 'D259Y', 'G262V', 'L265P', 'G266E', 'G266R', 'G266V', 'R267P', 'R267W', 'F270C', 'F270I', 'F270L', 'F270S', 'F270V', 'V272A', 'V272E', 'V272G', 'R273P', 'V274D', 'V274F', 'V274G', 'C275F', 'C275G', 'C275R', 'C275S', 'C275W', 'C275Y', 'P278H', 'P278L', 'P278R', 'P278S', 'P278T', 'G279E', 'G279R', 'G279V', 'G279W', 'D281G', 'R282P', 'R283P', 'T284I', 'T284P', 'L289P']
 - We aggregated all the variants that have at least one of the MAVISp modules with a predicted damaging effect (except for PTM.function) and retained only the ones with a Demask delta fitness >= 0.25 or <= -0.25 for a total of 1159 variants which could be of interest for further investigation: