KeyError with gofilter.py: Issue with .bed file?
kalavattam opened this issue · 2 comments
kalavattam commented
Thanks for your great software—I've been eager to try it out.
I've encountered an error when running gofilter.py. I'd like to ask for your advice for troubleshooting. I wonder if the error arises from the .bed file containing gene positions?
Calling gofilter.py:
python /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/src/dcHiC/dchic/gofilter.py \
-dir /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/results/kga0/2021_0226_pipeline_dcHiC \
-diffcompt /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/results/kga0/2021_0226_pipeline_dcHiC/DifferentialCompartment/MultiComparison_differential_compartments.bedGraph \
-config config_cardioD0.txt \
-outprefix u1_a1.cardioD0 \
-genome hg38 \
-geneBed /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/data/generate_annotation_model/gencode.v35.annotation.bed \
-runOption 1 \
-orientation 1
Head of gencode.v35.annotation.bed:
chr1 11868 14409 ENSG00000223972
chr1 14403 29570 ENSG00000227232
chr1 17368 17436 ENSG00000278267
chr1 29553 31109 ENSG00000243485
chr1 30365 30503 ENSG00000284332
chr1 34553 36081 ENSG00000237613
chr1 52472 53312 ENSG00000268020
chr1 57597 64116 ENSG00000240361
chr1 65418 71585 ENSG00000186092
chr1 89294 133723 ENSG00000238009
Error:
Slack Given In GO Analysis: 0
Rscript /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/src/dcHiC/dchic/cluster.r direction Active2Inactive cardioD2,cardioD5,cardioD14,endoD0,endoD2,endoD6,endoD14 cardioD0 /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/results/kga0/2021_0226_pipeline_dcHiC 1
[1] "1"
Rscript /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/src/dcHiC/dchic/cluster.r 0 /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/gencode.v35.annotation.bed u1_a1.cardioD0.bedGraph 2
[1] "2"
curl -H 'Content-Type: text/json' -d 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https://toppgene.cchmc.org/API/lookup
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 64912 0 46532 100 18380 32562 12862 0:00:01 0:00:01 --:--:-- 45393
curl -H 'Content-Type: text/json' -d '{"Genes":[105376686,85440,10207,163782,7398,106479731,100271142,54596,106480970,100422902,100422946,84938,27329,105378769,29929,23421,27022,107075109,199899,100996301,441887,100873288,102464823,102724319,1117,5016,79084,515,57413,27159,10390,128346,128338,79961,128344,106481431,149620,441897,106480360,100420342,100873292,140,26239,84648,4184,3713,6698,54544,353134,163778,353142,353145,254910,353135,353131,199834,353139,353140,353141,353143,353133,100129271,448834,101927988,450210,450209,450208,448835,353137,353144,110806278,450211,6279,6278,6706,114771,6707,6703,57115,6280,6283,6699,338324,6701,645922,127481,4014,574414,149018,6704,106479637,112488748,101928009,391102,6700,6705,2117,9826,149501,360155,440695,101929959,7582,104266963,728064,100312807,101929397,143341,100129482,107984178,101929445,106480081,106481458,100847014,1103,113218477,282966,6572,55753,101060581,100652748,106479006,267004,728407,100271422,109729125,109617009,101930591,56624,259230,728532,728990,100421577,9376,114571,117245,387775,387601,283238,644436,100127954,100533643,81539,54407,100129799,55089,100421550,387853,347902,91523,100233209,100127978,111082992,100506099,100288129,100616486,100616478,3071,5153,90070,9840,5502,117159,118430,644076,58158,441639,341416,121364,390327,390326,390323,283365,254783,403284,403282,254786,390321,403288,403285,81140,390318,390320,390322,4848,27345,106481192,101928062,100873208,100874501,100506622,100873817,6445,26278,100873808,100506680,100874124,100506697,100419955,51562,400206,253970,106480813,106480839,101101773,28473,28457,28452,100293211,101930405,28448,28447,28468,28445,28444,28442,28467,28455,28400,28434,28395,28432,28429,28394,28398,28426,28372,28431,28382,28374,28430,28348,28354,28351,28433,28441,28376,28347,28373,28371,28438,28470,28453,28355,28446,28366,28443,28346,28469,28353,28471,28369,28427,28440,28383,28435,28439,338005,102724971,28428,57289,102723170,28367,107548099,28350,2567,100873644,100420466,101928869,4948,100271207,9956,100132247,653786,5652,2521,112755,29108,6810,10295,84148,6524,3687,7041,64755,79798,339105,1339,3681,79759,9726,79001,3684,260434,283933,493829,146547,100652740,106479052,100132341,51327,10308,107983990,730196,100129315,100131641,100131118,100128384,100130603,102724018,102724127,100533705,28307,100873571,649159,106481738,100887074,731605,100507577,85320,94160,6477,443,8388,23108,84690,8392,8383,26189,8387,9596,390756,4994,8390,4991,4995,653166,100288728,8391,8386,100856809,40,100506677,3883,3881,8688,3882,8689,100653049,3884,8687,84616,100505724,83902,83901,81851,85290,3886,81870,81871,85289,85285,83900,728224,728255,100505753,100533177,100507608,653240,100132386,730755,81872,83896,83755,728279,83895,81850,106481644,85345,106480773,100505782,106480422,85343,728318,101930568,85280,85291,6093,80000,440487,106479619,100128324,284252,83539,361,147429,105372035,728606,102466874,5518,80110,162963,84436,90321,162962,102725206,284370,147657,147658,90317,693228,400713,9668,147660,102724105,102466984,100312842,150465,3552,3553,27178,84269,84172,56300,284958,6574,150468,100128413,7849,23550,150472,3557,27179,26525,27177,84639,200350,654433,106481552,6344,55240,165257,1622,140738,130355,100874111,107105282,106481050,30813,5834,26090,9837,22981,84532,955,284798,6789,10406,5266,6590,3787,6385,51604,6407,8785,11317,6406,27296,128488,149708,90196,107075105,140749,55861,767557,102465487,103504728,103504731,105377573,100128118,106479100,22987,10788,106480689,100873448,83989,285600,84250,79772,100533629,100270852,113523641,109729150,100873257,106478942,2037,9465,383,100421246,100271180,83861,117289,84624,102724053,105378083,100129518,29074,39,677812,4142,154197,9589,3482,677806,642738,100132803,106481866,6582,6581,6580,80350,729603,100271873,109504726,340252,51427,7697,102724456,2086,106481697,100127907,100418814,106480286,102465505,26,55365,3757,26157,28959,474344,55303,4846,474345,168537,100527949,170575,100288724,100874395,100874394,140545,64327,3110,64434,100506380,106480546,101927858,100129517,64433,23514,253986,106479928,100996586,106479109,100128541,80243,57094,100132812,106480785,116328,286189,6482,101927798,101927822,107075177,100873179,100131760,102724904,5239,286380,101060578,572558,8395,169693,116224,106479929,347097,105376072,101927015,5742,26468,4702,92400,347168,92399,158135,254956,100616312,23637,54542,254973,5082,392391,158131,392392,57684,392390,26735,138881,138882,138883,26737,10773,26740,692206,106481711,26742,100631239,26219,347169],"Categories":[{"Type": "GeneOntologyBiologicalProcess", "PValue": 0.05, "MinGenes": 1, "MaxGenes": 1500, "MaxResults": 30, "Correction": "FDR"}]}' https://toppgene.cchmc.org/API/enrich
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 57257 0 52651 100 4606 65081 5693 --:--:-- --:--:-- --:--:-- 70775
Traceback (most recent call last):
File "/Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/src/dcHiC/dchic/gofilter.py", line 154, in <module>
GeneList = results[a]['Genes'][0]['Symbol']
KeyError: 0
I encounter the same errors when using .bed files with gene names and Entrez IDs, e.g.,
chr1 11868 14409 DDX11L1
chr1 14403 29570 NA
chr1 17368 17436 MIR6859-1
chr1 29553 31109 NA
chr1 30365 30503 MIR1302-2
chr1 34553 36081 FAM138A
chr1 52472 53312 NA
chr1 57597 64116 NA
chr1 65418 71585 OR4F5
chr1 89294 133723 LOC100996442
chr1 11868 14409 100287102
chr1 14403 29570 NA
chr1 17368 17436 102466751
chr1 29553 31109 NA
chr1 30365 30503 100302278
chr1 34553 36081 645520
chr1 52472 53312 NA
chr1 57597 64116 NA
chr1 65418 71585 79501
chr1 89294 133723 100996442
When I use the .bed file in your hg38_goldenpathData directory from Dropbox, I encounter this error:
Slack Given In GO Analysis: 0
Rscript /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/src/dcHiC/dchic/cluster.r direction Active2Inactive cardioD2,cardioD5,cardioD14,endoD0,endoD2,endoD6,endoD14 cardioD0 /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/results/kga0/2021_0226_pipeline_dcHiC 1
[1] "1"
Rscript /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/src/dcHiC/dchic/cluster.r 0 /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/data/hg38_goldenpathData/hg38.refGene.bed u1_a1.cardioD0.bedGraph 2
[1] "2"
*****
***** ERROR: Requested column 7, but database file - only has fields 1 - 6.
Error in read.table(text = system(cmd, wait = T, intern = T), h = F) :
no lines available in input
Calls: mapGenes -> read.table
Execution halted
Head of the .bed in the hg38_goldenpathData, hg38.refGene.bed:
chr1 11874 11875
chr1 17435 17436
chr1 17435 17436
chr1 17435 17436
chr1 17435 17436
chr1 29369 29370
chr1 30366 30367
chr1 30366 30367
chr1 30366 30367
chr1 30366 30367
I tried a .bed with gene names and without NAs, similar to your mm10 mm10_gene_pos.bed; head of .bed without NAs:
chr1 11868 14409 DDX11L1
chr1 17368 17436 MIR6859-1
chr1 30365 30503 MIR1302-2
chr1 34553 36081 FAM138A
chr1 65418 71585 OR4F5
chr1 89294 133723 LOC100996442
chr1 187890 187958 MIR6859-2
chr1 450702 451697 OR4F29
chr1 586070 827796 LOC101928626
chr1 685678 686673 OR4F16
The call:
python /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/src/dcHiC/dchic/gofilter.py \
-dir /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/results/kga0/2021_0226_pipeline_dcHiC \
-diffcompt /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/results/kga0/2021_0226_pipeline_dcHiC/DifferentialCompartment/MultiComparison_differential_compartments.bedGraph \
-config config_cardioD0.txt \
-outprefix u1_a1.cardioD0 \
-genome hg38 \
-geneBed /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/gencode.v35.annotation.2.noNA.bed \
-runOption 1 \
-orientation 1
The error:
Slack Given In GO Analysis: 0
Rscript /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/src/dcHiC/dchic/cluster.r direction Active2Inactive cardioD2,cardioD5,cardioD14,endoD0,endoD2,endoD6,endoD14 cardioD0 /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/results/kga0/2021_0226_pipeline_dcHiC 1
[1] "1"
Rscript /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/src/dcHiC/dchic/cluster.r 0 /Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/gencode.v35.annotation.2.noNA.bed u1_a1.cardioD0.bedGraph 2
[1] "2"
curl -H 'Content-Type: text/json' -d '{"Symbols":["gene","loc105376686","dock7","kank4","l1td1","mir3116-1","mir3116-2","patj","usp1","angptl3","atg4c","linc01739","alg6","foxd3","foxd3-as1","itgb3bp","linc00466","loc102724319","mir6068","adora3","atp5pb","c1orf162","cept1","chi3l2","chia","chiap2","dennd2d","dram2","ovgp1","pgbp","pifo","tmigd3","wdr77","c1orf68","crct1","ivl","kprp","lce1a","lce1b","lce1c","lce1d","lce1e","lce1f","lce2a","lce2b","lce2c","lce2d","lce3a","lce3b","lce3c","lce3d","lce3e","lce4a","lce5a","lce6a","linc01527","smcp","sprr1a","sprr4","lelp1","loc101928009","lor","pglyrp3","pglyrp4","prr9","s100a12","s100a7","s100a7a","s100a8","s100a9","sprr1b","sprr2a","sprr2b","sprr2d","sprr2e","sprr2f","sprr2g","sprr3","arhgef11","cycsp52","etv3","etv3l","bms1","linc01264","linc01518","linc02623","mir5100","znf33b","znf37bp","agap6","c10orf53","chat","ercc6","linc00843","ogdhl","parg","slc18a3","timm23b","asah2","fam21ep","sgms1","washc2a","plaat5","slc22a10","slc22a24","slc22a25","slc22a8","slc22a9","slc38a1","slc38a2","slc38a4","amigo2","mir4494","mir4698","pced1b","pced1b-as1","dcd","glycam1","lacrt","mucl1","nckap1l","pde1b","ppp1r1a","tespa1","neurod4","or10a7","or6c1","or6c2","or6c3","or6c6","or6c65","or6c68","or6c70","or6c74","or6c75","or6c76","or9k2","cnot2","cnot2-dt","kcnmb4","linc00540","linc00327","sacs","sacs-as1","sgcg","linc00609","mbip","sfta3","linc00221","gabrg3","gabrg3-as1","oca2","hs3st2","npipb5","otoap1","armc5","bckdk","c16orf58","cox6a2","fus","itgad","itgam","itgax","kat8","prss36","prss53","prss8","pycard","pycard-as1","pydc1","slc5a2","stx1b","stx4","tgfb1i1","trim72","vkorc1","znf646","znf668","znf843","ahsp","cluhp3","frg2kp","vn1r3","znf267","znf720","tp53tg3d","abcc11","abcc12","lonp2","siah1","aspa","loc100288728","or1a1","or1a2","or1d2","or1d4","or1d5","or1e1","or1e2","or1e3","or1g1","or3a1","or3a2","or3a3","or3a4p","rap1gap2","spata22","aa06","asic2","krt31","krt32","krt33a","krt33b","krt34","krt35","krt36","krt37","krt38","krtap1-1","krtap1-3","krtap1-4","krtap1-5","krtap16-1","krtap17-1","krtap2-1","krtap2-2","krtap2-3","krtap2-4","krtap29-1","krtap3-1","krtap4-1","krtap4-11","krtap4-12","krtap4-2","krtap4-3","krtap4-4","krtap4-5","krtap4-6","krtap4-7","krtap4-8","krtap4-9","krtap9-1","krtap9-2","krtap9-3","krtap9-4","krtap9-6","krtap9-7","krtap9-8","krtap9-9","loc100505782","greb1l","rock1","aqp4","aqp4-as1","chst9","kctd1","loc105372035","mir8057","pcat18","mir643","mir6801","ppp2r1a","znf432","znf480","znf528","znf528-as1","znf534","znf578","znf610","znf614","znf615","znf616","znf766","znf836","znf841","znf880","chchd5","ckap2l","il1a","il1b","il36g","il37","nt5dc4","polr1b","slc20a1","ttl","cbwd2","foxd4l1","il1f10","il1rn","il36a","il36b","il36rn","pax8","pax8-as1","psd4","c1ql2","c2orf76","dbi","loc107105282","sctr","steap3","steap3-as1","tmem37","abhd12","acss1","entpd6","gins1","loc284798","ninl","pygb","vsx1","dbndd2","kcns1","matn4","mir6812","pi3","pigt","rbpjl","sdc4","semg1","semg2","slpi","stk4","sys1","sys1-dbndd2","tp53tg5","wfdc12","wfdc2","wfdc5","loc101930100","mir3648-2","temn3-as1","iqgap2","sv2c","fam172a","kiaa0825","mctp1","slf1","akap7","arg1","epb41l2","fndc1","linc02529","loc105378083","loc112267968","rsph3","tagap","acat2","igf2r","mas1","mrpl18","pnldc1","snora20","snora29","sod2","sod2-ot1","tcp1","wtap","airn","loc729603","lpal2","slc22a1","slc22a2","slc22a3","erv3-1","loc441239","mir6839","znf107","znf117","znf138","znf273","znf680","aoc1","gimap1","gimap1-gimap5","gimap2","gimap4","gimap5","gimap6","gimap7","kcnh2","nos3","tmem176a","tmem176b","linc00244","linc01006","lmbr1","loc101927858","mnx1","nom1","rnf32","spidr","cpa6","prex2","c8orf34","c8orf34-as1","loc101927798","loc101927822","st3gal1","loc102724904","cbwd3","foxd4l3","pgm5","pgm5-as1","fam122a","linc01506","pip5k1b","tmem252","tmem252-dt","lhx6","mir4478","morn5","mrrf","ndufa8","or1j1","ptgs1","rbm18","ttll11","gpr21","or1b1","or1j2","or1j4","or1k1","or1l1","or1l3","or1l4","or1l6","or1l8","or1n1","or1n2","or1q1","or5c1","pdcl","rc3h2","snord90","zbtb26","zbtb6"]}' https://toppgene.cchmc.org/API/lookup
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 32235 0 28191 100 4044 43774 6279 --:--:-- --:--:-- --:--:-- 50132
curl -H 'Content-Type: text/json' -d '{"Genes":[105376686,85440,163782,54596,100422902,100422946,10207,7398,27329,84938,105378769,29929,27022,100996301,23421,199899,102724319,102464823,140,515,128346,10390,1117,27159,149620,79961,128338,5016,441897,128344,57413,79084,100129271,54544,3713,448834,353131,353132,353133,353134,353135,353137,353139,26239,353140,353141,353142,353143,353144,84648,353145,199834,254910,448835,101927988,4184,6698,163778,149018,101928009,4017,114771,57115,574414,6283,6278,338324,6279,6280,6699,6700,6701,6703,6704,6705,6706,6707,9826,360155,2117,440695,9790,104266963,101929397,101929445,100847014,7582,100129482,414189,282966,1103,2074,102902672,55753,8505,6572,100652748,56624,100421577,259230,387680,117245,387775,283238,387601,9376,114571,81539,54407,55089,347902,100616478,100616486,91523,100233209,117159,644076,90070,118430,3071,5153,5502,9840,58158,121364,390321,341416,254786,283365,403282,403284,390327,254783,390323,390326,441639,4848,101928062,27345,100506622,100506697,26278,100506680,6445,101101773,51562,253970,338005,2567,101928869,4948,9956,100132247,653786,79798,10295,64755,1339,2521,3681,3684,3687,84148,146547,339105,5652,29108,100652740,260434,6524,112755,6810,7041,493829,79001,9726,79759,283933,51327,100132341,102724018,317702,10308,124411,729264,85320,94160,83752,6477,443,100288728,8383,26189,4991,653166,8386,8387,8388,8389,8390,4994,4995,8392,390756,23108,84690,100506677,40,3881,3882,3883,3884,3885,3886,8689,8688,8687,81851,81850,728255,83895,100505753,83902,81872,728279,730755,85294,100533177,83896,85285,653240,83755,85291,85290,84616,85289,81871,100132476,728224,100132386,728318,83899,83900,85280,100507608,100505724,83901,81870,100505782,80000,6093,361,147429,83539,284252,105372035,102466874,728606,693228,102466984,5518,9668,147657,84436,102724105,147658,147660,162963,80110,284370,90317,90321,162962,284371,400713,84269,150468,3552,3553,56300,27178,284958,84172,6574,150465,150472,200350,84639,3557,27179,27177,26525,7849,654433,23550,165257,130355,1622,6344,55240,100874111,140738,26090,84532,955,9837,284798,22981,5834,30813,55861,3787,8785,102465487,5266,51604,11317,6385,6406,6407,6590,6789,90196,767557,27296,128488,10406,149708,101930100,103504731,105377573,10788,22987,83989,285600,79772,84250,9465,383,2037,84624,102724053,105378083,112267968,83861,117289,39,3482,4142,29074,154197,677806,677812,6648,100129518,6950,9589,100271873,80350,6580,6582,6581,2086,441239,102465505,51427,51351,7697,10793,340252,26,170575,100527949,26157,55303,55340,474344,168537,3757,4846,55365,28959,64433,100506380,64327,3110,64434,140545,23514,57094,80243,116328,286189,101927798,101927822,6482,102724904,445571,286380,5239,572558,116224,101927015,8395,169693,105376072,26468,100616312,254956,92399,4702,347168,5742,92400,158135,2844,347169,26740,26219,392392,26737,26735,254973,392390,138881,138883,138882,158131,392391,5082,54542,692206,57684,10773],"Categories":[{"Type": "GeneOntologyBiologicalProcess", "PValue": 0.05, "MinGenes": 1, "MaxGenes": 1500, "MaxResults": 30, "Correction": "FDR"}]}' https://toppgene.cchmc.org/API/enrich
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 54105 0 51091 100 3014 69322 4089 --:--:-- --:--:-- --:--:-- 73313
Traceback (most recent call last):
File "/Volumes/SSHD/Dropbox/UW/projects/2020_endothelial-diff/src/dcHiC/dchic/gofilter.py", line 154, in <module>
GeneList = results[a]['Genes'][0]['Symbol']
KeyError: 0
ay-lab commented
Hi There!
Thank you so much for this feedback. The bed file you used in the format of "mm10_gene_pos.bed" is in the right format (the documentation has been updated & files have been added to the "files" folder to clarify this).
It appears there was a small error in the repo that should now be fixed. Could you try the new version?
kalavattam commented
Thanks, it's working well now!