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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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KeyError with gofilter.py: Issue with .bed file? #9

Closed kalavattam closed 3 years ago

kalavattam commented 3 years ago

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 3 years ago

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 3 years ago

Thanks, it's working well now!