Comments (7)
here's a fix for that.
seqcover.gz
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Thanks, for the fix. No trouble at all!
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thanks. working on a fix for this now.
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Thanks, I seem to be getting the same error message even with the new binary you attached.
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I just download this file that I put here and ran:
~/Downloads/seqcover report --genes CCDC39 --fasta $fasta d4s/HG00*.d4
and it completes without problem. Are you sure you got this version?
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Ah, it works without the hg19-flag, but throws an error when hg19 is added.
./seqcover report --genes CCDC39 --fasta $fasta samples/1_50_recal.per-base.d4 --background seqcover_out/seqcover_p5.d4 -r my_genes_report.html
[seqcover] read 1 sample coverage files
res:{"query":"ENSG00000145075","_id":"ENSG00000145075","_version":1,"genomic_pos":{"chr":"3","end":180870933,"ensemblgene":"ENSG00000145075","start":180614008,"strand":-1},"name":"coiled-coil domain containing 39","symbol":"CCDC39","exons":[{"txstart":180614008,"txend":180870933,"cdsstart":180870933,"cdsend":180870933,"position":[],"chr":"3","transcript":"NA","strand":-1}]}
res:{"query":"339829","_id":"339829","_version":1,"exons":[{"cdsend":180679380,"cdsstart":180614920,"chr":"3","position":[[180614007,180615077],[180616280,180616363],[180616515,180616695],[180616825,180616966],[180619258,180619365],[180619810,180619970],[180631468,180631592],[180641992,180642201],[180644119,180644257],[180647078,180647243],[180648164,180648359],[180651400,180651533],[180652162,180652266],[180654761,180654953],[180659451,180659580],[180659676,180659769],[180660569,180660728],[180661860,180662007],[180663866,180663986],[180679290,180679489]],"strand":-1,"transcript":"NM_181426","txend":180679489,"txstart":180614007}],"genomic_pos":{"chr":"3","end":180684942,"ensemblgene":"ENSG00000284862","start":180602858,"strand":-1},"name":"coiled-coil domain containing 39","symbol":"CCDC39"}
3 180613507 180679989
[seqcover] wrote report to:my_genes_report.html
./seqcover report --genes CCDC39 --fasta $fasta samples/1_50_recal.per-base.d4 --background seqcover_out/seqcover_p5.d4 --hg19
[seqcover] read 1 sample coverage files
tables.nim(262) []
Error: unhandled exception: key not found: exons_hg19 [KeyError]
from seqcover.
Hi, I have fixed that and several other cases as well. Sorry for the trouble, you're an early user, but we should be getting more stable soon. See attached binary for fixes.
seqcover.gz
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Related Issues (16)
- basic gene-plotting to-do. HOT 1
- summary table HOT 1
- use hash for linkable views HOT 3
- hilite samples+regions that are below lower threshold HOT 1
- switch json library for performance
- show chromosome HOT 1
- CDS bases below 7
- AssertionError with some genes HOT 3
- Increase visibility of selected sample trace
- ENH: add toggle button for line graph to set y-range to 95 pctile
- Feature suggestion - offline mode HOT 5
- Invalid integer exception HOT 4
- Error: unhandled exception: Connection refused [OSError] HOT 1
- Error: --hg19 coordinates HOT 5
- feature: MultiQC plugin
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