Genes with no exons

[oyvindbusk]

Some genes return no exons from the query, this gives the following error message.

tables.nim(262)          []
Error: unhandled exception: key not found: exons_hg19 [KeyError]

An example is CCDC39 ("_id": "ENSG00000145075") where the query returns the following results:

# http://mygene.info/v3/gene/ENSG00000145075?fields=name,symbol,exons
{"_id": "ENSG00000145075", "_version": 1, "name": "coiled-coil domain containing 39", "symbol": "CCDC39"}

[brentp]

thanks. working on a fix for this now.

[brentp]

here's a fix for that.
seqcover.gz

[oyvindbusk]

Thanks, I seem to be getting the same error message even with the new binary you attached.

[brentp]

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?

[oyvindbusk]

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]

[brentp]

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

[oyvindbusk]

Thanks, for the fix. No trouble at all!