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Kingsford-Group / squid

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
BSD 3-Clause "New" or "Revised" License
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SQUID annotation error #22

Closed AhmedArslan closed 4 years ago

AhmedArslan commented 4 years ago

I was facing a problem repeatedly while trying to annotate the output bedpe file:

here is my gft file:

chr12 refGene exon 98746968 98747158 . + . gene_id "Zc3h14"; transcript_id "NM_001160107"; exon_number "1"; exon_id "NM_001160107.1"; gene_name "Zc3h14"; chr12 refGene exon 98747480 98747522 . + . gene_id "Zc3h14"; transcript_id "NM_001160107"; exon_number "2"; exon_id "NM_001160107.2"; gene_name "Zc3h14";

my command: $ python AnnotateSQUIDOutput.py mm10.refGene.exon.gtf B.vcf_sv.txt B.anno.vcf

error:

Traceback (most recent call last): File "AnnotateSQUIDOutput.py", line 335, in glocater = GeneLocater(Transcripts, GeneTransMap) File "AnnotateSQUIDOutput.py", line 179, in init assert(len(set(chrnames)) == 1) AssertionError

Is there something, that I can do? Thanks.