Error with mRNA switch #4

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pjotrp opened this Issue Aug 10, 2012 · 2 comments

1 participant

@pjotrp
Owner

gff3-fetch mRNA m_hapla.WS232.genomic.fa m_hapla.WS232.annotations.gff3 > m_hapla.WS232.mRNA.fa

caused

/home/wrk/.gems/gems/bio-gff3-0.8.7/lib/bio/db/gff/digest/gffparser.rb:119:in block in each_mRNA_seq': undefined methodseqname' for #Array:0x00000000de79e8 (NoMethodError)

@pjotrp
Owner

This causes the parse error

new file:

MhA1_Contig0 Freeze3 mRNA 4027 5970 . + . ID=MhA1_Contig0.frz3.fgene1;Name=MhA1_Contig0.frz3.fgene1
MhA1_Contig0 Freeze3 CDS 4027 4090 15.97 + 0 Parent=MhA1_Contig0.frz3.fgene1

old file:

MhA1_Contig1133 WormBase mRNA 6237 7313 . + . ID=transcript:MhA1_Contig1133.frz3.gene3;Parent=gene:MhA1_Contig1133.frz3.gene3;Name=MhA1_Contig1133.frz3.gene3;
MhA1_Contig1133 WormBase CDS 6237 6353 . + 0 ID=cds:MhA1_Contig1133.frz3.gene3 Parent=transcript:MhA1_Contig1133.frz3.gene3

@pjotrp
Owner

The parent id is here MhA1_Contig0.frz3.fgene1, the child ID is MhA1_Contig0 4027 4090

INFO bio-gff3: Memory used BaseLine RAM 16M, VMEM 48M
INFO bio-gff3: ---- Digest DB and store data in mRNA Hash <>
INFO bio-gff3: Adding mRNA (validate)
INFO bio-gff3: Adding CDS (validate)

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