Preparation of transcripts.fa was failing when doing g2gtools extract --transcripts for single gene exons. So, added extra code/method to fix that error (see code and files below).
Also, it would be comprehensive to have :
transcripts[r['transcript_id']] = Transcript(r['transcript_id'], ......
on the code
transcripts[r['transcript_id']] = Transcript(r['ensembl_id'], r['seqid'], r['start'], r['end'], r['strand']) ....
since we are extracting transcripts.
Attached are the files and code to verify both the error and fix:
# there was problem with this code
$ python g2gtools extract -i MA625.Snp.Indels.patched.fa -db MA625-rawat.db --transcripts > MA625-rawat.transcripts.fa
Preparation of transcripts.fa was failing when doing
g2gtools extract --transcriptsfor single gene exons. So, added extra code/method to fix that error (see code and files below).transcripts[r['transcript_id']] = Transcript(r['transcript_id'], ......on the codetranscripts[r['transcript_id']] = Transcript(r['ensembl_id'], r['seqid'], r['start'], r['end'], r['strand']) ....since we are extracting transcripts.Attached are the files and code to verify both the error and fix:
Files:
MA625-rawat.db.gz MA625.Snp.Indels.patched.fa.fai.gz MA625.Snp.Indels.patched.fa.gz MA625-rawat.transcripts.fa.gz