[Biopython] gff3file
Atteyet-Alla.Yassin
Atteyet-Alla.Yassin at ukb.uni-bonn.de
Wed Jun 3 12:58:53 UTC 2015
I hope that is now right. I obtained the following erreor
>>> from Bio import SeqIO
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named 'Bio'
>>> with open("CP008802.out", "w") as output:
...
output.write("Seqname\tSource\tfeature\tStart\tEnd\tScore\tStrand\tFrame\tAttributes\n")
... for record in SeqIO.parse("CP008802.txt", "genbank"):
... print("Converting %s" % record.name)
... for f in record.features:
... if f.type != "gene":
... continue
... locus_tag = f.qualifiers["locus_tag"][0]
... if len(f.location.parts) > 1:
... print("What should we do for %s (compound location)?
%s" % (locus_tag, f.location))
... continue
...
output.write('%s\tGenBank\t%s\t%i\t%i\t0,000000\t%s\t.\tlocus_tag\t"%s";
transcript_id "%s"\n'
... % (record.name, f.type,
... f.location.start + 1, f.location.end,
f.location.strand,
... locus_tag, locus_tag))
... print("Done")
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