[Biopython] gff3file

[Iddo Friedberg]

Seems like you haven't installed biopython correctly. Your first error is
"no module named Bio". This can be because biopython is not installed, or
installed somewhere that your PYTHONPATH does not recognize. You would need
to properly install biopython before you can continue. See detailed
instructions here:
http://biopython.org/DIST/docs/install/Installation.html

Iddo Friedberg
http://iddo-friedberg.net
Sent from a machine that promotes typos
On Jun 3, 2015 9:29 AM, "Atteyet-Alla.Yassin" <
Atteyet-Alla.Yassin at ukb.uni-bonn.de> wrote:

> 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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