[BioPython] SeqIO.write() Multiple Calls for fasta

[Michiel de Hoon]

> for j in range(1, len(kogid)):
>     name = "EXT-CLB-" + kogid[j] + ".seq"
>     if os.path.exists(name):
>         handle = open(name, "rU")
>         records = list(SeqIO.parse(handle, "fasta"))

You don't need the 'list' here

>         for record in records:
>             speciesID = record.id.split('|')[0]
>             outFile = open(speciesID.split('-')[0] + ".seq", 'w')
>             SeqIO.write([record], outFile, "fasta")
>             outFile.close()
>             print "Added a record for" + speciesID.split('-')[0]
>     handle.close()

The handle.close() should be inside the "if" block, so with an additional four spaces of indentation. Though this is not important for the problem you mentioned. The only way I can see that the SeqIo.write overwrites a files is if speciesID.split('-')[0] + ".seq" results in the same file name for more than one of the records. It's not a SeqIO.write issue; if you comment out the SeqIO.write line, you'll probably end up with the exact same set of output files (all of them empty though).

--Michiel