[BioPython] error with Fasta.Record?

[Karin Lagesen]

I use the following code to read in a fasta file:

    genes = quick_FASTA_reader(geneFile)
    genelist = {}
    rec = Fasta.Record()
    iterator = 10001
    for entry in genes:
        g = ecoligene.EcoliGene(entry)
        oname = os.path.join(over300, str(iterator))
        if dofiles:
            rec.title, rec.sequence = entry
            print iterator, rec.title, rec.sequence
            ofile = open(oname, 'w')
            ofile.write(str(rec))
            ofile.close()

I do this with a test file:

adenine:18:38> cat /med/adenine/u2/projects/locator/gard/testfile
>1_dapB_to_carA_29196_29650
gtctataagtgccaaaaattacatgttttgtcttctgtttttgttgttttaatgtaaatt
ttgaccatttggtccacttttttctgctcgtttttatttcatgcaatc
>2_caiT_to_fixA_41932_42366
aattattattaacctcgtggacgcgttaatggctaactcataatgggtattcaataagct
gtattct
>3_caiT_to_fixA_41932_42366
aattattattaacctcgtggacgcgttaatggctaactcataatgggtattcaataagct
gtattctgtgattggtatcacatttttgtttcgggtgaatagagggcgttttttcgttaa
t
>4_caiT_to_fixA_41932_42366
aattattattaacctcgtggacgcgttaatggctaactcataatgggtattcaataagct
gtattctgtgattggtatcacatttttgtttcgggtgaatagagggcgttttttcgttaa
ttttgattaataatcagtttgttatgctctgttgtgagtaaaaaataacatctgac
>5_fruR_to_yabB_89033_89633
gcttcgcacgttggacgtaaaataaacaacgctgatattagccgtaaacatcgggttttt
tacctcggtatgccttgtgac
>6_fruR_to_yabB_89033_89633
aaacaacgctgatattagccgtaaacatcgggttttttacctcggtatgccttgtgac
>7_aroP_to_pdhR_121552_122091
gtttacatcaaagaagtttgaattgttacaaaaagacttccgtcagatcaagaataatgg
tatg
adenine:18:38>

And the files I get look like this:

adenine:18:37> cat /med/adenine/u2/projects/locator/gard/singles/10001
>1_dapB_to_carA_29196_29650
GTCTATAAGTGCCAAAAATTACATGTTTTGTCTTCTGTTTTTGTTGTTTTAATGTAAATT
adenine:18:37> cat /med/adenine/u2/projects/locator/gard/singles/10002
>2_caiT_to_fixA_41932_42366
AATTATTATTAACCTCGTGGACGCGTTAATGGCTAACTCATAATGGGTATTCAATAAGCT
adenine:18:37> cat /med/adenine/u2/projects/locator/gard/singles/10003
>3_caiT_to_fixA_41932_42366
AATTATTATTAACCTCGTGGACGCGTTAATGGCTAACTCATAATGGGTATTCAATAAGCT
GTATTCTGTGATTGGTATCACATTTTTGTTTCGGGTGAATAGAGGGCGTTTTTTCGTTAA
adenine:18:37> cat /med/adenine/u2/projects/locator/gard/singles/10004
>4_caiT_to_fixA_41932_42366
AATTATTATTAACCTCGTGGACGCGTTAATGGCTAACTCATAATGGGTATTCAATAAGCT
GTATTCTGTGATTGGTATCACATTTTTGTTTCGGGTGAATAGAGGGCGTTTTTTCGTTAA
adenine:18:37> cat /med/adenine/u2/projects/locator/gard/singles/10005
>5_fruR_to_yabB_89033_89633
GCTTCGCACGTTGGACGTAAAATAAACAACGCTGATATTAGCCGTAAACATCGGGTTTTT
adenine:18:38> cat /med/adenine/u2/projects/locator/gard/singles/10006
>6_fruR_to_yabB_89033_89633
adenine:18:38> cat /med/adenine/u2/projects/locator/gard/singles/10007
>7_aroP_to_pdhR_121552_122091
GTTTACATCAAAGAAGTTTGAATTGTTACAAAAAGACTTCCGTCAGATCAAGAATAATGG
adenine:18:38>

I try printing the rec object to test if the sequences are read in
correctly, and they are. Thus it seems to be a problem with writing
this object to file.

Is this something I do wrong, or is it something else?

Karin
-- 
Karin Lagesen, PhD student
karin.lagesen at labmed.uio.no