[Biopython] parsing fasta based on header

[Wibowo Arindrarto]

Hi Matthew,

You can use Python generators for this. Here's a rough example:

# generators for the two different groups
seq_1 = (r for r in SeqIO.parse(open('QHM-clean.fasta', 'rU'), 'fasta') if
r.id.startswith('1'))
seq_2 = (r for r in SeqIO.parse(open('QHM-clean.fasta', 'rU'), 'fasta') if
r.id.startswith('2'))

# seqs, filenames pair list
pairs = [(seq_1, 'file_1'), (seq_2, 'file_2')]

# the actual write
for seq, filename in pairs:
SeqIO.write(seq, open(filename, 'w'), 'fasta')

cheers,
Bowo


On Tue, Nov 1, 2011 at 20:19, Matthew MacManes <macmanes at gmail.com> wrote:

> Hi All,
>
> I have a large fasta file that I am trying to sort into multiple smaller
> files based on their ID's. The File starts like this:
>
> >1MUSgi|116063569|ref|NM_010065.2|
>
> AGGGG-TGGTTGACCATCAACAACATCGGCATCATG-AAGGGAGGCTCCAAGGAGTACTGGTTTGTGCTGACTGCTGAG-
> >2MUSgi|118130562|ref|NM_019880.3|
> CGGCCCGCGGCTCAGCCGTCGGCGCGCAGGATGGACGGCG-A
> >2MUSgi|118130562|ref|NM_019880.3|
>
> AGTTTAGCCAGGCCCTGGCCATCCGGAGCTACACCAAGTTTGTGATGGGGATTGCAGTGAGCATGCTGACCTACCCCTTCCTGCTCGTTGGAGATCTCATGGCAGTGAACAACCCTGGAGTAACCT
> >1HOMOgi|59853098|ref|NM_004408.2|
>
> GCATCCGCAAGGGCTGGCTGACTATCAATAATATTGGCATCATGAAAGGGGGCTCCAAGGAGTACTGGTTTGTGCTGACTGCTGAG-
> >1
>
> GGTGATCCGCAGGGGCTGGCTGACCATCAACAACATTGGCATCATGAAAGGGGGCTCCAAGGAGTACTGGTTCGTGCTCACTGCCGAGTCACTGTCCTGGTACAAGGACGAAGAGGAGAAAGAGAG
> >2
>
> CGCGCCAGCACCGGCCCGCGGCGCAGCCCTCGGCCCGCAGGATGGACGGCGCGTCCGGGGGCCTGGGCTCTGGGGATAGTGCC
>
> I want all of the ID's beginning with 1's to go on one file, ID's starting
> with 2's in another.
>
> I have been trying to use SeqIO
>
> for record in SeqIO.parse(open("QHM-clean.fasta", "rU"), "fasta") :
> for i in range(1,3):
>  if record.id %i:  #this needs to be changed "if record.id *STARTS WITH*
> %i"
>  print record.id
> output_handle = open("%i.fasta", "w") #naming in this manner does not seem
> to be allowed
>  SeqIO.write(output_handle, "fasta")
> output_handle.close()
>
> But this seems to be not working in many obvious ways... Can anybody help
> me out with some advice on how to proceed?
>
> Thanks a lot, Matt
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