[Biopython] Generator expression for SeqIO

[Willis, Jordan R]

Does the input.txt have fasta sequences in it and you want to write them to a file? This is what it looks like.

from Bio import SeqIO as sio

generator = sio.read('input.txt','fasta')


for i in generator:
print i.header
print i.seq

will give you header and sequence. You could of course write this to a file, but you seem to be inputting a fasta file just to write out another one.




Jordan Willis
Ph.D Candidate, CPB
Laboratory of Dr. James Crowe and Dr. Jens Meiler
11475 MRBIV
2213 Garland Ave.
Nashville, TN 37232
Cell: 816-674-5340
Office: 615-343-8263


On Dec 7, 2011, at 12:26 AM, Peter Cock wrote:

On Wed, Dec 7, 2011 at 4:41 AM, Mic <mictadlo at gmail.com<mailto:mictadlo at gmail.com>> wrote:
No worries is was perfect.

I have the following code and I do not know how to combine the *header* and
*seq* variables from the '*with*' statement with generator expression?

from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from pprint import pprint

if __name__ == '__main__':

   *with* open('input.txt') as f:
       for line in f:
           try:
               splited_line = line.split('\t')

               *header* = splited_line[0] +'_'+ splited_line[2]
               *seq* = splited_line[3]
           except IndexError:
               continue

   fasta_file = open('output.fasta', 'w')
   records = (SeqRecord(???), id=????, description="") for i in ???)

   SeqIO.write(records, fasta_file, "fasta")

Thank you in advance.

Are you trying to parse a tabular file, with three columns
(ID, sequence, description)?

I suggest you learn about generator functions in Python.

Peter

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