Re: concatenate fasta file

[Jean-Michel Pichavant]

PeroMHC wrote:

Hi All, I have  a simple problem that I hope somebody can help with. I
have an input file (a fasta file) that I need to edit..

Input file format

name 1

tactcatacatac

name 2

acggtggcat

name 3

gggtaccacgtt

I need to concatenate the sequences.. make them look like

concatenated

tactcatacatacacggtggcatgggtaccacgtt

thanks. Matt

A solution using regexp:

found = []
for line in open('seqfile.txt'):
   found += re.findall('^[acgtACGT]+$', line)

print found
> ['tactcatacatac', 'acggtggcat', 'gggtaccacgtt']

print ''.join(found)
> 'tactcatacatacacggtggcatgggtaccacgtt'


JM
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