concatenate fasta file

[PeroMHC]

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

 

[Roy Smith]

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

gggtaccacgtt

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

tactcatacatacacggtggcatgggtaccacgtt

thanks. Matt

Some quick ideas. First, try something along the lines of (not tested):

data=[]
for line in sys.stdin:
if line.startswith('>'):
continue
data.append(line.strip())
print ''.join(data)

Second, check out http://biopython.org/wiki/Main_Page. I'm sure somebody
has solved this problem before.

 

[Jean-Michel Pichavant]

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


gggtaccacgtt

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


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

 

[Grant Edwards]

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

gggtaccacgtt

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

tactcatacatacacggtggcatgggtaccacgtt

(echo "concantenated>"; grep '^ [actg]*$' inputfile | tr -d '\n'; echo) > outputfile