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ConradStack/pyfaidx.extract_by_name.py

Created September 30, 2017 02:06
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Extract sequences from a fasta file, preserving read name comments
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pyfaidx.extract_by_name.py
# Create a new fasta file given a fasta file and list of sequence names
# - outputting the long_name does/did not seem to work properly in the faidx script that is packaged with pyfaidx
from pyfaidx import *
# read fasta file
fa = Fasta('test.fa')
# test.read.names is newline-delimited list of sequence names, not including any text after the first space (i.e., the long_name)
with open('test.read.names') as f:
lines = [line.rstrip('\n') for line in f]
# loop over the list of read names and write the long_name (name + "comments") and sequence to a new fasta file.
with open('test.files.fasta', 'w') as outfile:
for key in lines:
read = fa[key]
# Write new fasta header for this subsequence to output file
outfile.write('>' + read.long_name + '\n')
# Write wrapped subsequence for output file
outfile.write( read[:].seq + '\n' )
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