#! /usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, absolute_import
# Standard modules
import os
import textwrap
FASTA_WIDTH = 60 # line width for fasta format
[docs]def read_fasta(name):
"""
Read fasta file and output sequences in a list.
Parameters
----------
name : str
Name of file containing sequences in fasta format.
Returns
-------
header_lst : list
List of headers (str)
sequence_lst : list
List of sequences (str)
"""
assert os.path.exists(name), name + ' does not exist'
sequence_lst = []
header_lst = []
header = ""
sequence = ""
with open(name, "rt") as f_in:
for line in f_in:
data = line.strip()
# jump empty lines
if not data:
continue
# store header and sequence when a new header
# (i.e. sequence) is found
if sequence and header and data.startswith(">"):
header_lst.append(header)
sequence_lst.append(sequence)
# reset header and sequence
header = ""
sequence = ""
# save header of sequence
if data.startswith(">"):
header = data[1:]
# save sequence
if ">" not in data:
sequence += data
# save last sequence
if header and sequence:
header_lst.append(header)
sequence_lst.append(sequence)
# outputs
assert len(header_lst) == len(sequence_lst), \
"cannot read same number of headers and sequences"
print("read %d sequences in %s" % (len(sequence_lst), name))
if len(sequence_lst) == 0:
print("WARNING: {} seems empty of sequence".format(name))
return header_lst, sequence_lst
[docs]def read_several_fasta(input_files):
"""
Read several fasta files
Note that each fasta file may contain several sequences.
Parameters
----------
input_files: a list of fasta file paths.
Returns
-------
pb_name: a list of the headers
pb_seq: a list of the sequences
"""
pb_seq = []
pb_name = []
for name in input_files:
header, seq = read_fasta(name)
pb_name += header
pb_seq += seq
return pb_name, pb_seq
[docs]def write_fasta_entry(outfile, sequence, comment, width=FASTA_WIDTH):
"""
Write a fasta entry (header + sequence) in an open file
Parameters
----------
name : file descriptor
The file descriptor to write in. It must allow writing.
sequence : str
Sequence to format.
comment : str
Comment to make header of sequence.
width : int
The width of a line. `FASTA_WIDTH` by default.
"""
print('>' + comment, file=outfile)
print(textwrap.fill(sequence, width=width), file=outfile)
[docs]def write_fasta(outfile, sequences, comments):
"""
Write fasta entries (header + sequence) in an open file
Parameters
----------
name : file descriptor
The file descriptor to write in. It must allow writing.
header_lst : list
List of headers (str)
sequence_lst : list
List of sequences (str)
"""
for sequence, comment in zip(sequences, comments):
write_fasta_entry(outfile, sequence, comment)