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sequences.py
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sequences.py
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"""Module with Fasta and Fastq modules and file readers
"""
# Classes
class Fasta(object):
"""Fasta object with name and sequence
"""
def __init__(self, name, sequence):
self.name = name
self.sequence = sequence
def write_to_file(self, handle):
handle.write(">" + self.name + "\n")
handle.write(self.sequence + "\n")
def __repr__(self):
return self.name + " " + self.sequence[:31]
class Fastq(object):
"""Fastq object with name, sequence, name2, and quality string
"""
def __init__(self, name, sequence, name2, quality):
self.name = name
self.sequence = sequence
self.name2 = name2
self.quality = quality
def getShortname(self, separator):
if separator:
self.temp = self.name.split(separator)
del(self.temp[-1])
return separator.join(self.temp)
else:
return self.name
def write_to_file(self, handle):
handle.write(self.name + "\n")
handle.write(self.sequence + "\n")
handle.write(self.name2 + "\n")
handle.write(self.quality + "\n")
def __repr__(self):
return self.name + " " + self.sequence[:31]
# Defining functions
def myopen(_file, mode="r"):
if _file.endswith(".gz"):
return gzip.open(_file, mode=mode)
else:
return open(_file, mode=mode)
def fasta_iterator(input_file):
"""Takes a fasta file input_file and returns a fasta iterator
"""
with myopen(input_file) as f:
sequence = ""
name = ""
begun = False
for line in f:
line = line.strip()
if line.startswith(">"):
if begun:
yield Fasta(name, sequence)
name = line[1:]
sequence = ""
begun = True
else:
sequence += line
if name != "":
yield Fasta(name, sequence)
def fastq_iterator(infile):
"""Takes a fastq file infile and returns a fastq object iterator
Requires fastq file with four lines per sequence and no blank lines.
"""
with myopen(infile) as f:
while True:
name = f.readline().strip()
if not name:
break
seq = f.readline().strip()
name2 = f.readline().strip()
qual = f.readline().strip()
yield Fastq(name, seq, name2, qual)