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digest_genome.py
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digest_genome.py
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#!/usr/bin/env python
"""
In silico digest of a fasta genome file to fastq format data files.
"""
import os
import gzip
from ..assemble.utils import comp
class DigestGenome(object):
"""
Digest a fasta genome file with one or two restriction enzymes to create
pseudo-fastq files to treat as samples in a RAD assembly.
Parameters
----------
fasta (str):
Path to a fasta genome file (optionally gzipped).
workdir (str):
Directory in which to write output fastq files. Will be created if
it does not yet exist.
name (str):
Name prefix for output files.
readlen (int):
The length of the sequenced read extending from the cut site when
creating fastq reads from the digested fragments.
re1 (str):
First restriction enzyme recognition site.
re2 (str):
Second restriction enzyme recognition site.
ncopies (int):
The number of copies to make for every digested copy to write to as
fastq reads in the output files.
nscaffolds (int, None):
Only the first N scaffolds (sorted in order from longest to shortest)
will be digested. If None then all scaffolds are digested.
Example:
--------
dg = ipa.digest_genome(
fasta="genome.fa",
workdir="digested_genomes",
name="quinoa",
re1="AATCGG",
re2="CCGG",
ncopies=5,
readlen=150,
paired=True,
)
dg.run()
"""
def __init__(
self,
fasta,
name="digested",
workdir="digested_genomes",
re1="CTGCAG",
re2=None,
ncopies=1,
readlen=150,
paired=True,
min_size=None,
max_size=None,
nscaffolds=None,
):
self.fasta = fasta
self.name = name
self.workdir = workdir
self.re1 = re1
self.re2 = re2
self.ncopies = ncopies
self.readlen = readlen
self.paired = paired
self.min_size = min_size
self.max_size = max_size
self.nscaffolds = nscaffolds
# use readlen as min_size if not entered
if not self.min_size:
self.min_size = self.readlen
if not self.max_size:
self.max_size = 9999999
def run(self):
"""
Parses the genome into scaffolds list and then cuts each into digested
chunks and saves as fastq.
"""
# counter
iloc = 0
# open output file for writing
if not os.path.exists(self.workdir):
os.makedirs(self.workdir)
handle1 = os.path.join(self.workdir, self.name + "_R1_.fastq.gz")
handle2 = os.path.join(self.workdir, self.name + "_R2_.fastq.gz")
out1 = gzip.open(handle1, 'w')
if self.paired:
out2 = gzip.open(handle2, 'w')
# load genome file
if self.fasta.endswith(".gz"):
fio = gzip.open(self.fasta)
scaffolds = fio.read().decode().split(">")[1:]
else:
fio = open(self.fasta)
scaffolds = fio.read().split(">")[1:]
# sort scaffolds by length
scaffolds = sorted(scaffolds, key=lambda x: len(x), reverse=True)
# iterate over scaffolds
for scaff in scaffolds[:self.nscaffolds]:
# get name
name, seq = scaff.split("\n", 1)
# no funny characters in names plz
name = name.replace(" ", "_").strip()
# makes seqs nice plz
seq = seq.replace("\n", "").upper()
# digest scaffold into fragments and discard scaff ends
bits = ["1{}1".format(i) for i in seq.split(self.re1)][1:-1]
# digest each fragment into second cut fragment
if not self.re2:
bits1 = []
for fragment in bits:
if len(fragment) > self.min_size:
# forward read on fragment
bits1.append((fragment[1:-1], 0, self.max_size))
bits = bits1
else:
bits1 = bits
bits = []
pos = 0
for fragment in bits1:
fbits = fragment.split(self.re2)
if len(fbits) > 1:
# remove the 1
fbit = fbits[0][1:] # 1----2
rbit = fbits[1][:-1] # 2----1
lef = len(fbit)
if (lef > self.min_size) and (lef <= self.max_size):
#pos = seq.index(fbit)
bits.append((fbit, pos, lef))
lef = len(rbit)
if (lef > self.min_size) and (lef <= self.max_size):
res = comp(rbit)[::-1]
#pos = seq.index(res)
bits.append((res, pos, lef))
# turn fragments into (paired) reads
fastq_r1s = []
fastq_r2s = []
for fragment in bits:
fragment, pos, end = fragment
r1 = fragment[:self.readlen]
r2 = comp(fragment[-self.readlen:])[::-1]
# write reads to a file
for copy in range(self.ncopies):
fastq = "@{name}_loc{loc}_rep{copy} 1:N:0:\n{read}\n+\n{qual}"
fastq = fastq.format(**{
'name': name,
'loc': iloc,
# 'pos': pos,
# 'end': end,
'copy': copy,
'read': r1,
'qual': "B" * len(r1),
})
fastq_r1s.append(fastq)
if self.paired:
fastq = "@{name}_loc{loc}_rep{copy} 2:N:0:\n{read}\n+\n{qual}"
fastq = fastq.format(**{
'name': name,
'loc': iloc,
'copy': copy,
'read': r2,
'qual': "B" * len(r2),
})
fastq_r2s.append(fastq)
iloc += 1
# write all bits of scaffold to disk
if fastq_r1s:
out1.write(("\n".join(fastq_r1s)).encode() + b"\n")
if self.paired:
out2.write("\n".join(fastq_r2s).encode() + b"\n")
# close handles
fio.close()
out1.close()
if self.paired:
out2.close()
# report stats
print("extracted reads from {} positions".format(iloc))