393 lines
14 KiB
Python
393 lines
14 KiB
Python
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#!/usr/bin/env python
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#
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# Copyright 2015, Daehwan Kim <infphilo@gmail.com>
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#
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# This file is part of HISAT 2.
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#
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# HISAT 2 is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# HISAT 2 is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with HISAT 2. If not, see <http://www.gnu.org/licenses/>.
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#
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import sys, math, random, re
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from collections import defaultdict, Counter
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from argparse import ArgumentParser, FileType
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"""
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"""
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def reverse_complement(seq):
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result = ""
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for nt in seq:
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base = nt
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if nt == 'A':
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base = 'T'
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elif nt == 'a':
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base = 't'
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elif nt == 'C':
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base = 'G'
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elif nt == 'c':
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base = 'g'
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elif nt == 'G':
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base = 'C'
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elif nt == 'g':
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base = 'c'
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elif nt == 'T':
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base = 'A'
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elif nt == 't':
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base = 'a'
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result = base + result
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return result
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"""
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"""
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def read_genome(genome_file):
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chr_dic = {}
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chr_name, sequence = "", ""
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for line in genome_file:
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if line[0] == ">":
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if chr_name and sequence:
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chr_dic[chr_name] = sequence
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chr_name = line.strip().split()[0][1:]
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sequence = ""
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else:
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sequence += line[:-1]
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if chr_name and sequence:
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chr_dic[chr_name] = sequence
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return chr_dic
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"""
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"""
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def read_snp(snp_file):
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snps = defaultdict(list)
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for line in snp_file:
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line = line.strip()
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if not line or line.startswith('#'):
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continue
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try:
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snpID, type, chr, pos, data = line.split('\t')
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chr = chr.split()[0]
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except ValueError:
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continue
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assert type in ["single", "deletion", "insertion"]
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if type == "deletion":
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data = int(data)
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snps[chr].append([snpID, type, int(pos), data])
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return snps
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"""
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"""
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def getSamAlignment(chr_seq, read_len, snp):
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snp_id, snp_type, snp_pos, snp_data = snp
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# Define MD, XM, NM, Zs, read_seq
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read_seq, MD, Zs = "", "", ""
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left_read_len = read_len / 2
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pos = snp_pos - left_read_len
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assert pos >= 0
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if snp_type == "single":
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cigar_str = "100M"
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read_seq = chr_seq[pos:pos+left_read_len] + snp_data + chr_seq[pos+left_read_len+1:pos+read_len]
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MD = "%d%s%d" % (left_read_len, chr_seq[pos+left_read_len], read_len - left_read_len - 1)
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Zs = "%d|S|%s" % (left_read_len, snp_id)
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elif snp_type == "deletion":
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del_len = int(snp_data)
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cigar_str = "%dM%dD%dM" % (left_read_len, del_len, read_len - left_read_len)
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read_seq = chr_seq[pos:pos+left_read_len] + chr_seq[pos+left_read_len+del_len:pos+read_len+del_len]
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MD = "%d^%s%d" % (left_read_len, chr_seq[pos+left_read_len:pos+left_read_len+del_len], read_len - left_read_len)
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Zs = "%d|D|%s" % (left_read_len, snp_id)
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else:
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assert snp_type == "insertion"
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ins_len = len(snp_data)
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assert ins_len < read_len
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cigar_str = "%dM%dI%dM" % (left_read_len, ins_len, read_len - left_read_len - ins_len)
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read_seq = chr_seq[pos:pos+left_read_len] + snp_data + chr_seq[pos+left_read_len:pos+read_len-ins_len]
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MD = "%d" % (read_len - ins_len)
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Zs = "%d|I|%s" % (left_read_len, snp_id)
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if len(read_seq) != read_len:
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print >> sys.stderr, "read length differs:", len(read_seq), "vs.", read_len
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print >> sys.stderr, pos, cigar_str, MD, Zs
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assert False
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ref_read_seq = chr_seq[pos:pos+read_len]
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return pos, cigar_str, MD, Zs, read_seq, ref_read_seq
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"""
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"""
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cigar_re = re.compile('\d+\w')
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def samRepOk(genome_seq, read_seq, chr, pos, cigar, MD, Zs):
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assert chr in genome_seq
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chr_seq = genome_seq[chr]
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assert pos < len(chr_seq)
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# Calculate XM and NM based on Cigar and Zs
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cigars = cigar_re.findall(cigar)
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cigars = [[int(cigars[i][:-1]), cigars[i][-1]] for i in range(len(cigars))]
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ref_pos, read_pos = pos, 0
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ann_ref_seq, ann_ref_rel, ann_read_seq, ann_read_rel = [], [], [], []
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for i in range(len(cigars)):
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cigar_len, cigar_op = cigars[i]
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if cigar_op == "M":
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partial_ref_seq = chr_seq[ref_pos:ref_pos+cigar_len]
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partial_read_seq = read_seq[read_pos:read_pos+cigar_len]
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assert len(partial_ref_seq) == len(partial_read_seq)
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ann_ref_seq += list(partial_ref_seq)
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ann_read_seq += list(partial_read_seq)
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for j in range(len(partial_ref_seq)):
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if partial_ref_seq[j] == partial_read_seq[j]:
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ann_ref_rel.append("=")
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ann_read_rel.append("=")
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else:
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ann_ref_rel.append("X")
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ann_read_rel.append("X")
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ref_pos += cigar_len
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read_pos += cigar_len
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elif cigar_op == "D":
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partial_ref_seq = chr_seq[ref_pos:ref_pos+cigar_len]
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ann_ref_rel += list(partial_ref_seq)
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ann_ref_seq += list(partial_ref_seq)
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ann_read_rel += (["-"] * cigar_len)
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ann_read_seq += (["-"] * cigar_len)
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ref_pos += cigar_len
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elif cigar_op == "I":
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partial_read_seq = read_seq[read_pos:read_pos+cigar_len]
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ann_ref_rel += (["-"] * cigar_len)
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ann_ref_seq += (["-"] * cigar_len)
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ann_read_rel += list(partial_read_seq)
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ann_read_seq += list(partial_read_seq)
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read_pos += cigar_len
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elif cigar_op == "N":
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ref_pos += cigar_len
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else:
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assert False
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assert len(ann_ref_seq) == len(ann_read_seq)
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assert len(ann_ref_seq) == len(ann_ref_rel)
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assert len(ann_ref_seq) == len(ann_read_rel)
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ann_Zs_seq = ["0" for i in range(len(ann_ref_seq))]
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Zss, Zs_i, snp_pos_add = [], 0, 0
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if Zs != "":
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Zss = Zs.split(',')
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Zss = [zs.split('|') for zs in Zss]
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ann_read_pos = 0
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for zs in Zss:
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zs_pos, zs_type, zs_id = zs
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zs_pos = int(zs_pos)
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for i in range(zs_pos):
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while ann_read_rel[ann_read_pos] == '-':
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ann_read_pos += 1
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ann_read_pos += 1
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if zs_type == "S":
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ann_Zs_seq[ann_read_pos] = "1"
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ann_read_pos += 1
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elif zs_type == "D":
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while ann_read_rel[ann_read_pos] == '-':
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ann_Zs_seq[ann_read_pos] = "1"
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ann_read_pos += 1
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elif zs_type == "I":
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while ann_ref_rel[ann_read_pos] == '-':
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ann_Zs_seq[ann_read_pos] = "1"
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ann_read_pos += 1
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else:
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assert False
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tMD, tXM, tNM = "", 0, 0
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match_len = 0
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i = 0
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while i < len(ann_ref_seq):
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if ann_ref_rel[i] == "=":
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assert ann_read_rel[i] == "="
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match_len += 1
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i += 1
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continue
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assert ann_read_rel[i] != "="
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if ann_ref_rel[i] == "X" and ann_read_rel[i] == "X":
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if match_len > 0:
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tMD += ("{}".format(match_len))
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match_len = 0
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tMD += ann_ref_seq[i]
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if ann_Zs_seq[i] == "0":
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tXM += 1
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tNM += 1
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i += 1
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else:
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assert ann_ref_rel[i] == "-" or ann_read_rel[i] == "-"
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if ann_ref_rel[i] == '-':
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while ann_ref_rel[i] == '-':
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if ann_Zs_seq[i] == "0":
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tNM += 1
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i += 1
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else:
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assert ann_read_rel[i] == '-'
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del_seq = ""
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while ann_read_rel[i] == '-':
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del_seq += ann_ref_seq[i]
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if ann_Zs_seq[i] == "0":
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tNM += 1
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i += 1
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if match_len > 0:
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tMD += ("{}".format(match_len))
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match_len = 0
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tMD += ("^{}".format(del_seq))
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if match_len > 0:
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tMD += ("{}".format(match_len))
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if tMD != MD:
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print >> sys.stderr, chr, pos, cigar, MD, Zs
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print >> sys.stderr, tMD
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assert False
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"""
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"""
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def simulate_reads(genome_file, snp_file, base_fname, \
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paired_end, read_len, frag_len, \
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num_frag, sanity_check, verbose):
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if read_len > frag_len:
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frag_len = read_len
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genome_seq = read_genome(genome_file)
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snps = read_snp(snp_file)
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chr_ids = genome_seq.keys()
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sam_file = open(base_fname + ".sam", "w")
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# Write SAM header
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print >> sam_file, "@HD\tVN:1.0\tSO:unsorted"
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for chr in genome_seq.keys():
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print >> sam_file, "@SQ\tSN:%s\tLN:%d" % (chr, len(genome_seq[chr]))
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read_file = open(base_fname + "_snp_1.fa", "w")
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ref_read_file = open(base_fname + "_ref_1.fa", "w")
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if paired_end:
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read2_file = open(base_fname + "_snp_2.fa", "w")
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ref_read2_file = open(base_fname + "_ref_2.fa", "w")
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cur_read_id = 1
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for chr in snps:
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assert chr in genome_seq
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chr_seq = genome_seq[chr]
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chr_len = len(chr_seq)
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if chr in snps:
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chr_snps = snps[chr]
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else:
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chr_snps = []
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for snp in chr_snps:
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# SAM specification (v1.4)
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# http://samtools.sourceforge.net/
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flag, flag2 = 99, 163 # 83, 147
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pos, cigar_str, MD, Zs, read_seq, ref_read_seq = getSamAlignment(chr_seq, read_len, snp)
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# pos2, cigar2_str, MD2, Zs2, read2_seq = getSamAlignment(chr_seq, frag_pos+frag_len-read_len, read_len, snp)
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if sanity_check:
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samRepOk(genome_seq, read_seq, chr, pos, cigar_str, MD, Zs)
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# samRepOk(genome_seq, read2_seq, chr, pos2, cigar2_str, MD2, Zs2)
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if Zs != "":
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Zs = ("\tZs:Z:{}".format(Zs))
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# if Zs2 != "":
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# Zs2 = ("\tZs:Z:{}".format(Zs2))
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read_id_str = "{}_{}_{}_{}".format(cur_read_id, chr, pos, cigar_str)
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print >> read_file, ">{}".format(read_id_str)
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print >> read_file, read_seq
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print >> sam_file, "{}\t{}\t{}\t{}\t255\t{}\t{}\t{}\t0\t{}\t*\tXM:i:0\tNM:i:0\tMD:Z:{}{}".format(read_id_str, flag, chr, pos + 1, cigar_str, chr, pos + 1, read_seq, MD, Zs)
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print >> ref_read_file, ">{}_{}_{}_100M".format(cur_read_id, chr, pos)
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print >> ref_read_file, ref_read_seq
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"""
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if paired_end:
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print >> read2_file, ">{}".format(cur_read_id)
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print >> read2_file, reverse_complement(read2_seq)
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print >> sam_file, "{}\t{}\t{}\t{}\t255\t{}\t{}\t{}\t0\t{}\t*\tXM:i:0\tNM:i:0\tMD:Z:{}{}".format(cur_read_id, flag2, chr, pos2 + 1, cigar2_str, chr, pos + 1, read2_seq, MD2, Zs2)
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"""
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cur_read_id += 1
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sam_file.close()
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read_file.close()
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ref_read_file.close()
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if paired_end:
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read2_file.close()
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ref_read2_file.close()
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if __name__ == '__main__':
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parser = ArgumentParser(
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description='Simulate reads from GENOME (fasta) and GTF files')
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|
parser.add_argument('genome_file',
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nargs='?',
|
||
|
|
type=FileType('r'),
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help='input GENOME file')
|
||
|
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parser.add_argument('snp_file',
|
||
|
|
nargs='?',
|
||
|
|
type=FileType('r'),
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||
|
|
help='input SNP file')
|
||
|
|
parser.add_argument('base_fname',
|
||
|
|
nargs='?',
|
||
|
|
type=str,
|
||
|
|
help='output base filename')
|
||
|
|
parser.add_argument('--paired-end',
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||
|
|
dest='paired_end',
|
||
|
|
action='store_true',
|
||
|
|
help='single-end reads (default: paired-end reads)')
|
||
|
|
parser.add_argument('-r', '--read-length',
|
||
|
|
dest='read_len',
|
||
|
|
action='store',
|
||
|
|
type=int,
|
||
|
|
default=100,
|
||
|
|
help='read length (default: 100)')
|
||
|
|
parser.add_argument('-f', '--fragment-length',
|
||
|
|
dest='frag_len',
|
||
|
|
action='store',
|
||
|
|
type=int,
|
||
|
|
default=250,
|
||
|
|
help='fragment length (default: 250)')
|
||
|
|
parser.add_argument('-n', '--num-fragment',
|
||
|
|
dest='num_frag',
|
||
|
|
action='store',
|
||
|
|
type=int,
|
||
|
|
default=1000000,
|
||
|
|
help='number of fragments (default: 1000000)')
|
||
|
|
parser.add_argument('--sanity-check',
|
||
|
|
dest='sanity_check',
|
||
|
|
action='store_true',
|
||
|
|
help='sanity check')
|
||
|
|
parser.add_argument('-v', '--verbose',
|
||
|
|
dest='verbose',
|
||
|
|
action='store_true',
|
||
|
|
help='also print some statistics to stderr')
|
||
|
|
parser.add_argument('--version',
|
||
|
|
action='version',
|
||
|
|
version='%(prog)s 2.1.0')
|
||
|
|
args = parser.parse_args()
|
||
|
|
if not args.genome_file or not args.snp_file:
|
||
|
|
parser.print_help()
|
||
|
|
exit(1)
|
||
|
|
simulate_reads(args.genome_file, args.snp_file, args.base_fname, \
|
||
|
|
args.paired_end, args.read_len, args.frag_len, \
|
||
|
|
args.num_frag, args.sanity_check, args.verbose)
|