233 lines
8.9 KiB
Python
233 lines
8.9 KiB
Python
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#!/usr/bin/env python
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import sys, os, subprocess
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import multiprocessing
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import string, re
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import platform
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from datetime import datetime, date, time
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import copy
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from argparse import ArgumentParser, FileType
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"""
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"""
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def evaluate(read_fname,
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verbose):
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aligners = [
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["hisat2", "", "", ""],
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["hisat2", "", "snp", ""],
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["bowtie2", "", "", ""],
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]
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num_threads = 3
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cwd = os.getcwd()
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genome = "genome"
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align_stat = []
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# for paired in [False, True]:
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for paired in [False]:
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base_fname = "common_snp_reads"
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type_sam_fname = base_fname + ".sam"
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type_read1_fname = base_fname + "_1.fa"
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type_read2_fname = base_fname + "_2.fa"
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type_read1_fname = read_fname
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def get_aligner_version(aligner, version):
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version = ""
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if aligner == "hisat2" or \
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aligner == "bowtie2":
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if version:
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cmd = ["%s_%s/%s" % (aligner, version, aligner)]
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else:
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cmd = ["%s/%s" % (aligner_bin_base, aligner)]
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cmd += ["--version"]
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cmd_process = subprocess.Popen(cmd, stdout=subprocess.PIPE)
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version = cmd_process.communicate()[0][:-1].split("\n")[0]
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version = version.split()[-1]
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elif aligner == "star":
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version = "2.4.2a"
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elif aligner == "gsnap":
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cmd = ["%s/gsnap" % (aligner_bin_base)]
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cmd_process = subprocess.Popen(cmd, stderr=subprocess.PIPE)
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version = cmd_process.communicate()[1][:-1].split("\n")[0]
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version = version.split()[2]
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elif aligner == "bwa":
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cmd = ["%s/bwa" % (aligner_bin_base)]
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cmd_process = subprocess.Popen(cmd, stderr=subprocess.PIPE)
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version = cmd_process.communicate()[1][:-1].split("\n")[2]
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version = version.split()[1]
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return version
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def get_aligner_cmd(aligner, type, index_type, version, read1_fname, read2_fname, out_fname, cmd_idx = 0):
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cmd = []
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if aligner == "hisat2":
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cmd = ["hisat2"]
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if num_threads > 1:
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cmd += ["-p", str(num_threads)]
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cmd += ["-f"]
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cmd += ["--no-spliced-alignment"]
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if index_type:
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index_cmd = "../grch38_snp_hisat2/genome_snp"
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else:
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index_cmd = "../grch38_hisat2/genome"
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cmd += [index_cmd]
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if paired:
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cmd += ["-1", read1_fname,
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"-2", read2_fname]
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else:
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cmd += [read1_fname]
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elif aligner == "star":
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cmd = ["%s/STAR" % (aligner_bin_base)]
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if num_threads > 1:
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cmd += ["--runThreadN", str(num_threads)]
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cmd += ["--genomeDir"]
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if cmd_idx == 0:
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if type == "gtf":
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cmd += ["%s/STAR%s/gtf" % (index_base, index_add)]
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else:
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cmd += ["%s/STAR%s" % (index_base, index_add)]
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else:
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assert cmd_idx == 1
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cmd += ["."]
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if desktop:
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cmd += ["--genomeLoad", "NoSharedMemory"]
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else:
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cmd += ["--genomeLoad", "LoadAndKeep"]
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if type == "x2":
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if cmd_idx == 1:
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cmd += ["--alignSJDBoverhangMin", "1"]
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cmd += ["--readFilesIn",
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read1_fname]
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if paired:
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cmd += [read2_fname]
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if paired:
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cmd += ["--outFilterMismatchNmax", "6"]
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else:
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cmd += ["--outFilterMismatchNmax", "3"]
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elif aligner == "bowtie2":
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cmd = ["bowtie2"]
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if num_threads > 1:
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cmd += ["-p", str(num_threads)]
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cmd += ["-f"]
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cmd += ["-x ../grch38_bowtie2/genome"]
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if paired:
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cmd += ["-1", read1_fname,
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"-2", read2_fname]
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else:
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cmd += [read1_fname]
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elif aligner == "gsnap":
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cmd = ["%s/gsnap" % (aligner_bin_base),
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"-A",
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"sam"]
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if num_threads > 1:
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cmd += ["-t", str(num_threads)]
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cmd += ["--max-mismatches=3",
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"-D", "%s/GSNAP%s" % (index_base, index_add),
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"-N", "1",
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"-d", genome,
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read1_fname]
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if paired:
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cmd += [read2_fname]
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elif aligner == "bwa":
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cmd = ["%s/bwa" % (aligner_bin_base)]
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if type in ["mem", "aln"]:
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cmd += [type]
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elif type == "sw":
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cmd += ["bwa" + type]
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if num_threads > 1:
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cmd += ["-t", str(num_threads)]
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cmd += ["%s/BWA%s/%s.fa" % (index_base, index_add, genome)]
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cmd += [read1_fname]
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if paired:
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cmd += [read2_fname]
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else:
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assert False
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return cmd
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for aligner, type, index_type, version in aligners:
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aligner_name = aligner + type
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if version != "":
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aligner_name += ("_%s" % version)
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if aligner == "hisat2" and index_type != "":
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aligner_name += ("_" + index_type)
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two_step = (aligner == "tophat2" or type == "x2" or (aligner in ["hisat2", "hisat"] and type == ""))
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print >> sys.stderr, "\t%s\t%s" % (aligner_name, str(datetime.now()))
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if paired:
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aligner_dir = aligner_name + "_paired"
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else:
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aligner_dir = aligner_name + "_single"
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if not os.path.exists(aligner_dir):
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os.mkdir(aligner_dir)
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os.chdir(aligner_dir)
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out_fname = base_fname + ".sam"
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duration = -1.0
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# Align all reads
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aligner_cmd = get_aligner_cmd(aligner, type, index_type, version, "../" + type_read1_fname, "../" + type_read2_fname, out_fname)
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start_time = datetime.now()
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if verbose:
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print >> sys.stderr, "\t", start_time, " ".join(aligner_cmd)
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if aligner in ["hisat2", "hisat", "bowtie", "bowtie2", "gsnap", "bwa"]:
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proc = subprocess.Popen(aligner_cmd, stdout=open(out_fname, "w"), stderr=subprocess.PIPE)
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else:
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proc = subprocess.Popen(aligner_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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proc.communicate()
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finish_time = datetime.now()
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duration = finish_time - start_time
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duration = duration.total_seconds()
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if verbose:
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print >> sys.stderr, "\t", finish_time, "finished:", duration
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assert os.path.exists(out_fname)
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correct_reads, correct_multi_reads, num_reads = 0, 0, 0
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prev_read_id = None
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for line in open(out_fname):
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if line.startswith('@'):
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continue
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read_id, flag, chr, pos, mapQ, cigar = line.split()[:6]
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if chr.startswith("chr"):
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chr = chr[3:]
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pos = int(pos) - 1
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true_chr, true_pos, true_cigar = read_id.split('_')[1:4]
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true_pos = int(true_pos)
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if read_id != prev_read_id:
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num_reads += 1
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if true_chr == chr and pos == true_pos and cigar == true_cigar:
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correct_multi_reads += 1
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if prev_read_id != read_id:
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correct_reads += 1
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prev_read_id = read_id
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print >> sys.stderr, "\tfirst: %d / %d (%.2f%%)" % (correct_reads, num_reads, float(correct_reads)/num_reads*100)
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print >> sys.stderr, "\tall: %d / %d (%.2f%%)" % (correct_multi_reads, num_reads, float(correct_multi_reads)/num_reads*100)
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os.chdir("..")
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"""
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"""
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if __name__ == "__main__":
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parser = ArgumentParser(
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description='test HISAT2, and compare HISAT2 with other popular aligners such as TopHat2, STAR, Bowtie1/2, GSNAP, BWA-mem, etc.')
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parser.add_argument('read_fname',
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nargs='?',
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type=str,
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help='input read file')
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parser.add_argument('-v', '--verbose',
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dest='verbose',
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action='store_true',
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help='also print some statistics to stderr')
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args = parser.parse_args()
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evaluate(args.read_fname,
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args.verbose)
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