view bin/bsf-call @ 2:f274c166e738 default tip

remove comments in bsfcall_wrapper.xml

#!/usr/bin/env python
"""
Bisulfighter::bsf-call

Bisulfighter (http://epigenome.cbrc.jp/bisulfighter)
by National Institute of Advanced Industrial Science and Technology (AIST)
is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
http://creativecommons.org/licenses/by-nc-sa/3.0/
"""

__version__= "1.3"

from optparse import OptionParser
import os
import sys
import re

prog = 'bsf-call'
usage = """%prog [options] refgenome read1 read2 ...
  example: %prog -o experiment.txt hg38.fa paired-sample1-1.fastq,paired-sample1-2.fastq"""
description = "A mapping of the read bisulfite treated by LAST, to detect methylated cytosine (mC) of the results, and outputs the detection result to the file."

op = OptionParser(prog=prog, usage=usage, description=description, version="%s-%s" % (prog, __version__))

op.add_option("-c", "--coverage", type="int", default=5, metavar="C",
              help="threshold of read coverate (default: %default)")

# op.add_option("-d", "--pe-direction", type="string", default="ff",
#               help="direction of paired-end probes: ff, fr, rf, rr (default: %default)")
# 
op.add_option("-l", "--lower-bound", type="float", default=0.05, metavar="L",
              help="threshold of mC ratio (default: %default)")

op.add_option("-p", "--multi-thread", type="int", default=1, metavar="P",
              help="number of threads (default: %default)")

op.add_option("-s", "", type="int", default=150, metavar="S",
              help="threshold of the alignment score at filtering (default: %default)")

op.add_option("-m", "", type="float", default=1e-9, metavar="M",
              help="threshold of the mismap probability at filtering (default: %default)")

# op.add_option("", "--last", type="string", default="", metavar="OPT1,OPT2,...",
#               help="options for LAST (lastal command)")
# 
op.add_option("-o", "", type="string", default="bsf-call.out", metavar="FILE",
              help="output file (default: bsf-call.out)")

op.add_option("-W", "", type="string", default="./bsfwork", metavar="WORKDIR",
              help="work directory (default: ./bsfwork)")

op.add_option("", "--work-auto", action="store_true", dest="auto_create_work_dir", default=False,
              help="create work directory automatically")

# op.add_option("-n", "", action="store_true", dest="use_cluster", default=False,
#               help="run bsf-call on pc cluster")
# 
# op.add_option("-q", "", type="string", default="", metavar="QUEUE_LIST",
#               help="queue list")
# 
op.add_option("-M", "", type="string", metavar="MAPPING_DIR",
              help="mapping result directory")

op.add_option("-T", "", type="string", metavar="LOCAL_DIR",
              help="local directory")

# op.add_option("-r", "", type="string", default="100M", metavar="SPLIT_READ_SIZE",
#               help="split read size")
# 
# op.add_option("", "--bam", action="store_true", dest="read_bam", default=False,
#               help="read BAM file for mC detection")
# 
# op.add_option("", "--sam", action="store_true", dest="read_sam", default=False,
#               help="read SAM file for mC detection")
# 
# op.add_option("-z", "--compress-prog", type="string", dest="z", metavar="COMPRESS_PROG", default="bzip2", 
#               help="compression program")

options, args = op.parse_args()

errors = []

work_dir = None
if options.W:
    work_dir = options.W
else:
    if not options.auto_create_work_dir:
        work_dir = "bsfwork"

if options.M:
    if len(args) < 1:
        op.error("\n  Reference genome is not specified.")

    for result_dir in options.M.split(","):
        if not os.path.exists(result_dir):
            errors.append("Mapping result directory: '%s' does not exist." % options.M)

    # if options.read_bam and options.read_sam:
    #     errors.append("--bam and --sam cannot be placed simultaneously.")

    ref_genome = args[0]
    reads = None
else:
    if len(args) < 2:
        op.error("\n  Reference genome and read sequence is not specified.")

    # if options.read_bam:
    #     errors.append("--bam option is specified but -M option is not specified.")

    # if options.read_sam:
    #     errors.append("--sam option is specified but -M option is not specified.")

    ref_genome = args[0]
    reads = args[1:]

    for read_files in reads:
        for read_file in read_files.split(','):
            if not os.path.exists(read_file):
                errors.append("Read file: '%s' does not exists." % read_file)

    if work_dir and os.path.exists(work_dir):
        errors.append("Working directory: '%s' already exists." % work_dir)

if not os.path.exists(ref_genome):
    errors.append("Reference genome: '%s' does not exists." % ref_genome)

# if options.read_bam or options.read_sam:
#     try:
#         import pysam
#     except:
#         errors.append("--bam or --sam is specified but pysam is not installed.")

if len(errors) > 0:
    op.error("\n  " + "\n  ".join(errors))

cmd_opts = {}
cmd_opts["coverage"] = options.coverage
# cmd_opts["pe_direction"] = options.pe_direction
cmd_opts["num_threads"] = options.multi_thread
cmd_opts["lower_bound"] = options.lower_bound
cmd_opts["aln_score_thres"] = options.s
cmd_opts["aln_mismap_prob_thres"] = options.m
cmd_opts["output"] = options.o
# cmd_opts["last_opts"] = options.last
cmd_opts["work_dir"] = work_dir
# cmd_opts["use_cluster"] = options.use_cluster
# cmd_opts["queue_list"] = options.q
cmd_opts["mapping_dir"] = options.M
cmd_opts["local_dir"] = options.T
# cmd_opts["split_read_size"] = options.r
# cmd_opts["read_bam"] = options.read_bam
# cmd_opts["read_sam"] = options.read_sam
# cmd_opts["compress_prog"] = options.z

try:
    sys.path.append('.');
    import bsfcall
except ImportError:
    errors.append("\"import bsfcall\" failed. Please be sure you have bsfcall.py in your python library path.");

import subprocess

# if not checkRunnable('last-map-probs'):
#     sys.exit(1)
# if not checkRunnable('last-pair-probs'):
#     sys.exit(1)
# if not checkRunnable(options.z):
#     sys.exit(1)

if len(errors) > 0:
    op.error("\n  " + "\n  ".join(errors))

# if cmd_opts["use_cluster"]:
#     cmd_opts["num_threads"] = 1
#     bsf_call = bsfcall.BsfCallCluster(ref_genome, reads, cmd_opts)
# else:
#     bsf_call = bsfcall.BsfCall(ref_genome, reads, cmd_opts)
bsf_call = bsfcall.BsfCall(ref_genome, reads, cmd_opts)

bsf_call.execute()

sys.exit(0)

def checkRunnable(cmd):
    for outline, errline in runProcess(cmd.split()):
        if (re.match(r'error: subProcess:', errline) is not None):
            print >>sys.stderr, '\"%s\" is not found.' % cmd
            return False
    return True

def runProcess(exe):
    try:
        p = subprocess.Popen(exe, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    except:
        yield (None, 'error: runProcess: \'%s\' failed.' % ' '.join(exe))
        return
    while (True):
        retcode = p.poll()
        if (retcode is not None):
           break
        outline = p.stdout.readline()
        errline = p.stderr.readline()
        yield (outline, errline)