diff STACKS_denovomap.py @ 0:d6ba40f6c824

first commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/STACKS_denovomap.py	Mon Aug 24 09:29:12 2015 +0000
@@ -0,0 +1,265 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
+import sys
+import re
+import os
+import tempfile
+import shutil
+import subprocess
+import glob
+import argparse
+from os.path import basename
+import zipfile
+import tarfile
+import gzip
+from galaxy.datatypes.checkers import *
+from stacks import *
+
+
+def __main__():
+
+    # arguments recuperation
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-p')
+    parser.add_argument('-b')
+    parser.add_argument('-r')
+    parser.add_argument('-s')
+    parser.add_argument('-O')
+    parser.add_argument('-m')
+    parser.add_argument('-P')
+    parser.add_argument('-M')
+    parser.add_argument('-N')
+    parser.add_argument('-n')
+    parser.add_argument('-t')
+    parser.add_argument('-H')
+    parser.add_argument('--bound_low')
+    parser.add_argument('--bound_high')
+    parser.add_argument('--alpha')
+    parser.add_argument('--logfile')
+    parser.add_argument('--compress_output')
+    parser.add_argument('--catalogsnps')
+    parser.add_argument('--catalogalleles')
+    parser.add_argument('--catalogtags')
+
+    # additionnal outputs
+    parser.add_argument('--total_output')
+    parser.add_argument('--tags_output')
+    parser.add_argument('--snps_output')
+    parser.add_argument('--alleles_output')
+    parser.add_argument('--matches_output')
+
+    options = parser.parse_args()
+
+    # create working directories
+
+    os.mkdir('inputs')
+    os.mkdir('job_outputs')
+    os.mkdir('galaxy_outputs')
+
+    cmd_line = []
+    cmd_line.append('denovo_map.pl')
+
+    # if genetic map
+
+    if options.p:
+
+        # parse config files
+
+        tab_parent_files = galaxy_config_to_tabfiles_for_STACKS(options.p)
+
+        # check if zipped files are into the tab and change tab content
+
+        extract_compress_files_from_tabfiles(tab_parent_files, 'inputs')
+
+        # check files extension (important to have .fq or .fasta files)
+
+        check_fastq_extension_and_add(tab_parent_files, 'inputs')
+
+        # create symlink into the temp dir
+
+        create_symlinks_from_tabfiles(tab_parent_files, 'inputs')
+
+        # parse the input dir and store all file names into a tab
+
+        fastq_files = []
+        for fastq_file in glob.glob('inputs/*'):
+            # if is a file (skip repository created after a decompression)
+            if os.path.isfile(fastq_file):
+                fastq_files.append(fastq_file)
+
+        fastq_files.sort()
+
+        # test if fastq are paired-end
+        if options.b == 'true':
+            for n in range(0, len(fastq_files), 2):
+                cmd_line.extend(['-p', fastq_files[n]])
+        else:
+            for myfastqfile in fastq_files:
+                cmd_line.extend(['-p', myfastqfile])
+
+    # if genetic map with progeny files
+
+    if options.r:
+
+        # parse config files
+        tab_progeny_files = galaxy_config_to_tabfiles_for_STACKS(options.r)
+
+        # check if zipped files are into the tab and change tab content
+        extract_compress_files_from_tabfiles(tab_progeny_files, 'inputs')
+
+        # check files extension (important to have .fq or .fasta files)
+        check_fastq_extension_and_add(tab_progeny_files, 'inputs')
+
+        # create symlink into the temp dir
+        create_symlinks_from_tabfiles(tab_progeny_files, 'inputs')
+
+        for key in tab_progeny_files:
+
+            # if is a file (skip repository created after a decompression)
+
+            if os.path.isfile('inputs/' + key):
+                cmd_line.extend(['-r', 'inputs/' + key])
+
+    # if population is checked
+    if options.s:
+
+        tab_individual_files = galaxy_config_to_tabfiles_for_STACKS(options.s)
+
+        # check if zipped files are into the tab and change tab content
+        extract_compress_files_from_tabfiles(tab_individual_files, 'inputs')
+
+        # check files extension (important to have .fq or .fasta files)
+        check_fastq_extension_and_add(tab_individual_files, 'inputs')
+
+        # create symlink into the temp dir
+        create_symlinks_from_tabfiles(tab_individual_files, 'inputs')
+
+        # create the command input line
+        for key in tab_individual_files:
+
+            # if is a file (skip repository created after a decompression)
+            if os.path.isfile('inputs/' + key):
+                cmd_line.extend(['-s', 'inputs/' + key])
+
+    # create the command line
+    cmd_line.extend([
+        '-S',
+        '-b',
+        '1',
+        '-T',
+        '4',
+        '-o',
+        'job_outputs/'
+        ])
+
+    if options.O:
+        cmd_line.extend(['-O', options.O])
+
+    if options.m and options.m != '-1':
+        cmd_line.extend(['-m', options.m])
+
+    if options.P and options.P != '-1':
+        cmd_line.extend(['-P', options.P])
+
+    if options.M and options.M != '-1':
+        cmd_line.extend(['-M', options.M])
+
+    if options.N and options.N != '-1':
+        cmd_line.extend(['-N', options.N])
+
+    if options.n and options.n != '-1':
+        cmd_line.extend(['-n', options.n])
+
+    if options.t and options.t == 'true':
+        cmd_line.append('-t')
+
+    if options.H and options.H == 'true':
+        cmd_line.append('-H')
+
+    ## SNP model 
+    if options.bound_low:
+        cmd_line.extend(['--bound_low', options.bound_low])
+        cmd_line.extend(['--bound_high', options.bound_high])
+
+    if options.alpha:
+        cmd_line.extend(['--alpha', options.alpha])
+
+    # launch the command line
+    print "[CMD_LINE] : "+' '.join(cmd_line)    
+
+    p = subprocess.call(cmd_line)
+
+    # postprocesses
+    try:
+        shutil.move('job_outputs/denovo_map.log', options.logfile)
+    except:
+        sys.stderr.write('Error in denovo_map execution; Please read the additional output (stdout)\n')
+        sys.exit(1)
+
+    # go inside the outputs dir
+    os.chdir('job_outputs')
+
+    # move files
+    for i in glob.glob('*'):
+        if re.search('catalog.snps.tsv$', i):
+            shutil.copy(i, options.catalogsnps)
+        if re.search('catalog.alleles.tsv$', i):
+            shutil.copy(i, options.catalogalleles)
+        if re.search('catalog.tags.tsv$', i):
+            shutil.copy(i, options.catalogtags)
+
+    list_files = glob.glob('*')
+
+    # if compress output is total
+    if options.compress_output == 'total':
+
+        mytotalzipfile = zipfile.ZipFile('total.zip.temp', 'w',
+                allowZip64=True)
+
+        for i in list_files:
+            mytotalzipfile.write(os.path.basename(i))
+
+        # return the unique archive
+        shutil.move('total.zip.temp', options.total_output)
+    elif options.compress_output == 'categories':
+
+    # if compress output is by categories
+        mytagszip = zipfile.ZipFile('tags.zip.temp', 'w', allowZip64=True)
+        mysnpszip = zipfile.ZipFile('snps.zip.temp', 'w', allowZip64=True)
+        myalleleszip = zipfile.ZipFile('alleles.zip.temp', 'w', allowZip64=True)
+        mymatcheszip = zipfile.ZipFile('matches.zip.temp', 'w', allowZip64=True)
+
+        for i in list_files:
+            # for each type of files
+            if re.search("tags\.tsv$", i) and not re.search('batch', i):
+                mytagszip.write(os.path.basename(i))
+                os.remove(i)
+            elif re.search("snps\.tsv$", i) and not re.search('batch', i):
+                mysnpszip.write(os.path.basename(i))
+                os.remove(i)
+            elif re.search("alleles\.tsv$", i) and not re.search('batch', i):
+                myalleleszip.write(os.path.basename(i))
+                os.remove(i)
+            elif re.search("matches\.tsv$", i) and not re.search('batch', i):
+                mymatcheszip.write(os.path.basename(i))
+                os.remove(i)
+            else:
+                shutil.move(os.path.basename(i), '../galaxy_outputs')
+
+        # return archives....
+        shutil.move('tags.zip.temp', options.tags_output)
+        shutil.move('snps.zip.temp', options.snps_output)
+        shutil.move('alleles.zip.temp', options.alleles_output)
+        shutil.move('matches.zip.temp', options.matches_output)
+    else:
+    # else no compression
+        for i in list_files:
+            shutil.move(os.path.basename(i), '../galaxy_outputs')
+
+
+if __name__ == '__main__':
+    __main__()
+
+