Mercurial > repos > bgruening > bismark

diff bismark_pretty_report/bismark2report_wrapper.py @ 7:fcadce4d9a06 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bismark_pretty_report/bismark2report_wrapper.py	Sat May 06 13:18:09 2017 -0400
@@ -0,0 +1,122 @@
+#!/usr/bin/python
+
+import argparse
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+import logging
+
+def cleanup_before_exit(tmp_dir):
+    if tmp_dir and os.path.exists(tmp_dir):
+        shutil.rmtree(tmp_dir)
+
+def get_arg():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--tool_dir', dest='tool_dir', action='store', nargs=1, metavar='tool_dir', type=str)
+    parser.add_argument('--alignment_report', dest='alignment_report', action='store', nargs=1, metavar='alignment_report', type=str)
+    parser.add_argument('--dedup_report', dest='dedup_report', action='store', nargs=1, metavar='dedup_report', type=str)
+    parser.add_argument('--splitting_report', dest='splitting_report', action='store', nargs=1, metavar='splitting_report', type=str)
+    parser.add_argument('--mbias_report', dest='mbias_report', action='store', nargs=1, metavar='mbias_report', type=str)
+    parser.add_argument('--nucleotide_report', dest='nucleotide_report', action='store', nargs=1, metavar='nucleotide_report', type=str)
+    parser.add_argument('--output_html_report', dest='output_html_report', action='store', nargs=1, metavar='output_html_report', type=str)
+    parser.add_argument('--output_html_report_link', dest='output_html_report_link', action='store', nargs=1, metavar='output_html_report_link', type=str)
+    parser.add_argument('--log_report', dest='log_report', action='store', nargs=1, metavar='log_report', type=str)
+    parser.add_argument('--output_dir', dest='job_dir', action='store', nargs=1, metavar='job_dir', type=str)
+    args = parser.parse_args()
+    return args
+
+def create_and_write_html_link(job_dir, output_html_report_link, tmp_dir):
+    """
+    Web browsers don't allow to open a link pointing to the absolute path of a local html file FROM a website page;
+    The only way to make such link functional is to integrate the local file inside the web structure of the site.
+    Galaxy has been designed such that the child_dir <dataset_[0-9]+_files> of the output_dir is considered as the root
+    of the html base tag (i.e <base href="/" /> for the current job running.
+    The function proceeds the following steps:
+    #1. Extracts the galaxy dir where the output files are stored
+    #2. Creating a child dir <dataset_[0-9]+_files> in this output_dir is needed because it is considered as the root of the html base tag
+    #   We can extract the exact name of this child dir from the jobs_directory name
+    #3. Moves the html file in this child_dir
+    """
+    output_path_list = output_html_report_link.split('/')
+    output_path = '/'.join(output_path_list[0:-1])
+    html_root = job_dir.split('/')[-1]
+    final_dir = os.path.join(output_path, html_root)
+    os.makedirs(final_dir)
+    shutil.move(os.path.join(tmp_dir, 'html_report'), os.path.join(final_dir, 'html_report.html'))
+
+    html_report = open(output_html_report_link, 'wb')
+    html_report.write('<!DOCTYPE html>\n')
+    html_report.write('<head>\n')
+    html_report.write('\t<meta http-equiv="content-type" content="text/html; charset=UTF-8">\n')
+    html_report.write('\t\t<base href="/" />\n')
+    html_report.write('\t\t<a href="html_report.html/" target="_blank">Link to Bismark Pretty Report Page</a>\n')
+    html_report.write('</head>')
+    html_report.close()
+
+def __main__():
+    args = get_arg()
+
+    tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='')
+
+    if args.log_report:
+        logging.basicConfig(level=logging.INFO, filename=args.log_report[0], filemode="a+", format='%(message)s')
+    else:
+        logging.basicConfig(level=logging.INFO, filename=os.path.join(tmp_dir, 'log_report.txt'), filemode="a+", format='%(message)s')
+
+    alignment_option = '--alignment_report'
+    alignment_report = args.alignment_report[0]
+    if args.dedup_report:
+        dedup_option = '--dedup_report'
+        dedup_report = args.dedup_report[0]
+    else:
+        dedup_option = ''
+        dedup_report = ''
+    if args.splitting_report:
+        splitting_option = '--splitting_report'
+        splitting_report = args.splitting_report[0]
+    else:
+        splitting_option = ''
+        splitting_report = ''
+    if args.mbias_report:
+        mbias_option = '--mbias_report'
+        mbias_report = args.mbias_report[0]
+    else:
+        mbias_option = ''
+        mbias_report = ''
+    if args.nucleotide_report:
+        nucleotide_option = '--nucleotide_report'
+        nucleotide_report = args.nucleotide_report[0]
+    else:
+        nucleotide_option = ''
+        nucleotide_report = ''
+
+    proc = subprocess.Popen(['perl', os.path.join(args.tool_dir[0], 'bismark2report'), alignment_option, alignment_report, dedup_option, dedup_report,\
+                             splitting_option, splitting_report, mbias_option, mbias_report, nucleotide_option, nucleotide_report,\
+                             '--dir', tmp_dir, '--output', 'html_report'],\
+                             stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+    proc_out, proc_err = proc.communicate()
+
+    cmd = 'perl %s %s %s %s %s %s %s %s %s %s %s --output html_report --dir %s'\
+          % (os.path.join(args.tool_dir[0], 'bismark2report'), alignment_option, alignment_report, dedup_option, dedup_report,\
+             splitting_option, splitting_report, mbias_option, mbias_report, nucleotide_option, nucleotide_report, tmp_dir)
+
+    logging.info('COMMAND LINE:\n\n%s' % cmd)
+    logging.info("__________________________________________________________________\n")
+    logging.info("BISMARK PRETTY REPORT STDOUT:\n\n%s" % proc_out)
+    if proc_err:
+        logging.critical("__________________________________________________________________\n")
+        logging.critical("BISMARK PRETTY REPORT ERROR:\n\n%s" % proc_err)
+        sys.exit("Bismark pretty report crashed with the folowing error message:\n%s" % proc_err)
+
+    if args.output_html_report:
+        shutil.copy(os.path.join(tmp_dir, 'html_report'), args.output_html_report[0])
+
+    #This function writes a link towards the Bismark html page inside an html file.
+    #This is needed because the direct visualization of the Bismark html report via Galaxy is ugly
+    create_and_write_html_link(args.job_dir[0], args.output_html_report_link[0], tmp_dir)
+
+    cleanup_before_exit(tmp_dir)
+
+if __name__=="__main__": __main__()
\ No newline at end of file