--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ALFA/ALFA_wrapper.py	Thu Oct 27 04:42:59 2016 -0400
@@ -0,0 +1,194 @@
+#!/usr/bin/python
+
+import argparse
+import logging
+import os
+import re
+import shutil
+import subprocess
+import sys
+import tempfile
+
+def exit_and_explain(msg):
+    logging.critical(msg)
+    sys.exit(msg)
+
+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('--project_name', dest='project_name', action='store', nargs=1, metavar='project_name', type=str)
+    #Input 1: Annotation File
+    parser.add_argument('--index', dest='indexes', action='store', nargs=2, metavar=('stranded_index_filename', 'unstranded_index_filename'), type=str)
+    parser.add_argument('--bi_index', dest='bi_indexes', action='store', nargs=1, metavar='built_in_indexes_dir_path', type=str )
+    parser.add_argument('--annotation', dest='annotation_file', action='store', nargs=1, metavar='annotation_gtf_file', type=str )
+    #Input 2: Mapped Reads
+    parser.add_argument('--reads_format', dest='reads_format', action='store', nargs=1, choices=['bam', 'bedgraph'], metavar='reads_format', type=str)
+    parser.add_argument('--reads', dest='reads', action='store', nargs='+', metavar=('bam_file1 label1',""), type=str)
+    parser.add_argument('--strandness', dest='strandness', action='store', nargs=1, default=['unstranded'], choices=['unstranded', 'forward', 'reverse'], metavar='strandness', type=str)
+    #Output files
+    parser.add_argument('--output_pdf', dest='output_pdf', action='store', nargs=1, metavar='output_pdf_filename', type=str)
+    parser.add_argument('--output_svg', dest='output_svg', action='store', nargs=2, metavar=('categories_svg_filename', 'biotypes_svg_filename'), type=str)
+    parser.add_argument('--output_png', dest='output_png', action='store', nargs=2, metavar=('categories_png_filename', 'biotypes_png_filename'), type=str)
+    parser.add_argument('--output_count', dest='output_count', action='store', nargs=1, metavar='output_count_filename', type=str)
+    parser.add_argument('--output_index', dest='output_indexes', action='store', nargs=2, metavar=('output_stranded_index_filename', 'output_unstranded_index_filename'), type=str)
+    #Output Options
+    parser.add_argument('--categories_depth', dest='categories_depth', action='store', nargs=1, default=[3], choices=range(1,5), metavar='categories_depth', type=int)
+    parser.add_argument('--plot_format', dest='plot_format', action='store', nargs=1, choices=['pdf', 'png', 'svg'], metavar='plot_format', type=str)
+    parser.add_argument('--threshold', dest='threshold', action='store', nargs=2, metavar=('yMin', 'yMax'), type=float)
+    #Internal variables
+    parser.add_argument('--log_report', dest='log_report', action='store', nargs=1, metavar='log_filename', type=str)
+    parser.add_argument('--galaxy_root', dest='GALAXY_ROOT_DIR', action='store', nargs=1, metavar='galaxy_root_path', type=str)
+    parser.add_argument('--tool_dir', dest='GALAXY_TOOL_DIR', action='store', nargs=1, metavar='galaxy_tool_dir_path', type=str)
+    args = parser.parse_args()
+    return args
+
+def make_tmp_dir(galaxy_root):
+    parent_dir = os.path.join(galaxy_root, 'database/tmp/')
+    if os.path.exists(parent_dir):
+        tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='', dir=parent_dir)
+    else:
+        tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='', dir='.')
+    return tmp_dir
+
+def mv_and_rename_user_indexes(stranded_index, unstranded_index):
+    index='index'
+    shutil.copy(stranded_index, index + '.stranded.index')
+    shutil.copy(unstranded_index, index + '.unstranded.index')
+    return index
+
+def get_input2_args(reads_list, format):
+    n = len(reads_list)
+    if n%2 != 0:
+        exit_and_explain('Problem with pairing reads filename and reads label')
+    input2_args='-i'
+    k = 0
+    reads_filenames = [''] * (n/2)
+    reads_labels = [''] * (n/2)
+    for i in range(0, n, 2):
+        reads_filenames[k] = reads_list[i].split('__fname__')[1]
+        reads_labels[k] = reads_list[i+1].split('__label__')[1]
+        if not reads_labels[k]:
+            reads_labels[k] = 'sample_%s' % str(k+1)
+        input2_args='%s %s %s' % (input2_args, reads_filenames[k], reads_labels[k])
+        k += 1
+    if format == 'bedgraph':
+        input2_args = input2_args + ' --bedgraph'
+    return input2_args, reads_filenames, reads_labels
+
+def redirect_errors(alfa_out, alfa_err):
+    # When the option --n is enabled, alfa prints '### End of the program' in stderr even if the process worked-
+    # The following lines to avoid the tool from crashing in this case
+    if alfa_err and not re.search('### End of program', alfa_err):
+        # When alfa prints '### End of program' in stdout, all the messages in stderr are considered
+        # as warnings and not as errors.
+        if re.search('### End of program', alfa_out):
+            logging.warning("The script ALFA.py encountered the following warning:\n\n%s" % alfa_err)
+            logging.info("\n******************************************************************\n")
+        # True errors make the script exits
+        else:
+            exit_and_explain("The script ALFA.py encountered the following error:\n\n%s" % alfa_err)
+
+def merge_count_files(reads_labels):
+    merged_count_file = open('count_file.txt', 'wb')
+    for i in range(0, len(reads_labels)):
+        current_count_file = open(reads_labels[i] + '.categories_counts', 'r')
+        reads_label = reads_labels[i]
+        merged_count_file.write('##LABEL: %s\n\n' % reads_label)
+        merged_count_file.write(current_count_file.read())
+        merged_count_file.write('__________________________________________________________________\n')
+        current_count_file.close()
+    merged_count_file.close()
+    return 'count_file.txt'
+
+def main():
+    args = get_arg()
+
+    if not (args.output_pdf or args.output_png or args.output_svg or args.output_indexes or args.output_count):
+        exit_and_explain('Error: no output to return\nProcess Aborted\n')
+
+    tmp_dir = make_tmp_dir(args.GALAXY_TOOL_DIR[0])
+    os.chdir(tmp_dir)
+
+    logging.basicConfig(level=logging.INFO, filename=args.log_report[0], filemode="a+", format='%(message)s')
+
+    alfa_path = os.path.join(args.GALAXY_TOOL_DIR[0], 'ALFA.py')
+
+    #INPUT1: Annotation File
+    if args.indexes:
+        # The indexes submitted by the user must exhibit the suffix '.(un)stranded.index' and will be called by alfa by their prefix
+        index = mv_and_rename_user_indexes(args.indexes[0], args.indexes[1])
+        input1_args = '-g %s' % index
+    elif args.bi_indexes:
+        input1_args = '-g %s' % args.bi_indexes[0]
+    elif args.annotation_file:
+        input1_args = '-a %s' % args.annotation_file[0]
+    else:
+        exit_and_explain('No annotation file submitted !')
+
+    #INPUT 2: Mapped Reads
+    if args.reads:
+        input2_args, reads_filenames, reads_labels = get_input2_args(args.reads, args.reads_format[0])
+        strandness = '-s %s' % args.strandness[0]
+    else:
+        exit_and_explain('No reads submitted !')
+
+    ##Output options
+    categories_depth = '-d %s' % args.categories_depth[0]
+    if not (args.output_pdf or args.output_png or args.output_svg):
+        output_args = '--n'
+    else:
+        if args.output_pdf:
+            output_args = '--pdf plot.pdf'
+        if args.output_png:
+            output_args = '--png plot'
+        if args.output_svg:
+            output_args = '--svg plot'
+        if args.threshold:
+            output_args = '%s -t %.3f %.3f' % (output_args, args.threshold[0], args.threshold[1])
+
+    ##Run alfa
+    cmd = 'python %s %s %s %s %s %s' % (alfa_path, input1_args, input2_args, strandness, categories_depth, output_args)
+    logging.info("__________________________________________________________________\n")
+    logging.info("Alfa execution")
+    logging.info("__________________________________________________________________\n")
+    logging.info("Command Line:\n%s\n" % cmd)
+    logging.info("------------------------------------------------------------------\n")
+    alfa_result = subprocess.Popen(args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    alfa_out, alfa_err =  alfa_result.communicate()
+
+    ##Handle stdout, warning, errors...
+    redirect_errors(alfa_out, alfa_err)
+
+    logging.info("Alfa prompt:\n%s" % alfa_out)
+
+    ##Redirect outputs
+    if args.output_pdf:
+        shutil.move('plot.pdf', args.output_pdf[0])
+    if args.output_png:
+        shutil.move('plot' + '.categories.png', args.output_png[0])
+        shutil.move('plot' + '.biotypes.png', args.output_png[1])
+    if args.output_svg:
+        shutil.move('plot' + '.categories.svg', args.output_svg[0])
+        shutil.move('plot' + '.biotypes.svg', args.output_svg[1])
+    if args.output_count:
+        count_filename = merge_count_files(reads_labels)
+        shutil.move(count_filename, args.output_count[0])
+    if args.output_indexes:
+        if args.annotation_file:
+            indexes_regex = re.compile('.*\.index')
+            indexes = filter(indexes_regex.search, os.listdir('.'))
+            indexes.sort()
+            shutil.move(indexes[0], args.output_indexes[0])
+            shutil.move(indexes[1], args.output_indexes[1])
+        if args.indexes:
+            shutil.move(index + '.stranded.index', args.output_indexes[0])
+            shutil.move(index + '.unstranded.index', args.output_indexes[1])
+        if args.bi_indexes:
+            shutil.move(args.bi_indexes[0] + '.stranded.index', args.output_index[0])
+            shutil.move(args.bi_indexes[1] + '.unstranded.index', args.output_index[1])
+
+    cleanup_before_exit(tmp_dir)
+main()
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