--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sRbowtie.py	Tue May 26 18:36:09 2015 -0400
@@ -0,0 +1,189 @@
+#!/usr/bin/env python
+# small RNA oriented bowtie wrapper
+# version 1.5 17-7-2014: arg parser implementation
+# Usage sRbowtie.py <1 input_fasta_file> <2 alignment method> <3 -v mismatches> <4 out_type> <5 buildIndexIfHistory> <6 fasta/bowtie index> <7 bowtie output> <8 ali_fasta> <9 unali_fasta> <10 --num-threads \${GALAXY_SLOTS:-4}>
+# current rev: for bowtie __norc, move from --supress 2,6,7,8 to --supress 6,7,8. Future Parser must be updated to take into account this standardisation
+# Christophe Antoniewski <drosofff@gmail.com>
+
+import sys
+import os
+import subprocess
+import tempfile
+import shutil
+import argparse
+
+
+def Parser():
+    the_parser = argparse.ArgumentParser(
+        description="bowtie wrapper for small fasta reads")
+    the_parser.add_argument(
+        '--input', action="store", type=str, help="input file")
+    the_parser.add_argument(
+        '--input-format', dest="input_format", action="store", type=str, help="fasta or fastq")
+    the_parser.add_argument('--method', action="store", type=str,
+                            help="RNA, unique, multiple, k_option, n_option, a_option")
+    the_parser.add_argument('--v-mismatches', dest="v_mismatches", action="store",
+                            type=str, help="number of mismatches allowed for the alignments")
+    the_parser.add_argument(
+        '--output-format', dest="output_format", action="store", type=str, help="tabular, sam, bam")
+    the_parser.add_argument(
+        '--output', action="store", type=str, help="output file path")
+    the_parser.add_argument(
+        '--index-from', dest="index_from", action="store", type=str, help="indexed or history")
+    the_parser.add_argument('--index-source', dest="index_source",
+                            action="store", type=str, help="file path to the index source")
+    the_parser.add_argument(
+        '--aligned', action="store", type=str, help="aligned read file path, maybe None")
+    the_parser.add_argument('--unaligned', action="store",
+                            type=str, help="unaligned read file path, maybe None")
+    the_parser.add_argument('--num-threads', dest="num_threads",
+                            action="store", type=str, help="number of bowtie threads")
+    args = the_parser.parse_args()
+    return args
+
+
+def stop_err(msg):
+    sys.stderr.write('%s\n' % msg)
+    sys.exit()
+
+
+def bowtieCommandLiner(alignment_method="RNA", v_mis="1", out_type="tabular",
+                       aligned="None", unaligned="None", input_format="fasta", input="path",
+                       index="path", output="path", pslots="4"):
+    if input_format == "fasta":
+        input_format = "-f"
+    elif (input_format == "fastq") or (input_format == "fastqsanger"):
+        input_format = "-q"
+    else:
+        raise Exception('input format must be one of fasta or fastq')
+    if alignment_method == "RNA":
+        x = "-v %s -M 1 --best --strata -p %s --norc --suppress 6,7,8" % (
+            v_mis, pslots)
+    elif alignment_method == "unique":
+        x = "-v %s -m 1 -p %s --suppress 6,7,8" % (v_mis, pslots)
+    elif alignment_method == "multiple":
+        x = "-v %s -M 1 --best --strata -p %s --suppress 6,7,8" % (
+            v_mis, pslots)
+    elif alignment_method == "k_option":
+        x = "-v %s -k 1 --best -p %s --suppress 6,7,8" % (v_mis, pslots)
+    elif alignment_method == "n_option":
+        x = "-n %s -M 1 --best -p %s --suppress 6,7,8" % (v_mis, pslots)
+    elif alignment_method == "a_option":
+        x = "-v %s -a --best -p %s --suppress 6,7,8" % (v_mis, pslots)
+    if aligned == "None" and unaligned == "None":
+        fasta_command = ""
+    elif aligned != "None" and unaligned == "None":
+        fasta_command = " --al %s" % aligned
+    elif aligned == "None" and unaligned != "None":
+        fasta_command = " --un %s" % unaligned
+    else:
+        fasta_command = " --al %s --un %s" % (aligned, unaligned)
+    x = x + fasta_command
+    if out_type == "tabular":
+        return "bowtie %s %s %s %s > %s" % (x, index, input_format, input, output)
+    elif out_type == "sam":
+        return "bowtie %s -S %s %s %s > %s" % (x, index, input_format, input, output)
+    elif out_type == "bam":
+        return "bowtie %s -S %s %s %s |samtools view -bS - > %s" % (
+            x, index, input_format, input, output)
+
+
+def bowtie_squash(fasta):
+    # make temp directory for bowtie indexes
+    tmp_index_dir = tempfile.mkdtemp()
+    ref_file = tempfile.NamedTemporaryFile(dir=tmp_index_dir)
+    ref_file_name = ref_file.name
+    # by default, delete the temporary file, but ref_file.name is now stored
+    # in ref_file_name
+    ref_file.close()
+    # symlink between the fasta source file and the deleted ref_file name
+    os.symlink(fasta, ref_file_name)
+    # bowtie command line, which will work after changing dir
+    # (cwd=tmp_index_dir)
+    cmd1 = 'bowtie-build -f %s %s' % (ref_file_name, ref_file_name)
+    try:
+        FNULL = open(os.devnull, 'w')
+        # a path string for a temp file in tmp_index_dir. Just a string
+        tmp = tempfile.NamedTemporaryFile(dir=tmp_index_dir).name
+        # creates and open a file handler pointing to the temp file
+        tmp_stderr = open(tmp, 'wb')
+        # both stderr and stdout of bowtie-build are redirected in  dev/null
+        proc = subprocess.Popen(
+            args=cmd1, shell=True, cwd=tmp_index_dir, stderr=FNULL, stdout=FNULL)
+        returncode = proc.wait()
+        tmp_stderr.close()
+        FNULL.close()
+        sys.stdout.write(cmd1 + "\n")
+    except Exception as e:
+        # clean up temp dir
+        if os.path.exists(tmp_index_dir):
+            shutil.rmtree(tmp_index_dir)
+            stop_err('Error indexing reference sequence\n' + str(e))
+    # no Cleaning if no Exception, tmp_index_dir has to be cleaned after
+    # bowtie_alignment()
+    # bowtie fashion path without extention
+    index_full_path = os.path.join(tmp_index_dir, ref_file_name)
+    return tmp_index_dir, index_full_path
+
+
+def bowtie_alignment(command_line, flyPreIndexed=''):
+    # make temp directory just for stderr
+    tmp_index_dir = tempfile.mkdtemp()
+    tmp = tempfile.NamedTemporaryFile(dir=tmp_index_dir).name
+    tmp_stderr = open(tmp, 'wb')
+    # conditional statement for sorted bam generation viewable in Trackster
+    if "samtools" in command_line:
+        # recover the final output file name
+        target_file = command_line.split()[-1]
+        path_to_unsortedBam = os.path.join(tmp_index_dir, "unsorted.bam")
+        path_to_sortedBam = os.path.join(tmp_index_dir, "unsorted.bam.sorted")
+        first_command_line = " ".join(
+            command_line.split()[:-3]) + " -o " + path_to_unsortedBam + " - "
+        # example: bowtie -v 0 -M 1 --best --strata -p 12 --suppress 6,7,8 -S
+        # /home/galaxy/galaxy-dist/bowtie/Dmel/dmel-all-chromosome-r5.49 -f
+        # /home/galaxy/galaxy-dist/database/files/003/dataset_3460.dat
+        # |samtools view -bS -o /tmp/tmp_PgMT0/unsorted.bam -
+        # generates an "unsorted.bam.sorted.bam file", NOT an
+        # "unsorted.bam.sorted" file
+        second_command_line = "samtools sort  %s %s" % (
+            path_to_unsortedBam, path_to_sortedBam)
+        # fileno() method return the file descriptor number of tmp_stderr
+        p = subprocess.Popen(
+            args=first_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno())
+        returncode = p.wait()
+        sys.stdout.write("%s\n" % first_command_line + str(returncode))
+        p = subprocess.Popen(
+            args=second_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno())
+        returncode = p.wait()
+        sys.stdout.write("\n%s\n" % second_command_line + str(returncode))
+        if os.path.isfile(path_to_sortedBam + ".bam"):
+            shutil.copy2(path_to_sortedBam + ".bam", target_file)
+    else:
+        p = subprocess.Popen(
+            args=command_line, shell=True, stderr=tmp_stderr.fileno())
+        returncode = p.wait()
+        sys.stdout.write(command_line + "\n")
+    tmp_stderr.close()
+    # cleaning if the index was created in the fly
+    if os.path.exists(flyPreIndexed):
+        shutil.rmtree(flyPreIndexed)
+    # cleaning tmp files and directories
+    if os.path.exists(tmp_index_dir):
+        shutil.rmtree(tmp_index_dir)
+    return
+
+
+def __main__():
+    args = Parser()
+    F = open(args.output, "w")
+    if args.index_from == "history":
+        tmp_dir, index_path = bowtie_squash(args.index_source)
+    else:
+        tmp_dir, index_path = "dummy/dymmy", args.index_source
+    command_line = bowtieCommandLiner(args.method, args.v_mismatches, args.output_format,
+                                      args.aligned, args.unaligned, args.input_format, args.input, 
+                                      index_path, args.output, args.num_threads)
+    bowtie_alignment(command_line, flyPreIndexed=tmp_dir)
+    F.close()
+if __name__ == "__main__":
+    __main__()