diff sRbowtie.py @ 0:64064dccdb11 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sRbowtie.py	Mon Nov 03 10:24:38 2014 -0500
@@ -0,0 +1,123 @@
+#!/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 <[e-mail]>
+
+import sys, os, subprocess, tempfile, shutil, 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 fasta file")
+  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="path", index="path", output="path", pslots="4"):
+    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 -f %s > %s" % (x, index, input, output)
+    elif out_type=="sam":
+        return "bowtie %s -S %s -f %s > %s" % (x, index, input, output)
+    elif out_type=="bam":
+        return "bowtie %s -S %s -f %s |samtools view -bS - > %s" % (x, index, input, output)
+
+def bowtie_squash(fasta):
+  tmp_index_dir = tempfile.mkdtemp() # make temp directory for bowtie indexes
+  ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
+  ref_file_name = ref_file.name
+  ref_file.close() # by default, delete the temporary file, but ref_file.name is now stored in ref_file_name
+  os.symlink( fasta, ref_file_name ) # symlink between the fasta source file and the deleted ref_file name
+  cmd1 = 'bowtie-build -f %s %s' % (ref_file_name, ref_file_name ) # bowtie command line, which will work after changing dir (cwd=tmp_index_dir)
+  try:
+    FNULL = open(os.devnull, 'w')
+    tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name # a path string for a temp file in tmp_index_dir. Just a string
+    tmp_stderr = open( tmp, 'wb' ) # creates and open a file handler pointing to the temp file
+    proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=FNULL, stdout=FNULL ) # both stderr and stdout of bowtie-build are redirected in  dev/null
+    returncode = proc.wait()
+    tmp_stderr.close()
+    FNULL.close()
+    sys.stdout.write(cmd1 + "\n")
+  except Exception, 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()
+  index_full_path = os.path.join(tmp_index_dir, ref_file_name) # bowtie fashion path without extention
+  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:
+    target_file = command_line.split()[-1] # recover the final output file name
+    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 -
+    second_command_line = "samtools sort  %s %s" % (path_to_unsortedBam, path_to_sortedBam) # generates an "unsorted.bam.sorted.bam file", NOT an "unsorted.bam.sorted" file
+    p = subprocess.Popen(args=first_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno()) # fileno() method return the file descriptor number of tmp_stderr
+    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, index_path, args.output, args.num_threads)
+  bowtie_alignment(command_line, flyPreIndexed=tmp_dir)
+  F.close()
+if __name__=="__main__": __main__()