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1 #!/usr/bin/env python
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2 # small RNA oriented bowtie wrapper
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3 # version 1.5 17-7-2014: arg parser implementation
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4 # 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}>
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5 # 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
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6 # Christophe Antoniewski <drosofff@gmail.com>
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7
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8 import sys, os, subprocess, tempfile, shutil, argparse
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9
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10 def Parser():
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11 the_parser = argparse.ArgumentParser(description="bowtie wrapper for small fasta reads")
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12 the_parser.add_argument('--input', action="store", type=str, help="input fasta file")
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13 the_parser.add_argument('--method', action="store", type=str, help="RNA, unique, multiple, k_option, n_option, a_option")
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14 the_parser.add_argument('--v-mismatches', dest="v_mismatches", action="store", type=str, help="number of mismatches allowed for the alignments")
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15 the_parser.add_argument('--output-format', dest="output_format", action="store", type=str, help="tabular, sam, bam")
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16 the_parser.add_argument('--output', action="store", type=str, help="output file path")
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17 the_parser.add_argument('--index-from', dest="index_from", action="store", type=str, help="indexed or history")
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18 the_parser.add_argument('--index-source', dest="index_source", action="store", type=str, help="file path to the index source")
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19 the_parser.add_argument('--aligned', action="store", type=str, help="aligned read file path, maybe None")
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20 the_parser.add_argument('--unaligned', action="store", type=str, help="unaligned read file path, maybe None")
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21 the_parser.add_argument('--num-threads', dest="num_threads", action="store", type=str, help="number of bowtie threads")
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22 args = the_parser.parse_args()
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23 return args
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24
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25 def stop_err( msg ):
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26 sys.stderr.write( '%s\n' % msg )
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27 sys.exit()
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28
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29 def bowtieCommandLiner (alignment_method="RNA", v_mis="1", out_type="tabular", aligned="None", unaligned="None", input="path", index="path", output="path", pslots="4"):
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30 if alignment_method=="RNA":
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31 x = "-v %s -M 1 --best --strata -p %s --norc --suppress 6,7,8" % (v_mis, pslots)
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32 elif alignment_method=="unique":
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33 x = "-v %s -m 1 -p %s --suppress 6,7,8" % (v_mis, pslots)
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34 elif alignment_method=="multiple":
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35 x = "-v %s -M 1 --best --strata -p %s --suppress 6,7,8" % (v_mis, pslots)
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36 elif alignment_method=="k_option":
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37 x = "-v %s -k 1 --best -p %s --suppress 6,7,8" % (v_mis, pslots)
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38 elif alignment_method=="n_option":
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39 x = "-n %s -M 1 --best -p %s --suppress 6,7,8" % (v_mis, pslots)
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40 elif alignment_method=="a_option":
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41 x = "-v %s -a --best -p %s --suppress 6,7,8" % (v_mis, pslots)
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42 if aligned == "None" and unaligned == "None": fasta_command = ""
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43 elif aligned != "None" and unaligned == "None": fasta_command= " --al %s" % aligned
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44 elif aligned == "None" and unaligned != "None": fasta_command = " --un %s" % unaligned
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45 else: fasta_command = " --al %s --un %s" % (aligned, unaligned)
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46 x = x + fasta_command
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47 if out_type == "tabular":
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48 return "bowtie %s %s -f %s > %s" % (x, index, input, output)
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49 elif out_type=="sam":
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50 return "bowtie %s -S %s -f %s > %s" % (x, index, input, output)
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51 elif out_type=="bam":
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52 return "bowtie %s -S %s -f %s |samtools view -bS - > %s" % (x, index, input, output)
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53
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54 def bowtie_squash(fasta):
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55 tmp_index_dir = tempfile.mkdtemp() # make temp directory for bowtie indexes
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56 ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
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57 ref_file_name = ref_file.name
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58 ref_file.close() # by default, delete the temporary file, but ref_file.name is now stored in ref_file_name
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59 os.symlink( fasta, ref_file_name ) # symlink between the fasta source file and the deleted ref_file name
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60 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)
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61 try:
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62 FNULL = open(os.devnull, 'w')
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63 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name # a path string for a temp file in tmp_index_dir. Just a string
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64 tmp_stderr = open( tmp, 'wb' ) # creates and open a file handler pointing to the temp file
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65 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
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66 returncode = proc.wait()
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67 tmp_stderr.close()
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68 FNULL.close()
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69 sys.stdout.write(cmd1 + "\n")
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70 except Exception, e:
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71 # clean up temp dir
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72 if os.path.exists( tmp_index_dir ):
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73 shutil.rmtree( tmp_index_dir )
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74 stop_err( 'Error indexing reference sequence\n' + str( e ) )
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75 # no Cleaning if no Exception, tmp_index_dir has to be cleaned after bowtie_alignment()
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76 index_full_path = os.path.join(tmp_index_dir, ref_file_name) # bowtie fashion path without extention
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77 return tmp_index_dir, index_full_path
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78
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79 def bowtie_alignment(command_line, flyPreIndexed=''):
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80 # make temp directory just for stderr
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81 tmp_index_dir = tempfile.mkdtemp()
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82 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
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83 tmp_stderr = open( tmp, 'wb' )
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84 # conditional statement for sorted bam generation viewable in Trackster
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85 if "samtools" in command_line:
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86 target_file = command_line.split()[-1] # recover the final output file name
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87 path_to_unsortedBam = os.path.join(tmp_index_dir, "unsorted.bam")
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88 path_to_sortedBam = os.path.join(tmp_index_dir, "unsorted.bam.sorted")
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89 first_command_line = " ".join(command_line.split()[:-3]) + " -o " + path_to_unsortedBam + " - "
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90 # 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 -
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91 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
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92 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
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93 returncode = p.wait()
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94 sys.stdout.write("%s\n" % first_command_line + str(returncode))
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95 p = subprocess.Popen(args=second_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno())
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96 returncode = p.wait()
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97 sys.stdout.write("\n%s\n" % second_command_line + str(returncode))
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98 if os.path.isfile(path_to_sortedBam + ".bam"):
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99 shutil.copy2(path_to_sortedBam + ".bam", target_file)
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100 else:
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101 p = subprocess.Popen(args=command_line, shell=True, stderr=tmp_stderr.fileno())
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102 returncode = p.wait()
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103 sys.stdout.write(command_line + "\n")
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104 tmp_stderr.close()
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105 ## cleaning if the index was created in the fly
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106 if os.path.exists( flyPreIndexed ):
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107 shutil.rmtree( flyPreIndexed )
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108 # cleaning tmp files and directories
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109 if os.path.exists( tmp_index_dir ):
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110 shutil.rmtree( tmp_index_dir )
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111 return
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112
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113 def __main__():
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114 args = Parser()
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115 F = open (args.output, "w")
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116 if args.index_from == "history":
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117 tmp_dir, index_path = bowtie_squash(args.index_source)
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118 else:
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119 tmp_dir, index_path = "dummy/dymmy", args.index_source
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120 command_line = bowtieCommandLiner(args.method, args.v_mismatches, args.output_format, args.aligned, args.unaligned, args.input, index_path, args.output, args.num_threads)
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121 bowtie_alignment(command_line, flyPreIndexed=tmp_dir)
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122 F.close()
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123 if __name__=="__main__": __main__()
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