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1 #!/usr/bin/env python
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2 # generic bowtie wrapper for bowtie, small RNA oriented
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3 # version 1 17-1-2014
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4 # Usage sRbowtie_wrapper.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>
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5
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6 import sys, re, os, subprocess, shlex, tempfile, shutil
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7
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8 def stop_err( msg ):
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9 sys.stderr.write( '%s\n' % msg )
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10 sys.exit()
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11
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12 def bowtieCommandLiner (alignment_method, v_mis, out_type, aligned, unaligned, input, index, output):
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13 if alignment_method=="RNA":
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14 x = "-v %s -M 1 --best --strata -p 12 --norc --suppress 2,6,7,8" % v_mis
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15 elif alignment_method=="unique":
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16 x = "-v %s -m 1 -p 12 --suppress 6,7,8" % v_mis
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17 elif alignment_method=="multiple":
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18 x = "-v %s -M 1 --best --strata -p 12 --suppress 6,7,8" % v_mis
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19 elif alignment_method=="k_option":
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20 x = "-v %s -k 1 --best -p 12 --suppress 6,7,8" % v_mis
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21 elif alignment_method=="n_option":
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22 x = "-n %s -M 1 --best -p 12 --suppress 6,7,8" % v_mis
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23 elif alignment_method=="a_option":
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24 x = "-v %s -a --best -p 12 --suppress 6,7,8" % v_mis
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25 if aligned == "None" and unaligned == "None": fasta_command = ""
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26 elif aligned != "None" and unaligned == "None": fasta_command= " --al %s" % aligned
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27 elif aligned == "None" and unaligned != "None": fasta_command = " --un %s" % unaligned
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28 else: fasta_command = " --al %s --un %s" % (aligned, unaligned)
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29 x = x + fasta_command
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30 if out_type == "tabular":
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31 return "bowtie %s %s -f %s > %s" % (x, index, input, output)
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32 elif out_type=="sam":
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33 return "bowtie %s -S %s -f %s > %s" % (x, index, input, output)
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34 elif out_type=="bam":
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35 return "bowtie %s -S %s -f %s |samtools view -bS - > %s" % (x, index, input, output)
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36
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37 def bowtie_squash(fasta):
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38 # make temp directory for placement of indices and copy reference file there if necessary
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39 tmp_index_dir = tempfile.mkdtemp()
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40 ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
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41 ref_file_name = ref_file.name
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42 ref_file.close() # by default, this action delete the temporary file !
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43 os.symlink( fasta, ref_file_name ) # now there is a symlink between the fasta source file and the deleted ref_file name
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44 cmd1 = 'bowtie-build -f %s %s' % (ref_file_name, ref_file_name ) # this will work with the bowtie command line but we have to change the working dir !
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45 try:
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46 FNULL = open(os.devnull, 'w')
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47 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name # a full path temp file to tmp_index_dir is created. just a string
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48 tmp_stderr = open( tmp, 'wb' ) # creates and open the file handler
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49 proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=FNULL, stdout=FNULL ) # fileno() method return the file descriptor number of tmp_stderr / stderr=tmp_stderr.fileno()
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50 # here I played a while a finish by redirecting everythin in dev/null. Clean later tmp_stderr calls
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51 returncode = proc.wait()
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52 tmp_stderr.close()
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53 FNULL.close()
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54 sys.stdout.write(cmd1 + "\n")
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55 except Exception, e:
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56 # clean up temp dir
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57 if os.path.exists( tmp_index_dir ):
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58 shutil.rmtree( tmp_index_dir )
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59 stop_err( 'Error indexing reference sequence\n' + str( e ) )
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60 # no Cleaning if no Exception, to be cleaned later after bowtie alignment
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61 index_full_path = os.path.join(tmp_index_dir, ref_file_name) # bowtie fashion path (without extention) ...
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62 return tmp_index_dir, index_full_path
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63
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64 def bowtie_alignment(command_line, flyPreIndexed=''):
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65 # make temp directory just for stderr
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66 tmp_index_dir = tempfile.mkdtemp()
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67 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
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68 tmp_stderr = open( tmp, 'wb' )
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69 # conditional statement for sorted bam generation viewable in Trackster
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70 if "samtools" in command_line:
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71 target_file = command_line.split()[-1] # recover the final output file name
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72 path_to_unsortedBam = os.path.join(tmp_index_dir, "unsorted.bam")
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73 path_to_sortedBam = os.path.join(tmp_index_dir, "unsorted.bam.sorted")
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74 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 -
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75 second_command_line = "samtools sort %s %s" % (path_to_unsortedBam, path_to_sortedBam) # Be carreful : this indeed will generate an unsorted.bam.sorted.bam file, NOT a unsorted.bam.sorted file
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76 p = subprocess.Popen(args=first_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno())
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77 returncode = p.wait()
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78 sys.stdout.write("%s\n" % first_command_line + str(returncode))
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79 p = subprocess.Popen(args=second_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno())
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80 returncode = p.wait()
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81 sys.stdout.write("\n%s\n" % second_command_line + str(returncode))
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82 if os.path.isfile(path_to_sortedBam + ".bam"):
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83 shutil.copy2(path_to_sortedBam + ".bam", target_file)
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84 else:
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85 p = subprocess.Popen(args=command_line, shell=True, stderr=tmp_stderr.fileno())
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86 returncode = p.wait()
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87 sys.stdout.write(command_line + "\n")
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88 tmp_stderr.close()
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89 ## cleaning if the index was created in the fly
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90 if os.path.exists( flyPreIndexed ):
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91 shutil.rmtree( flyPreIndexed )
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92 # cleaning tmp files and directories
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93 if os.path.exists( tmp_index_dir ):
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94 shutil.rmtree( tmp_index_dir )
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95 return
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96
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97 def __main__():
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98 F = open (sys.argv[-3], "w")
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99 if sys.argv[5] == "history":
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100 tmp_dir, index_path = bowtie_squash(sys.argv[6])
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101 else:
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102 tmp_dir, index_path = "dummy/dymmy", sys.argv[6]
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103 command_line = bowtieCommandLiner(sys.argv[2], sys.argv[3], sys.argv[4], sys.argv[-2], sys.argv[-1], sys.argv[1], index_path, sys.argv[7])
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104 bowtie_alignment(command_line, flyPreIndexed=tmp_dir)
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105 F.close()
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106 if __name__=="__main__": __main__()
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