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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
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9 import os
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10 import subprocess
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11 import tempfile
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12 import shutil
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13 import argparse
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14
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15
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16 def Parser():
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17 the_parser = argparse.ArgumentParser(
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18 description="bowtie wrapper for small fasta reads")
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19 the_parser.add_argument(
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20 '--input', action="store", type=str, help="input file")
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21 the_parser.add_argument(
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22 '--input-format', dest="input_format", action="store", type=str, help="fasta or fastq")
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23 the_parser.add_argument('--method', action="store", type=str,
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24 help="RNA, unique, multiple, k_option, n_option, a_option")
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25 the_parser.add_argument('--v-mismatches', dest="v_mismatches", action="store",
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26 type=str, help="number of mismatches allowed for the alignments")
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27 the_parser.add_argument(
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28 '--output-format', dest="output_format", action="store", type=str, help="tabular, sam, bam")
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29 the_parser.add_argument(
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30 '--output', action="store", type=str, help="output file path")
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31 the_parser.add_argument(
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32 '--index-from', dest="index_from", action="store", type=str, help="indexed or history")
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33 the_parser.add_argument('--index-source', dest="index_source",
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34 action="store", type=str, help="file path to the index source")
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35 the_parser.add_argument(
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36 '--aligned', action="store", type=str, help="aligned read file path, maybe None")
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37 the_parser.add_argument('--unaligned', action="store",
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38 type=str, help="unaligned read file path, maybe None")
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39 the_parser.add_argument('--num-threads', dest="num_threads",
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40 action="store", type=str, help="number of bowtie threads")
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41 args = the_parser.parse_args()
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42 return args
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43
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44
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45 def stop_err(msg):
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46 sys.stderr.write('%s\n' % msg)
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47 sys.exit()
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48
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49
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50 def bowtieCommandLiner(alignment_method="RNA", v_mis="1", out_type="tabular",
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51 aligned="None", unaligned="None", input_format="fasta", input="path",
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52 index="path", output="path", pslots="4"):
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53 if input_format == "fasta":
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54 input_format = "-f"
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55 elif (input_format == "fastq") or (input_format == "fastqsanger"):
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56 input_format = "-q"
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57 else:
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58 raise Exception('input format must be one of fasta or fastq')
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59 if alignment_method == "RNA":
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60 x = "-v %s -M 1 --best --strata -p %s --norc --suppress 6,7,8" % (
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61 v_mis, pslots)
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62 elif alignment_method == "unique":
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63 x = "-v %s -m 1 -p %s --suppress 6,7,8" % (v_mis, pslots)
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64 elif alignment_method == "multiple":
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65 x = "-v %s -M 1 --best --strata -p %s --suppress 6,7,8" % (
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66 v_mis, pslots)
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67 elif alignment_method == "k_option":
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68 x = "-v %s -k 1 --best -p %s --suppress 6,7,8" % (v_mis, pslots)
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69 elif alignment_method == "n_option":
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70 x = "-n %s -M 1 --best -p %s --suppress 6,7,8" % (v_mis, pslots)
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71 elif alignment_method == "a_option":
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72 x = "-v %s -a --best -p %s --suppress 6,7,8" % (v_mis, pslots)
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73 if aligned == "None" and unaligned == "None":
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74 fasta_command = ""
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75 elif aligned != "None" and unaligned == "None":
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76 fasta_command = " --al %s" % aligned
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77 elif aligned == "None" and unaligned != "None":
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78 fasta_command = " --un %s" % unaligned
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79 else:
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80 fasta_command = " --al %s --un %s" % (aligned, unaligned)
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81 x = x + fasta_command
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82 if out_type == "tabular":
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83 return "bowtie %s %s %s %s > %s" % (x, index, input_format, input, output)
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84 elif out_type == "sam":
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85 return "bowtie %s -S %s %s %s > %s" % (x, index, input_format, input, output)
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86 elif out_type == "bam":
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87 return "bowtie %s -S %s %s %s |samtools view -bS - > %s" % (
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88 x, index, input_format, input, output)
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89
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90
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91 def bowtie_squash(fasta):
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92 # make temp directory for bowtie indexes
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93 tmp_index_dir = tempfile.mkdtemp()
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94 ref_file = tempfile.NamedTemporaryFile(dir=tmp_index_dir)
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95 ref_file_name = ref_file.name
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96 # by default, delete the temporary file, but ref_file.name is now stored
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97 # in ref_file_name
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98 ref_file.close()
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99 # symlink between the fasta source file and the deleted ref_file name
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100 os.symlink(fasta, ref_file_name)
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101 # bowtie command line, which will work after changing dir
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102 # (cwd=tmp_index_dir)
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103 cmd1 = 'bowtie-build -f %s %s' % (ref_file_name, ref_file_name)
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104 try:
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105 FNULL = open(os.devnull, 'w')
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106 # a path string for a temp file in tmp_index_dir. Just a string
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107 tmp = tempfile.NamedTemporaryFile(dir=tmp_index_dir).name
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108 # creates and open a file handler pointing to the temp file
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109 tmp_stderr = open(tmp, 'wb')
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110 # both stderr and stdout of bowtie-build are redirected in dev/null
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111 proc = subprocess.Popen(
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112 args=cmd1, shell=True, cwd=tmp_index_dir, stderr=FNULL, stdout=FNULL)
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113 returncode = proc.wait()
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114 tmp_stderr.close()
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115 FNULL.close()
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116 sys.stdout.write(cmd1 + "\n")
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117 except Exception as e:
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118 # clean up temp dir
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119 if os.path.exists(tmp_index_dir):
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120 shutil.rmtree(tmp_index_dir)
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121 stop_err('Error indexing reference sequence\n' + str(e))
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122 # no Cleaning if no Exception, tmp_index_dir has to be cleaned after
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123 # bowtie_alignment()
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124 # bowtie fashion path without extention
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125 index_full_path = os.path.join(tmp_index_dir, ref_file_name)
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126 return tmp_index_dir, index_full_path
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127
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128
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129 def bowtie_alignment(command_line, flyPreIndexed=''):
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130 # make temp directory just for stderr
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131 tmp_index_dir = tempfile.mkdtemp()
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132 tmp = tempfile.NamedTemporaryFile(dir=tmp_index_dir).name
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133 tmp_stderr = open(tmp, 'wb')
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134 # conditional statement for sorted bam generation viewable in Trackster
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135 if "samtools" in command_line:
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136 # recover the final output file name
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137 target_file = command_line.split()[-1]
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138 path_to_unsortedBam = os.path.join(tmp_index_dir, "unsorted.bam")
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139 path_to_sortedBam = os.path.join(tmp_index_dir, "unsorted.bam.sorted")
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140 first_command_line = " ".join(
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141 command_line.split()[:-3]) + " -o " + path_to_unsortedBam + " - "
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142 # example: bowtie -v 0 -M 1 --best --strata -p 12 --suppress 6,7,8 -S
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143 # /home/galaxy/galaxy-dist/bowtie/Dmel/dmel-all-chromosome-r5.49 -f
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144 # /home/galaxy/galaxy-dist/database/files/003/dataset_3460.dat
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145 # |samtools view -bS -o /tmp/tmp_PgMT0/unsorted.bam -
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146 # generates an "unsorted.bam.sorted.bam file", NOT an
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147 # "unsorted.bam.sorted" file
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148 second_command_line = "samtools sort %s %s" % (
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149 path_to_unsortedBam, path_to_sortedBam)
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150 # fileno() method return the file descriptor number of tmp_stderr
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151 p = subprocess.Popen(
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152 args=first_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno())
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153 returncode = p.wait()
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154 sys.stdout.write("%s\n" % first_command_line + str(returncode))
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155 p = subprocess.Popen(
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156 args=second_command_line, cwd=tmp_index_dir, shell=True, stderr=tmp_stderr.fileno())
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157 returncode = p.wait()
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158 sys.stdout.write("\n%s\n" % second_command_line + str(returncode))
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159 if os.path.isfile(path_to_sortedBam + ".bam"):
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160 shutil.copy2(path_to_sortedBam + ".bam", target_file)
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161 else:
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162 p = subprocess.Popen(
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163 args=command_line, shell=True, stderr=tmp_stderr.fileno())
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164 returncode = p.wait()
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165 sys.stdout.write(command_line + "\n")
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166 tmp_stderr.close()
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167 # cleaning if the index was created in the fly
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168 if os.path.exists(flyPreIndexed):
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169 shutil.rmtree(flyPreIndexed)
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170 # cleaning tmp files and directories
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171 if os.path.exists(tmp_index_dir):
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172 shutil.rmtree(tmp_index_dir)
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173 return
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174
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175
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176 def __main__():
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177 args = Parser()
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178 F = open(args.output, "w")
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179 if args.index_from == "history":
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180 tmp_dir, index_path = bowtie_squash(args.index_source)
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181 else:
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182 tmp_dir, index_path = "dummy/dymmy", args.index_source
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183 command_line = bowtieCommandLiner(args.method, args.v_mismatches, args.output_format,
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184 args.aligned, args.unaligned, args.input_format, args.input,
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185 index_path, args.output, args.num_threads)
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186 bowtie_alignment(command_line, flyPreIndexed=tmp_dir)
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187 F.close()
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188 if __name__ == "__main__":
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189 __main__()
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