Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate amplicon_analysis_pipeline.py @ 1:1c1902e12caf draft

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Updated to version 1.2.1.0
author pjbriggs
date Wed, 25 Apr 2018 03:54:00 -0400
parents 47ec9c6f44b8
children 3ab198df8f3f
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47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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1 #!/usr/bin/env python
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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2 #
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3 # Wrapper script to run Amplicon_analysis_pipeline.sh
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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4 # from Galaxy tool
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5
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6 import sys
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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7 import os
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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8 import argparse
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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9 import subprocess
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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10 import glob
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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11
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12 class PipelineCmd(object):
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13 def __init__(self,cmd):
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14 self.cmd = [str(cmd)]
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15 def add_args(self,*args):
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16 for arg in args:
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17 self.cmd.append(str(arg))
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18 def __repr__(self):
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19 return ' '.join([str(arg) for arg in self.cmd])
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20
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21 def ahref(target,name=None,type=None):
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22 if name is None:
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23 name = os.path.basename(target)
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24 ahref = "<a href='%s'" % target
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25 if type is not None:
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26 ahref += " type='%s'" % type
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27 ahref += ">%s</a>" % name
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28 return ahref
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29
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30 def check_errors():
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31 # Errors in Amplicon_analysis_pipeline.log
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32 with open('Amplicon_analysis_pipeline.log','r') as pipeline_log:
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33 log = pipeline_log.read()
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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34 if "Names in the first column of Metatable.txt and in the second column of Final_name.txt do not match" in log:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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35 print_error("""*** Sample IDs don't match dataset names ***
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36
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37 The sample IDs (first column of the Metatable file) don't match the
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38 supplied sample names for the input Fastq pairs.
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39 """)
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40 # Errors in pipeline output
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41 with open('pipeline.log','r') as pipeline_log:
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42 log = pipeline_log.read()
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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43 if "Errors and/or warnings detected in mapping file" in log:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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44 with open("Metatable_log/Metatable.log","r") as metatable_log:
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45 # Echo the Metatable log file to the tool log
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46 print_error("""*** Error in Metatable mapping file ***
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47
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48 %s""" % metatable_log.read())
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49 elif "No header line was found in mapping file" in log:
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50 # Report error to the tool log
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51 print_error("""*** No header in Metatable mapping file ***
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52
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53 Check you've specified the correct file as the input Metatable""")
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54
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55 def print_error(message):
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56 width = max([len(line) for line in message.split('\n')]) + 4
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57 sys.stderr.write("\n%s\n" % ('*'*width))
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58 for line in message.split('\n'):
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59 sys.stderr.write("* %s%s *\n" % (line,' '*(width-len(line)-4)))
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60 sys.stderr.write("%s\n\n" % ('*'*width))
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61
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62 def clean_up_name(sample):
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63 # Remove trailing "_L[0-9]+_001" from Fastq
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64 # pair names
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65 split_name = sample.split('_')
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66 if split_name[-1] == "001":
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67 split_name = split_name[:-1]
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68 if split_name[-1].startswith('L'):
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69 try:
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70 int(split_name[-1][1:])
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71 split_name = split_name[:-1]
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72 except ValueError:
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73 pass
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74 return '_'.join(split_name)
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75
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76 def list_outputs(filen=None):
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77 # List the output directory contents
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78 # If filen is specified then will be the filename to
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79 # write to, otherwise write to stdout
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80 if filen is not None:
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81 fp = open(filen,'w')
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82 else:
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83 fp = sys.stdout
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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84 results_dir = os.path.abspath("RESULTS")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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85 fp.write("Listing contents of output dir %s:\n" % results_dir)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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86 ix = 0
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87 for d,dirs,files in os.walk(results_dir):
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88 ix += 1
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89 fp.write("-- %d: %s\n" % (ix,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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90 os.path.relpath(d,results_dir)))
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91 for f in files:
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92 ix += 1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
93 fp.write("---- %d: %s\n" % (ix,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
94 os.path.relpath(f,results_dir)))
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
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95 # Close output file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
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96 if filen is not None:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
97 fp.close()
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
98
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
99 if __name__ == "__main__":
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
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100 # Command line
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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101 print "Amplicon analysis: starting"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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102 p = argparse.ArgumentParser()
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
103 p.add_argument("metatable",
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
104 metavar="METATABLE_FILE",
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
105 help="Metatable.txt file")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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106 p.add_argument("fastq_pairs",
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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107 metavar="SAMPLE_NAME FQ_R1 FQ_R2",
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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108 nargs="+",
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
109 default=list(),
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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110 help="Triplets of SAMPLE_NAME followed by "
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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111 "a R1/R2 FASTQ file pair")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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112 p.add_argument("-g",dest="forward_pcr_primer")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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113 p.add_argument("-G",dest="reverse_pcr_primer")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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114 p.add_argument("-q",dest="trimming_threshold")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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115 p.add_argument("-O",dest="minimum_overlap")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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116 p.add_argument("-L",dest="minimum_length")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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117 p.add_argument("-l",dest="sliding_window_length")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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118 p.add_argument("-P",dest="pipeline",
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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119 choices=["vsearch","uparse","qiime"],
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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120 type=str.lower,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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121 default="vsearch")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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122 p.add_argument("-S",dest="use_silva",action="store_true")
1
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123 p.add_argument("-H",dest="use_homd",action="store_true")
0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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124 p.add_argument("-r",dest="reference_data_path")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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125 p.add_argument("-c",dest="categories_file")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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126 args = p.parse_args()
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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127
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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128 # Build the environment for running the pipeline
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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129 print "Amplicon analysis: building the environment"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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130 metatable_file = os.path.abspath(args.metatable)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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131 os.symlink(metatable_file,"Metatable.txt")
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132 print "-- made symlink to Metatable.txt"
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pjbriggs
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133
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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134 # Link to Categories.txt file (if provided)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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135 if args.categories_file is not None:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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136 categories_file = os.path.abspath(args.categories_file)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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137 os.symlink(categories_file,"Categories.txt")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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138 print "-- made symlink to Categories.txt"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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139
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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140 # Link to FASTQs and construct Final_name.txt file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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141 sample_names = []
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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142 with open("Final_name.txt",'w') as final_name:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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143 fastqs = iter(args.fastq_pairs)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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144 for sample_name,fqr1,fqr2 in zip(fastqs,fastqs,fastqs):
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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145 sample_name = clean_up_name(sample_name)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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146 r1 = "%s_R1_.fastq" % sample_name
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
147 r2 = "%s_R2_.fastq" % sample_name
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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diff changeset
148 os.symlink(fqr1,r1)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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149 os.symlink(fqr2,r2)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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diff changeset
150 final_name.write("%s\n" % '\t'.join((r1,sample_name)))
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
151 final_name.write("%s\n" % '\t'.join((r2,sample_name)))
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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diff changeset
152 sample_names.append(sample_name)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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diff changeset
153
1
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diff changeset
154 # Reference database
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parents: 0
diff changeset
155 if args.use_silva:
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diff changeset
156 ref_database = "silva"
1c1902e12caf Updated to version 1.2.1.0
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diff changeset
157 elif args.use_homd:
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diff changeset
158 ref_database = "homd"
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diff changeset
159 else:
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160 ref_database = "gg"
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diff changeset
161
0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
162 # Construct the pipeline command
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
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163 print "Amplicon analysis: constructing pipeline command"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
164 pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
165 if args.forward_pcr_primer:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
166 pipeline.add_args("-g",args.forward_pcr_primer)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
167 if args.reverse_pcr_primer:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
168 pipeline.add_args("-G",args.reverse_pcr_primer)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
169 if args.trimming_threshold:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
170 pipeline.add_args("-q",args.trimming_threshold)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
171 if args.minimum_overlap:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
172 pipeline.add_args("-O",args.minimum_overlap)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
173 if args.minimum_length:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
174 pipeline.add_args("-L",args.minimum_length)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
175 if args.sliding_window_length:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
176 pipeline.add_args("-l",args.sliding_window_length)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
177 if args.reference_data_path:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
178 pipeline.add_args("-r",args.reference_data_path)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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diff changeset
179 pipeline.add_args("-P",args.pipeline)
1
1c1902e12caf Updated to version 1.2.1.0
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parents: 0
diff changeset
180 if ref_database == "silva":
0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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diff changeset
181 pipeline.add_args("-S")
1
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parents: 0
diff changeset
182 elif ref_database == "homd":
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parents: 0
diff changeset
183 pipeline.add_args("-H")
0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
184
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
185 # Echo the pipeline command to stdout
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
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186 print "Running %s" % pipeline
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
187
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
188 # Run the pipeline
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
189 with open("pipeline.log","w") as pipeline_out:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
190 try:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
191 subprocess.check_call(pipeline.cmd,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
192 stdout=pipeline_out,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
193 stderr=subprocess.STDOUT)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
194 exit_code = 0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
195 print "Pipeline completed ok"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
196 except subprocess.CalledProcessError as ex:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
197 # Non-zero exit status
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
198 sys.stderr.write("Pipeline failed: exit code %s\n" %
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
199 ex.returncode)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
200 exit_code = ex.returncode
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
201 except Exception as ex:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
202 # Some other problem
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
203 sys.stderr.write("Unexpected error: %s\n" % str(ex))
1
1c1902e12caf Updated to version 1.2.1.0
pjbriggs
parents: 0
diff changeset
204 exit_code = 1
0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
205
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
206 # Write out the list of outputs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
207 outputs_file = "Pipeline_outputs.txt"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
208 list_outputs(outputs_file)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
209
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
210 # Check for log file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
211 log_file = "Amplicon_analysis_pipeline.log"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
212 if os.path.exists(log_file):
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
213 print "Found log file: %s" % log_file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
214 if exit_code == 0:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
215 # Create an HTML file to link to log files etc
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
216 # NB the paths to the files should be correct once
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
217 # copied by Galaxy on job completion
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
218 with open("pipeline_outputs.html","w") as html_out:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
219 html_out.write("""<html>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
220 <head>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
221 <title>Amplicon analysis pipeline: log files</title>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
222 <head>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
223 <body>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
224 <h1>Amplicon analysis pipeline: log files</h1>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
225 <ul>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
226 """)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
227 html_out.write(
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
228 "<li>%s</li>\n" %
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
229 ahref("Amplicon_analysis_pipeline.log",
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
230 type="text/plain"))
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
231 html_out.write(
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
232 "<li>%s</li>\n" %
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
233 ahref("pipeline.log",type="text/plain"))
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
234 html_out.write(
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
235 "<li>%s</li>\n" %
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
236 ahref("Pipeline_outputs.txt",
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
237 type="text/plain"))
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
238 html_out.write(
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
239 "<li>%s</li>\n" %
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
240 ahref("Metatable.html"))
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
241 html_out.write("""<ul>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
242 </body>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
243 </html>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
244 """)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
245 else:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
246 # Check for known error messages
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
247 check_errors()
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
248 # Write pipeline stdout to tool stderr
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
249 sys.stderr.write("\nOutput from pipeline:\n")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
250 with open("pipeline.log",'r') as log:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
251 sys.stderr.write("%s" % log.read())
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
252 # Write log file contents to tool log
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
253 print "\nAmplicon_analysis_pipeline.log:"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
254 with open(log_file,'r') as log:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
255 print "%s" % log.read()
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
256 else:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
257 sys.stderr.write("ERROR missing log file \"%s\"\n" %
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
258 log_file)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
259
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
260 # Handle FastQC boxplots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
261 print "Amplicon analysis: collating per base quality boxplots"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
262 with open("fastqc_quality_boxplots.html","w") as quality_boxplots:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
263 # PHRED value for trimming
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
264 phred_score = 20
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
265 if args.trimming_threshold is not None:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
266 phred_score = args.trimming_threshold
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
267 # Write header for HTML output file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
268 quality_boxplots.write("""<html>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
269 <head>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
270 <title>Amplicon analysis pipeline: Per-base Quality Boxplots (FastQC)</title>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
271 <head>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
272 <body>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
273 <h1>Amplicon analysis pipeline: Per-base Quality Boxplots (FastQC)</h1>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
274 """)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
275 # Look for raw and trimmed FastQC output for each sample
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
276 for sample_name in sample_names:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
277 fastqc_dir = os.path.join(sample_name,"FastQC")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
278 quality_boxplots.write("<h2>%s</h2>" % sample_name)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
279 for d in ("Raw","cutdapt_sickle/Q%s" % phred_score):
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
280 quality_boxplots.write("<h3>%s</h3>" % d)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
281 fastqc_html_files = glob.glob(
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
282 os.path.join(fastqc_dir,d,"*_fastqc.html"))
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
283 if not fastqc_html_files:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
284 quality_boxplots.write("<p>No FastQC outputs found</p>")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
285 continue
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
286 # Pull out the per-base quality boxplots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
287 for f in fastqc_html_files:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
288 boxplot = None
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
289 with open(f) as fp:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
290 for line in fp.read().split(">"):
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
291 try:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
292 line.index("alt=\"Per base quality graph\"")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
293 boxplot = line + ">"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
294 break
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
295 except ValueError:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
296 pass
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
297 if boxplot is None:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
298 boxplot = "Missing plot"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
299 quality_boxplots.write("<h4>%s</h4><p>%s</p>" %
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
300 (os.path.basename(f),
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
301 boxplot))
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
302 quality_boxplots.write("""</body>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
303 </html>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
304 """)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
305
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
306 # Handle additional output when categories file was supplied
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
307 if args.categories_file is not None:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
308 # Alpha diversity boxplots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
309 print "Amplicon analysis: indexing alpha diversity boxplots"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
310 boxplots_dir = os.path.abspath(
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
311 os.path.join("RESULTS",
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
312 "%s_%s" % (args.pipeline.title(),
1
1c1902e12caf Updated to version 1.2.1.0
pjbriggs
parents: 0
diff changeset
313 ref_database),
0
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
314 "Alpha_diversity",
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
315 "Alpha_diversity_boxplot",
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
316 "Categories_shannon"))
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
317 print "Amplicon analysis: gathering PDFs from %s" % boxplots_dir
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
318 boxplot_pdfs = [os.path.basename(pdf)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
319 for pdf in
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
320 sorted(glob.glob(
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
321 os.path.join(boxplots_dir,"*.pdf")))]
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
322 with open("alpha_diversity_boxplots.html","w") as boxplots_out:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
323 boxplots_out.write("""<html>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
324 <head>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
325 <title>Amplicon analysis pipeline: Alpha Diversity Boxplots (Shannon)</title>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
326 <head>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
327 <body>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
328 <h1>Amplicon analysis pipeline: Alpha Diversity Boxplots (Shannon)</h1>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
329 """)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
330 boxplots_out.write("<ul>\n")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
331 for pdf in boxplot_pdfs:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
332 boxplots_out.write("<li>%s</li>\n" % ahref(pdf))
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
333 boxplots_out.write("<ul>\n")
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
334 boxplots_out.write("""</body>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
335 </html>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
336 """)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
337
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
338 # Finish
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
339 print "Amplicon analysis: finishing, exit code: %s" % exit_code
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
340 sys.exit(exit_code)