Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/tools/mothur/mothur_wrapper.py @ 1:fcc0778f6987

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Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:35:35 -0400
parents 3202a38e44d9
children e990ac8a0f58
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0
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1 #!/usr/bin/env python
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2
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3 """
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4 http://www.mothur.org/
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5
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6 Supports mothur version
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7 mothur v.1.15.0
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8
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9 Class encapsulating Mothur galaxy tool.
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10 Expect each invocation to include:
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11 Here is an example call to this script with an explanation before each param :
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12 mothur_wrapper.py
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13 # name of a mothur command, this is required
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14 --cmd='summary.shared'
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15 # Galaxy output dataset list, these are output files that can be determined before the command is run
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16 # The items in the list are separated by commas
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17 # Each item contains a regex to match the output filename and a galaxy dataset filepath in which to copy the data (separated by :)
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18 --result='^mothur.\S+\.logfile$:'/home/galaxy/data/database/files/002/dataset_2613.dat,'^\S+\.summary$:'/home/galaxy/data/database/files/002/dataset_2614.dat
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19 # Galaxy output dataset extra_files_path direcotry in which to put all output files
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20 --outputdir='/home/galaxy/data/database/files/002/dataset_2613_files'
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21 # The id of one of the galaxy outputs (e.g. the mothur logfile) used for dynamic dataset generation
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22 # http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
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23 --datasetid='2578'
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24 # The galaxy directory in which to copy all output files for dynamic dataset generation
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25 --new_file_path='/home/galaxy/data/database/tmp'
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26 # specifies files to copy to the new_file_path
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27 # The list is separated by commas
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28 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
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29 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output
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30 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
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31 # Many mothur commands first require data to be read into memory using: read.otu, read.dist, or read.tree
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32 # This prequisite command and its params are prefixed with 'READ_'
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33 --READ_cmd='read.otu'
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34 --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat
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35 --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat'
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36 --READ_label='unique,0.07'
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37 """
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38 # import pkg_resources;
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39 import logging, os, string, sys, tempfile, glob, shutil, types, urllib, optparse, re
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40 import shlex, subprocess
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41 from stat import *
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42
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43 log = logging.getLogger( __name__ )
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44
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45 assert sys.version_info[:2] >= ( 2, 4 )
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46
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47 debug = False
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48 #debug = True
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49 max_processors = 1
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50
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51 def stop_err( msg ):
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52 sys.stderr.write( "%s\n" % msg )
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53 sys.exit()
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54
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55 def __main__():
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56 # tranform the logfile into html
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57 def logfile_to_html(logfile_path,htmlfile_path,tmp_input_dir_name,tmp_output_dir_name,title="Mothur Logfile"):
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58 if debug: print >> sys.stdout, 'logfile_to_html %s -> %s' % (logfile_path, htmlfile_path)
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59 if debug: print >> sys.stdout, 'logfile_to_html input_dir: %s' % tmp_input_dir_name
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60 if debug: print >> sys.stdout, 'logfile_to_html output_dir: %s' % tmp_output_dir_name
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61 txt = open(logfile_path,'r')
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62 in_pat = re.sub('[^a-zA-Z0-9_/]','.',tmp_input_dir_name) + '/(.+)'
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63 out_pat = re.sub('[^a-zA-Z0-9_/]','.',tmp_output_dir_name) + '/(.+)'
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64 html = open(htmlfile_path,'w')
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65 html.write("<html><head><title>%s</title></head>\n<body>\n<pre>\n" % title)
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66 try:
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67 for line in txt:
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68 if line.find('set.dir') >= 0:
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69 continue
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70 elif line.find('put directory to ') >= 0:
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71 continue
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72 elif line.startswith('Type ') :
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73 continue
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74 elif line.find(tmp_output_dir_name) >= 0:
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75 line = re.sub(out_pat,'<a href="\\1">\\1</a>',line)
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76 elif line.find(tmp_input_dir_name) >= 0:
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77 line = re.sub(in_pat,'\\1',line)
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78 html.write(line)
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79 except Exception, e:
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80 print(str(e))
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81 pass
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82 html.write('</pre>\n</body>\n</html>\n')
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83 html.close()
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84 #Overide the processors option
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85 def processors_callback(option, opt, value, parser):
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86 val = value if value <= max_processors else max_processors
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87 setattr(parser.values, option.dest, val)
0
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88 #Strip out "(xx)" confidence values from a taxonomy list
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89 def remove_confidence_callback(option, opt, value, parser):
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90 # val = "'" + re.sub('\(\d+\)','',value) + "'"
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91 setattr(parser.values, option.dest, re.sub('\(\d+\)','',value))
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92 #Mothur separates items in a list of values with hyphens
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93 def multi_val_callback(option, opt, value, parser):
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94 setattr(parser.values, option.dest, '-'.join(value.split(',')))
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95 #Handle list arguments that may contain dataset files
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96 def prepare_input(value,input_dir):
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97 """
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98 Mothur requires items in a list of input values to be separated by hyphens
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99 Change list separator from comma to hyphen
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100 If those items are files, copy them to the input dir.
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101 """
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102 if input_dir != None and value != None and isinstance(value, str):
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103 vals = []
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104 for val in value.split(','):
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105 if val[0] == '/' and os.path.isfile(val):
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106 (dir,fname) = os.path.split(val)
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107 try:
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108 os.symlink(val,os.path.join(input_dir,fname))
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109 except:
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110 shutil.copy(val,os.path.join(input_dir,fname))
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111 vals.append(fname)
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112 if debug: print >> sys.stderr, "scp %s %s" % (val, os.path.join(input_dir,fname))
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113 else:
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114 vals.append(val)
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115 return '-'.join(vals)
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116 return value
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117 #Parse Command Line and get a list of params
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118 # Prefix is used to differentiate between prerequisite commands: read.otu, read.dist, read.tree
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119 def get_params(cmd, options, input_dir, prefix=''):
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120 if debug: print >> sys.stderr, options
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121 params = []
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122 for opt in cmd_dict[cmd]['required']:
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123 if debug: print >> sys.stderr, opt
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124 if isinstance(opt,list): # One of these must be present
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125 missing = True
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126 for sel in opt:
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127 # if debug: print >> sys.stderr, sel
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128 try:
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129 value = prepare_input(getattr(options,prefix+sel), input_dir)
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130 if value != None:
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131 params.append('%s=%s' % (sel,value))
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132 missing = False
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133 except Exception, e:
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134 stop_err('Illegal option for cmd %s : %s %s' % (cmd,sel,e))
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135 if missing:
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136 stop_err('Missing a required parameter for %s, need one of %s' % (cmd,opt))
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137 else: # This option is required
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138 try:
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139 value = prepare_input(getattr(options,prefix+opt), input_dir)
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140 # if debug: print >> sys.stderr, value
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141 if value != None:
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142 params.append('%s=%s' % (opt,value))
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143 else:
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144 stop_err('Missing a required parameter for %s : %s' % (cmd,opt))
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145 except Exception, e:
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146 stop_err('Illegal option %s %s' % (opt,e))
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147 if 'optional' in cmd_dict[cmd]:
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148 for opt in cmd_dict[cmd]['optional']:
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149 # if debug: print >> sys.stderr, opt
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150 try:
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151 value = prepare_input(getattr(options,prefix+opt), input_dir)
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152 # if debug: print >> sys.stderr, value
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153 if value != None:
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154 params.append('%s=%s' % (opt,value))
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155 except Exception, e:
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156 # should distinguish between READ_ opts and cmd opts
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157 # stop_err('Illegal option for %s : %s' % (cmd,opt))
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158 pass
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159 return params
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160 """
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161 The command dict has a dict for each mothur command with required and options arguments
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162 The top level list of required arguments is interpreted that each value item is required and any list item represents a choice of arguments
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163 This covers many, but not all of the argument dependency requirements.
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164 For example - read.dist required a phylip or (column and name) argument.
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165 The complexity of inputs should be handled by the glaxy tool xml file.
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166 """
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167 cmd_dict = dict()
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168 cmd_dict['merge.files'] = dict({'required' : ['input','output']})
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169 cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : ['output']})
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170 cmd_dict['merge.groups'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label']})
0
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171 cmd_dict['summary.seqs'] = dict({'required' : ['fasta'],
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172 'outputs' : ['.names']})
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173 cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']})
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174 cmd_dict['degap.seqs'] = dict({'required' : ['fasta']})
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175 cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['names']})
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176 cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','names'], 'optional' : []})
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177 cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['keep','short']})
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178 cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']})
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179 cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','processors']})
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180 cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['group','oligos','qfile','qaverage','qthreshold','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast']})
0
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181 cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]})
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182 cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
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183 cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
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184 cmd_dict['align.seqs'] = dict({'required' : ['candidate','template'], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','processors']})
0
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185 cmd_dict['align.check'] = dict({'required' : ['fasta','map']})
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186 cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['names','diffs']})
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187 cmd_dict['bin.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','label','group']})
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188 cmd_dict['classify.seqs'] = dict({'required' : ['fasta','template','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','processors']})
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189 cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']})
0
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190 # label=0.01-0.02-0.03 from 0.01,0.02,0.03 string.replace(options.label,',','-')
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191 cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']})
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192 cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','template'], 'optional' : ['filter','mask','window','numwanted','processors']})
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193 cmd_dict['chimera.check'] = dict({'required' : ['fasta','template'], 'optional' : ['ksize','svg','name','increment','processors']})
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194 cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','template'], 'optional' : ['conservation','quantile','filter','mask','window','increment','processors']})
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195 cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','template'], 'optional' : ['name','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','processors']})
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196 cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','processors']})
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197 cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']})
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198 cmd_dict['read.dist'] = dict({'required' : [['phylip','column']], 'optional' : ['name','cutoff','hard','precision','sim','group']})
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199 cmd_dict['read.otu'] = dict({'required' : [['rabund','sabund','list','shared','relabund']], 'optional' : ['label','group','groups','ordergroup']})
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200 cmd_dict['read.tree'] = dict({'required' : ['tree'], 'optional' : ['name','group']})
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201 cmd_dict['cluster'] = dict({'required' : [] , 'optional' : ['method','cutoff','hard','precision']})
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202 cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund']})
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203 cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent']})
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204 cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','timing','processors']})
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205 cmd_dict['metastats'] = dict({'required' : ['design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']})
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206 cmd_dict['summary.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','groupmode','processors']})
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207 cmd_dict['summary.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','all','distance']})
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208 cmd_dict['collect.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','freq']})
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209 cmd_dict['collect.shared'] = dict({'required' : [], 'optional' : ['calc','label','freq','groups','all']})
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210 cmd_dict['rarefaction.single'] = dict({'required' : [], 'optional' : ['calc','abund','iters','label','freq','processors']})
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211 cmd_dict['rarefaction.shared'] = dict({'required' : [], 'optional' : ['label','iters','groups','jumble']})
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212 cmd_dict['normalize.shared'] = dict({'required' : [], 'optional' : ['label','method','norm','groups']})
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213 cmd_dict['dist.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','output']})
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214 cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']})
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215 cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : []})
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216 cmd_dict['tree.shared'] = dict({'required' : [], 'optional' : ['groups','calc','cutoff','precision','label']})
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217 cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','processors']})
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218 cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','processors']})
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219 cmd_dict['parsimony'] = dict({'required' : [], 'optional' : ['groups','iters','random','processors']})
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220 cmd_dict['sffinfo'] = dict({'required' : ['sff'], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']})
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221 cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : []})
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222 cmd_dict['heatmap.bin'] = dict({'required' : [], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']})
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223 cmd_dict['heatmap.sim'] = dict({'required' : [], 'optional' : ['calc','phylip','column','name','label','groups']})
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224 cmd_dict['venn'] = dict({'required' : [], 'optional' : ['calc','label','groups','nseqs','permute']})
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225 cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : []})
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226 cmd_dict['pca'] = dict({'required' : [], 'optional' : ['label','groups','metric']})
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227 cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']})
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228 cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']})
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229 cmd_dict['get.group'] = dict({'required' : [], 'optional' : []})
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230 cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']})
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231 cmd_dict['phylo.diversity'] = dict({'required' : [],'optional' : ['groups','iters','freq','processors','scale','rarefy','collect','summary','processors']})
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232 cmd_dict['get.oturep'] = dict({'required' : ['fasta','list'], 'optional' : ['phylip','column','name','label','group','groups','sorted','precision','cutoff','large','weighted']})
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233 cmd_dict['get.relabund'] = dict({'required' : [],'optional' : ['scale','label','groups']})
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234 cmd_dict['libshuff'] = dict({'required' : [],'optional' : ['iters','form','step','cutoff']})
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235 # clearcut options not needed in galaxy: 'version','verbose','quiet','stdout'
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236 cmd_dict['clearcut'] = dict({'required' : [['list','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']})
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237 cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
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238 cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
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239 cmd_dict['bootstrap.shared'] = dict({'required' : [], 'optional' : ['calc','groups','iters','label']})
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240 """
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241 Mothur 1.15
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242 """
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243 cmd_dict['cluster.classic'] = dict({'required' : [] , 'optional' : ['method','cutoff','hard','precision']})
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244 cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']})
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245 cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']})
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246 cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
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diff changeset
247 cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
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248 cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']})
0
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249 cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']})
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250
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251 cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']})
0
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252 cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label']})
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253 cmd_dict['indicator'] = dict({'required' : ['tree',['shared','relabund']], 'optional' : ['groups','label','design']})
0
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254 parser = optparse.OptionParser()
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255 # Options for managing galaxy interaction
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256 parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' )
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257 parser.add_option( '--cmd', dest='cmd', help='The mothur command' )
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258 parser.add_option( '--inputdir', dest='inputdir', help='The directory in which to work' )
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259 parser.add_option( '--outputdir', dest='outputdir', help='The directory in which to work' )
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260 parser.add_option( '--tmpdir', dest='tmpdir', help='The directory in which to work' )
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261 parser.add_option( '--tempdefault', dest='tempdefault', help='The default directory in which to search for input' )
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262 parser.add_option( '--result', dest='result', help='The name pattern and destination for each output file' )
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263 parser.add_option( '--new_file_path', dest='new_file_path', help='The Galaxy new_file_path, dir for extra output datasets' )
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264 parser.add_option( '--datasetid', dest='datasetid', help='The Galaxy new_file_path, dir for extra output datasets' )
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diff changeset
265 parser.add_option( '--new_datasets', dest='new_datasets', help='The name pattern and datatype ext for ouputs' )
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266 # Options for prerequisite Read commands
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267 parser.add_option( '--READ_cmd', dest='READ_cmd', help='The mothur command' )
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268 # required arguments for Read.dist
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269 parser.add_option( '--READ_phylip', dest='READ_phylip', help='' )
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270 parser.add_option( '--READ_column', dest='READ_column', help='' )
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diff changeset
271 # required arguments for Read.otu
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272 parser.add_option( '--READ_rabund', dest='READ_rabund', help='' )
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273 parser.add_option( '--READ_sabund', dest='READ_sabund', help='' )
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274 parser.add_option( '--READ_list', dest='READ_list', help='' )
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275 parser.add_option( '--READ_shared', dest='READ_shared', help='' )
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diff changeset
276 parser.add_option( '--READ_relabund', dest='READ_relabund', help='' )
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diff changeset
277 # required arguments for Read.tree
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278 parser.add_option( '--READ_tree', dest='READ_tree', help='' )
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diff changeset
279 # optional arguments for Read cmds
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280 parser.add_option( '--READ_name', dest='READ_name', help='' )
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diff changeset
281 parser.add_option( '--READ_cutoff', dest='READ_cutoff', type="float", help='' )
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282 parser.add_option( '--READ_hard', dest='READ_hard', help='' )
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diff changeset
283 parser.add_option( '--READ_precision', dest='READ_precision', type="int", help='' )
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diff changeset
284 parser.add_option( '--READ_sim', dest='READ_sim', help='' )
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diff changeset
285 parser.add_option( '--READ_group', dest='READ_group', help='' )
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diff changeset
286 parser.add_option( '--READ_groups', dest='READ_groups', help='' )
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diff changeset
287 parser.add_option( '--READ_ordergroup', dest='READ_ordergroup', help='')
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diff changeset
288 parser.add_option( '--READ_label', dest='READ_label', help='' )
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diff changeset
289 # Parameter specified in mothur
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diff changeset
290 parser.add_option( '--numbases', dest='numbases', type="int", help='Number of base to allow' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
291 parser.add_option( '--fasta', dest='fasta', help='fasta file paths' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
292 parser.add_option( '--fastq', dest='fastq', help='fastq file paths' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
293 parser.add_option( '--qfile', dest='qfile', help='Sequence read quality file (454 platform)' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
294 parser.add_option( '--qaverage', dest='qaverage', type="int", help='Remove sequences that have an average quality below the value' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
295 parser.add_option( '--qthreshold', dest='qthreshold', type="int", help='If at any point a base call in a sequence has a quality score below the value provided to the option, the sequence is terminated' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
296 parser.add_option( '--qtrim', dest='qtrim', help='For sequence below qthreshold, false to scrap file, true to trimmed and in trim file' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
297 parser.add_option( '--flip', dest='flip', help='If true, reverse complement the sequences' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
298 parser.add_option( '--maxambig', dest='maxambig', type="int", help='Number of ambiguous base calls to allow' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
299 parser.add_option( '--maxhomop', dest='maxhomop', type="int", help='Maximun homopolymer length allowed' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
300 parser.add_option( '--minlength', dest='minlength', type="int", help='Minimun sequence length' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
301 parser.add_option( '--maxlength', dest='maxlength', type="int", help='Maximun sequence length' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
302 parser.add_option( '--oligos', dest='oligos', help='The oligos option takes a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier.' )
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diff changeset
303 parser.add_option( '--bdiffs', dest='bdiffs', type="int", help='Number of barcode differences to allow' )
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diff changeset
304 parser.add_option( '--pdiffs', dest='pdiffs', type="int", help='Number of primer differences to allow' )
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diff changeset
305 parser.add_option( '--tdiffs', dest='tdiffs', type="int", help='Total number of barcode and primer differences to allow' )
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diff changeset
306 parser.add_option( '--diffs', dest='diffs', type="int", help='Number of mismatched bases to allow between sequences in a group' )
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diff changeset
307 parser.add_option( '--allfiles', dest='allfiles', help='T - generate fasta and group for each barcode' )
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diff changeset
308 parser.add_option( '--name', dest='name', help='A file containing a 2 column table: name, and comma separated list of represetatives' )
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diff changeset
309 parser.add_option( '--accnos', dest='accnos', help='A file containing a list of names' )
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diff changeset
310 parser.add_option( '--groups', dest='groups', help='pairwise group labels' )
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diff changeset
311 parser.add_option( '--group', dest='group', help='A file containing a list of names' )
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diff changeset
312 parser.add_option( '--list', dest='list', help='A file containing a list of names' )
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diff changeset
313 parser.add_option( '--alignreport', dest='alignreport', help='A align.report file ' )
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314 parser.add_option( '--taxonomy', dest='taxonomy', help='A Taxonomy file' )
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diff changeset
315 parser.add_option( '--reftaxonomy', dest='reftaxonomy', help='A Taxonomy file' )
0
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diff changeset
316 parser.add_option( '--taxon', dest='taxon', help='A Taxon' )
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diff changeset
317 parser.add_option( '--taxlevel', dest='taxlevel', type="int", help='A Taxonomy level' )
0
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318 # parser.add_option( '--taxon', dest='taxon', action="callback", callback=remove_confidence_callback, help='A Taxon' )
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diff changeset
319 parser.add_option( '--candidate', dest='candidate', help=' file ' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
320 parser.add_option( '--template', dest='template', help=' file ' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
321 parser.add_option( '--dups', dest='dups', help='if True also apply to the aliases from the names files' )
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diff changeset
322 parser.add_option( '--keep', dest='keep', help='Either front or back to specify the which end of the sequence to keep' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
323 parser.add_option( '--search', dest='search', help='Method for finding the template sequence: kmer, blast, suffix' )
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diff changeset
324 parser.add_option( '--ksize', dest='ksize', type="int", help='Size of kmers (5 - 12)' )
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diff changeset
325 parser.add_option( '--align', dest='align', help='Alignment method: needleman, blastn, gotoh' )
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diff changeset
326 parser.add_option( '--match', dest='match', type="float", help='Reward for a match, default is +1.0' )
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diff changeset
327 parser.add_option( '--mismatch', dest='mismatch', type="float", help='Penalty for a mismatch, default is -1.0' )
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diff changeset
328 parser.add_option( '--gapopen', dest='gapopen', type="float", help='Penalty for a opening, default is -2.0' )
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diff changeset
329 parser.add_option( '--gapextend', dest='gapextend', type="float", help='Penalty for extending a gap, default is -1.0' )
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diff changeset
330 parser.add_option( '--precision', dest='precision', type="int", help='' )
0
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diff changeset
331 parser.add_option( '--threshold', dest='threshold', type="float", help='Cutoff at which an alignment is deemed bad and the reverse complement may be tried, 0.0 - 1.0 default 0.50' )
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diff changeset
332 parser.add_option( '--map', dest='map', help='File containing the secondary structure map.' )
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diff changeset
333 parser.add_option( '--label', dest='label', type='string', action="callback", callback=multi_val_callback, help='Distance levels you would like a output files created for(separated by commas or dashes)' )
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diff changeset
334 parser.add_option( '--filter', dest='filter', help='If true, a 50% soft filter will be applied' )
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diff changeset
335 parser.add_option( '--correction', dest='correction', help='If true, square root of the distances is used instead of the distance value' )
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diff changeset
336 parser.add_option( '--window', dest='window', type="int", help='Window size for searching for chimeras, default is 1/4 sequence length' )
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diff changeset
337 parser.add_option( '--increment', dest='increment', type="int", help='How far you move each window while finding chimeric sequences, default is 25' )
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diff changeset
338 parser.add_option( '--mask', dest='mask', help='A file containing one sequence you wish to use as a mask for the your sequences' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
339 parser.add_option( '--numwanted', dest='numwanted', type="int", help='How many sequences you would each query sequence compared with' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
340 parser.add_option( '--start', dest='start', type="int", help='Remove sequences that start after thisposition' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
341 parser.add_option( '--end', dest='end', type="int", help='Remove sequences that end before this position' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
342 parser.add_option( '--criteria', dest='criteria', type="int", help='Percentage of sequences to match' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
343 parser.add_option( '--optimize', dest='optimize', help='List of parameters to optimize' )
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diff changeset
344 parser.add_option( '--vertical', dest='vertical', help='Ignore any column that only contains gap characters, "-" or "."' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
345 parser.add_option( '--trump', dest='trump', help='Remove a column if the trump character is found at that position in any sequence of the alignment.' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
346 parser.add_option( '--soft', dest='soft', type='int', help='Soft Mask - percentage required to retain column. (0-100)' )
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diff changeset
347 parser.add_option( '--hard', dest='hard', help='Hard Column Filter - A file should only contain one line consisting of 0 and 1 chars' )
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diff changeset
348 parser.add_option( '--calc', dest='calc', help='Calc Method - Gap Penality' )
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349 parser.add_option( '--countends', dest='countends', help='Penalize terminal gaps' )
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350 # parser.add_option( '--cutoff', dest='cutoff', type="float", help='Distance Cutoff threshold, discard larger distances' )
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diff changeset
351 parser.add_option( '--cutoff', dest='cutoff', help='Distance Cutoff threshold, discard larger distances' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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352 parser.add_option( '--countgaps', dest='countgaps', help='count gaps as bases' )
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353 parser.add_option( '--output', dest='output', help='Format for output' )
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diff changeset
354 parser.add_option( '--method', dest='method', help='Method to use for analysis - cluster' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
355 parser.add_option( '--splitmethod', dest='splitmethod', help='Method to split a distance file - cluster.split' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
356 parser.add_option( '--abund', dest='abund', type='int', help='Threshold for rare to Abundant OTU classification' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
357 parser.add_option( '--size', dest='size', type='int', help='Size - sample size' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
358 parser.add_option( '--groupmode', dest='groupmode', help='Collate groups into one result table' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
359 parser.add_option( '--all', dest='all', help='Calculate for all' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
360 parser.add_option( '--freq', dest='freq', type="float", help='Frequency of sequences to choose, as fraction is 0.0 - 1.0 or iteration if int > 1' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
361 parser.add_option( '--iters', dest='iters', type='int', help='Iterations of randomizations' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
362 parser.add_option( '--maxiters', dest='maxiters', type='int', help='Iterations of randomizations' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
363 parser.add_option( '--jumble', dest='jumble', help='If false, just a collector curve across the samples' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
364 parser.add_option( '--conservation', dest='conservation', help='Template frequency information' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
365 parser.add_option( '--quantile', dest='quantile', help='Template quantile information' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
366 parser.add_option( '--parents', dest='parents', type='int', help='Number of Parents to investigate' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
367 parser.add_option( '--minsim', dest='minsim', type='int', help='Minimum simarity (0-100 percent)' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
368 parser.add_option( '--mincov', dest='mincov', type='int', help='Minimum coverage (0-100 percent)' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
369 parser.add_option( '--minbs', dest='minbs', type='int', help='Minimum bootstrap support (0-100 percent)' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
370 parser.add_option( '--minsnp', dest='minsnp', type='int', help='Minimum SNPs to sample(0-100 percent)' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
371 parser.add_option( '--mindim', dest='mindim', type='int', help='Minimum dimensions' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
372 parser.add_option( '--maxdim', dest='maxdim', type='int', help='Maximum dimensions' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
373 parser.add_option( '--percent', dest='percent', type='int', help='(0-100 percent)' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
374 parser.add_option( '--divergence', dest='divergence', type='float', help='Divergence cutoff for chimera determination' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
375 parser.add_option( '--sff', dest='sff', help='Sff file' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
376 parser.add_option( '--sfftxt', dest='sfftxt', help='Generate a sff.txt file' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
377 parser.add_option( '--flow', dest='flow', help='Generate a flowgram file' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
378 parser.add_option( '--trim', dest='trim', help='Whether sequences and quality scores are trimmed to the clipQualLeft and clipQualRight values' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
379 parser.add_option( '--input', dest='input', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
380 parser.add_option( '--phylip', dest='phylip', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
381 parser.add_option( '--column', dest='column', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
382 parser.add_option( '--sorted', dest='sorted', help='Input is presorted' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
383 parser.add_option( '--showabund', dest='showabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
384 parser.add_option( '--short', dest='short', help='Keep sequences that are too short to chop' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
385 parser.add_option( '--distance', dest='distance', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
386 parser.add_option( '--scale', dest='scale', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
387 parser.add_option( '--numotu', dest='numotu', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
388 parser.add_option( '--fontsize', dest='fontsize', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
389 parser.add_option( '--neqs', dest='neqs', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
390 parser.add_option( '--permute', dest='permute', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
391 parser.add_option( '--rarefy', dest='rarefy', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
392 parser.add_option( '--collect', dest='collect', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
393 parser.add_option( '--summary', dest='summary', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
394 parser.add_option( '--large', dest='large', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
395 parser.add_option( '--shuffle', dest='shuffle', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
396 parser.add_option( '--neighbor', dest='neighbor', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
397 parser.add_option( '--expblen', dest='expblen', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
398 parser.add_option( '--expdist', dest='expdist', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
399 parser.add_option( '--ntrees', dest='ntrees', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
400 parser.add_option( '--DNA', dest='DNA', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
401 parser.add_option( '--protein', dest='protein', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
402 parser.add_option( '--kimura', dest='kimura', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
403 parser.add_option( '--jukes', dest='jukes', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
404 parser.add_option( '--matrixout', dest='matrixout', help='' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
405 parser.add_option( '--nseqs', dest='nseqs', help='' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
406 parser.add_option( '--bygroup', dest='bygroup', help='' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
407 parser.add_option( '--design', dest='design', help='' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
408 parser.add_option( '--sets', dest='sets', help='' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
409 parser.add_option( '--metric', dest='metric', help='' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
410 parser.add_option( '--epsilon', dest='epsilon', help='' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
411 parser.add_option( '--axes', dest='axes', help='table of name column followed by columns of axis values' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
412 parser.add_option( '--numaxes', dest='numaxes', help='the number of axes' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
413 parser.add_option( '--metadata', dest='metadata', help='data table with columns of floating-point values' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
414 parser.add_option( '--basis', dest='basis', help='what the summary file represents' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
415 parser.add_option( '--keepfirst', dest='keepfirst', help='trimming' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
416 parser.add_option( '--removelast', dest='removelast', help='trimming' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
417 parser.add_option( '--persample', dest='persample', help='sub sample option' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
418 parser.add_option( '--timing', dest='timing', help='timing option' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
419 parser.add_option( '--processors', dest='processors', type='int', action='callback', callback=processors_callback, help='Number of processors to use' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
420 # include read.otu options
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
421 parser.add_option( '--rabund', dest='rabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
422 parser.add_option( '--sabund', dest='sabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
423 parser.add_option( '--shared', dest='shared', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
424 parser.add_option( '--relabund', dest='relabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
425 parser.add_option( '--ordergroup', dest='ordergroup', help='')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
426 # include read.tree options
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
427 parser.add_option( '--tree', dest='tree', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
428
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
429 (options, args) = parser.parse_args()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
430 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
431 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
432 # print >> sys.stderr, options # so will appear as blurb for file
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
433 if options.debug != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
434 debug = options.debug
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
435 params = []
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
436 inputdir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
437 outputdir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
438 tmp_dir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
439 tempdefault = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
440 # Report exception if no command is given
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
441 if options.cmd == None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
442 stop_err('No mothur command given')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
443 # Read directory options
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
444 if options.tmpdir != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
445 if not os.path.isdir(options.tmpdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
446 os.makedirs(options.tmpdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
447 tmp_dir = options.tmpdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
448 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
449 tmp_dir = tempfile.mkdtemp()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
450 if options.inputdir != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
451 if not os.path.isdir(options.inputdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
452 os.makedirs(options.inputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
453 inputdir = options.inputdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
454 if options.outputdir != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
455 if not os.path.isdir(options.outputdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
456 os.makedirs(options.outputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
457 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
458 outputdir = os.path.join(tmp_dir,'out')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
459 os.symlink(options.outputdir,outputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
460 except Exception, e:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
461 print >> sys.stderr, e
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
462 outputdir = options.outputdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
463 # Set directories
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
464 if inputdir == None or not os.path.isdir(inputdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
465 inputdir = tmp_dir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
466 if outputdir == None or not os.path.isdir(outputdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
467 outputdir = tempfile.mkdtemp()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
468 if options.tempdefault != None and os.path.isdir(options.tempdefault):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
469 tempdefault = ', tempdefault=%s' % options.tempdefault
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
470 # params.append('set.dir(input=%s,output=%s%s)' % (inputdir,outputdir,tempdefault))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
471 params.append('set.dir(output=%s%s)' % (outputdir,tempdefault))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
472 # Check for prerequisite read command
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
473 if options.READ_cmd != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
474 read_cmd_opts = ','.join(get_params(options.READ_cmd,options,inputdir,prefix='READ_'))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
475 params.append('%s(%s)' % (options.READ_cmd,read_cmd_opts))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
476 # Check for command options
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
477 cmd_opts = ','.join(get_params(options.cmd,options,inputdir))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
478 # print >> sys.stderr, cmd_opts
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
479 # print >> sys.stderr, params # so will appear as blurb for file
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
480 params.append('%s(%s)' % (options.cmd,cmd_opts))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
481 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
482 # Generate the mothur commandline
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
483 # http://www.mothur.org/wiki/Command_line_mode
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
484 cmdline = 'mothur "#' + '; '.join(params) + '"'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
485 # print >> sys.stdout, '%s' % cmdline
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
486 if tmp_dir == None or not os.path.isdir(tmp_dir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
487 tmp_dir = tempfile.mkdtemp()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
488 tmp_stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.err' ).name
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
489 tmp_stderr = open( tmp_stderr_name, 'wb' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
490 tmp_stdout_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.out' ).name
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
491 tmp_stdout = open( tmp_stdout_name, 'wb' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
492 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno() )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
493 # proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
494 returncode = proc.wait()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
495 tmp_stderr.close()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
496 # get stderr, allowing for case where it's very large
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
497 tmp_stderr = open( tmp_stderr_name, 'rb' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
498 stderr = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
499 buffsize = 1048576
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
500 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
501 while True:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
502 stderr += tmp_stderr.read( buffsize )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
503 if not stderr or len( stderr ) % buffsize != 0:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
504 break
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
505 except OverflowError:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
506 pass
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
507 tmp_stderr.close()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
508 if returncode != 0:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
509 raise Exception, stderr
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
510 stdout = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
511 # Parse stdout to provide info
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
512 tmp_stdout.close()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
513 tmp_stdout = open( tmp_stdout_name, 'rb' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
514 info = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
515 if options.cmd.startswith('chimera') and not options.cmd.endswith('check'):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
516 pattern = '^.*$'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
517 if options.cmd == 'chimera.slayer':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
518 # gi|11093931|MNE12|AF293003 yes
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
519 pattern = '\S.*\tyes$'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
520 elif options.cmd == 'chimera.bellerophon':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
521 # gi|11093939|MNB2|AF293011 is a suspected chimera at breakpoint 2195
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
522 pattern = '\S.* suspected chimera .*'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
523 elif options.cmd == 'chimera.ccode':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
524 # gi|11093940|MNF8|AF293012 was found have at least one chimeric window.
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
525 pattern = '\S.* chimeric window.*'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
526 elif options.cmd == 'chimera.pintail':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
527 pattern = '\S.*chimera.*Yes'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
528 # move new generated template .freq and .quan files to outputdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
529 chimera_count = 0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
530 for line in tmp_stdout:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
531 if re.match(pattern,line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
532 chimera_count += 1
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
533 info += "Chimeras: %d" % chimera_count
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
534 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
535 found_begin = False
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
536 for line in tmp_stdout:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
537 if line.find(outputdir) >= 0:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
538 continue
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
539 if re.match('^Processing.*',line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
540 continue
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
541 if re.match('.*\.\.\.\s*$',line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
542 continue
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
543 if re.match('^\d*\s*$',line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
544 continue
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
545 if re.match('Output .*',line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
546 break
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
547 if found_begin:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
548 info += "%s" % line
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
549 if re.match('mothur > ' + options.cmd + '\(.*\)', line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
550 found_begin = True
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
551 tmp_stdout.close()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
552 print >> sys.stdout, info
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
553 # Collect output files
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
554 flist = os.listdir(outputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
555 if debug: print >> sys.stdout, '%s' % flist
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
556 # process option result first
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
557 # These are the known galaxy datasets listed in the --result= param
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
558 if len(flist) > 0 and options.result:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
559 # items in list are separated by commas
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
560 for output in options.result.split(','):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
561 # Each item has a regex pattern and a file path to a galaxy dataset
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
562 (pattern,path) = output.split(':')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
563 if debug: print >> sys.stdout, '%s -> %s' % (pattern,path)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
564 if path == None or path == 'None':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
565 continue
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
566 found = False
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
567 for fname in flist:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
568 if debug: print >> sys.stdout, 'outdir %s match: %s' % (fname,re.match(pattern,fname))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
569 if re.match(pattern,fname):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
570 found = True
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
571 flist.remove(fname)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
572 fpath = os.path.join(outputdir,fname)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
573 if fname.endswith('.logfile'):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
574 # Make the logfile into html
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
575 logfile_to_html(fpath,path,inputdir,outputdir,title="Mothur %s Logfile" % options.cmd)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
576 elif False and outputdir == options.outputdir:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
577 # Use a hard link if outputdir is the extra_files_path
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
578 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
579 os.link(fpath, path)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
580 except:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
581 shutil.copy2(fpath, path)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
582 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
583 shutil.copy2(fpath, path)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
584 break
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
585 # chimera.pintail e.g. generates files in the working dir that we might want to save
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
586 if not found:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
587 for fname in os.listdir(tmp_dir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
588 if debug: print >> sys.stdout, 'tmpdir %s match: %s' % (fname,re.match(pattern,fname))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
589 if re.match(pattern,fname):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
590 fpath = os.path.join(tmp_dir,fname)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
591 shutil.copy2(fpath, path)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
592 break
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
593 # Handle the dynamically generated galaxy datasets
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
594 # http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
595 # --new_datasets= specifies files to copy to the new_file_path
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
596 # The list items are separated by commas
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
597 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
598 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
599 if options.new_datasets != None and options.new_file_path != None and options.datasetid != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
600 datasets = options.new_datasets.split(',')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
601 for output in options.new_datasets.split(','):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
602 (pattern,ext) = output.split(':');
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
603 for fname in flist:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
604 m = re.match(pattern,fname)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
605 if m:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
606 fpath = os.path.join(outputdir,fname)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
607 if len(m.groups()) > 0:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
608 root = m.groups()[0]
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
609 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
610 # remove the ext from the name if it exists, galaxy will add back later
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
611 # remove underscores since galaxy uses that as a field separator for dynamic datasets
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
612 root = re.sub('\.?'+ext+'$','',fname).replace('_','').replace('.','')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
613 # filename pattern required by galaxy
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
614 fn = "%s_%s_%s_%s_%s" % ( 'primary', options.datasetid, root, 'visible', ext )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
615 if debug: print >> sys.stdout, '> %s' % fpath
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
616 if debug: print >> sys.stdout, '< %s' % os.path.join(options.new_file_path,fn)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
617 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
618 os.link(fpath, os.path.join(options.new_file_path,fn))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
619 except:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
620 shutil.copy2(fpath, os.path.join(options.new_file_path,fn))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
621 except Exception, e:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
622 msg = str(e) + stderr
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
623 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
624 if len(msg) < 50 and stdout != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
625 # include the last line of stdout
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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626 msg += stdout.splitlines()[-1]
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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627 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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628 stop_err( 'Error running ' + msg)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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629 finally:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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630 # Only remove temporary directories
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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631 # Enclose in try block, so we don't report error on stale nfs handles
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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632 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
633 if outputdir != options.outputdir and os.path.exists(outputdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
634 if os.path.islink(outputdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
635 os.remove(outputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
636 shutil.rmtree(os.path.dirname(outputdir))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
637 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
638 shutil.rmtree(outputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
639 if inputdir != options.inputdir and os.path.exists(inputdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
640 shutil.rmtree(inputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
641 except:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
642 pass
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
643
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
644
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
645 if __name__ == "__main__": __main__()