Mercurial > repos > tomnl > dma_filelist_generation

annotate dma-filelist-generation.py @ 3:19152a319f68 draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 578fd07833b93847193666c11744ba0bca1aaf57-dirty
author tomnl
date Thu, 03 May 2018 06:44:16 -0400
parents 6a2bb42acfe4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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6a2bb42acfe4 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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1 import argparse
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2 import textwrap
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3 import os
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4 import re
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5 import collections
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6 import csv
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7 from operator import itemgetter
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8
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9 def check_folder(in_dir, reg_string):
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10 filelist = []
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11 for f in os.listdir(in_dir):
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12
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13 if re.match(reg_string, f, re.IGNORECASE):
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15 fn, fe = os.path.splitext(f)
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16 fnl = fn.split("_")
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17 filename = fn
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18 fullpth = os.path.join(in_dir, f)
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19 wells = fnl[0]
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23 if re.match("^.*pos.*", f, re.IGNORECASE):
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24 polarity = "pos"
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25 elif re.match("^.*neg.*", f, re.IGNORECASE):
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26 polarity = "neg"
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27 else:
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28 error_message = "Files need to have either 'pos' or 'neg' in the file name"
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29 print error_message
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30 return 1, error_message, "", ""
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31 if re.match("^.*blank.*", f, re.IGNORECASE):
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32 sample_type = "blank"
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33 else:
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34 sample_type = "sample"
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35
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37 filelist.append([wells, sample_type, polarity, filename, fullpth])
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38
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39 return filelist
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40
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41 def get_filelist(filesin, o, file_type='mzML', create_filelist=True):
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42
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43 filedict = collections.OrderedDict()
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44
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45
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46 if file_type=="mzML":
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47 reg_string = "^.*mzML$"
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48 else:
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49 reg_string = "^.*raw$"
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50
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51 if isinstance(filesin, list):
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52 filelist = []
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53 for f in filesin:
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54 filelist.extend(check_folder(f, reg_string))
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55 else:
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56 filelist = check_folder(filesin, reg_string)
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57
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58 # Turn filelist into a dictionary
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59 for f1 in filelist:
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60 well = f1[0]
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61 filedict[well] = []
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62 for f2 in filelist:
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63 if well == f2[0]:
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64 filedict[well].append(f2[1:len(f2)+1])
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65
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66
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67
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68 filelist = sorted(filelist, key=itemgetter(0, 1))
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69
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70 for k, v in filedict.iteritems():
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71 classes = [i[0] for i in v]
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72 classes.sort()
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73 if not classes == ['blank', 'sample']:
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74 error_message = "!!!!ERROR!!!! Blank and sample required for each well, file type {}".format(file_type)
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75 print error_message
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76 return 1, error_message, "", ""
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77
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78 print 'files of type {} checked, files OK'.format(file_type)
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79
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80 if create_filelist:
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81
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82 outname = write_filedict(filedict, o, file_type)
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83 print 'filelist created in folder {}, using file type {}, full path {}'.format(o, file_type, outname)
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84
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85 return 0, "files OK", filedict, filelist
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86
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87 def write_filedict(filedict, out_dir, file_type, file_spacing='tsv'):
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88
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89 outname = os.path.join(out_dir,'filelist_{}.{}'.format(file_type, file_spacing))
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90
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91 if file_spacing=='tsv':
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92 delim = '\t'
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93 elif file_spacing=='csv':
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94 delim = ','
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95 else:
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96 delim = ','
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97
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98
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99 with open(outname, 'wb') as csvfile:
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100 w = csv.writer(csvfile, delimiter=delim)
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101
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102 w.writerow(['filename','classLabel', 'multilist', 'multilistLabel'])
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103 c = 1
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104 for k, v in filedict.iteritems():
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105 for i in v:
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106 w.writerow([os.path.basename(i[3]), i[0], c, k])
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107 c +=1
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108
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109 return outname
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110
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111
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112 def main():
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113
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114 p = argparse.ArgumentParser(prog='PROG',
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115 formatter_class=argparse.RawDescriptionHelpFormatter,
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116 description='''Create filelist for DMA DIMS nearline workflow''',
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117 epilog=textwrap.dedent('''
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118 -------------------------------------------------------------------------
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119
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120 Example Usage
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121
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122 python dma-filelist-generation.py -i [dir with sample files], [dir with blank files] -o .
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123
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124 '''))
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125
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126 p.add_argument('-i', dest='i', help='dir with sample files', nargs = '*', required=True)
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127 p.add_argument('-o', dest='o', help='out dir', required=True)
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128 p.add_argument('--check_mzml', dest='check_mzml', action='store_true')
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129 p.add_argument('--check_raw', dest='check_raw', action='store_true')
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130 p.add_argument('--create_filelist_mzml', dest='create_filelist_mzml', action='store_true')
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131 p.add_argument('--create_filelist_raw', dest='create_filelist_raw', action='store_true')
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132
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133 args = p.parse_args()
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134
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135 if not os.path.exists(args.o):
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136 os.makedirs(args.o)
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137 print args.o
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138
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139 if not args.check_mzml and not args.check_raw:
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140 print '--check_mzml or --check_raw (or both) are required as inputs'
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141 exit()
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142
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143 if args.check_mzml:
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144 get_filelist(args.i, args.o, file_type='mzML', create_filelist=args.create_filelist_mzml)
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145
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146 if args.check_raw:
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147
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148 get_filelist(args.i, args.o, file_type='raw', create_filelist=args.create_filelist_raw)
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149
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150
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151
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152 if __name__ == '__main__':
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153 main()
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154