Mercurial > repos > stevecassidy > maus

annotate items_to_bpf.py @ 6:28df10f22b51 draft default tip

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planemo upload commit 72cee9103c0ae4acb5794afaed179bea2c729f2c-dirty
author stevecassidy
date Sat, 11 Mar 2017 21:38:41 -0500
parents c87ee3aec57b
children
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1 from __future__ import print_function
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2 import argparse
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3 import os
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4 import csv
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5 import re
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6
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7
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8 def parser():
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9 parser = argparse.ArgumentParser(description="Generate BPF Orthographic Transcription from Item List")
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10 parser.add_argument('--item_list', required=True, action="store", type=str, help="File containing list of item URLs")
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11 parser.add_argument('--lexicon', required=True, action="store", type=str, help="File containing lexicon (tsv)")
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12 parser.add_argument('--output_path', required=True, action="store", type=str, help="Path to output file")
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13 return parser.parse_args()
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14
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15 def read_item_list(filename):
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16 """Read an item list from a file
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17 which should be a tabular formatted file
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18 with one column header ItemURL.
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19 Return an instance of ItemGroup"""
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20
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21 with open(filename) as fd:
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22 csvreader = csv.DictReader(fd, dialect='excel-tab')
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23 if 'ItemURL' not in csvreader.fieldnames:
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24 return None
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25 if 'Prompt' not in csvreader.fieldnames:
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26 return None
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27 itemurls = []
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28 for row in csvreader:
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29 itemurls.append((row['Prompt'], row['ItemURL']))
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30
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31 return itemurls
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32
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33 # this file name pattern allows galaxy to discover the dataset designation and type
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34 FNPAT = "%(designation)s#%(ext)s"
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35
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36 def galaxy_name(itemurl, ext):
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37 """Construct a filename suitable for dataset discovery
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38 by Galaxy.
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39
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40 @type itemurl: C{String}
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41 @param itemurl: the item URL from Alveo
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42
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43 @type ext: C{String}
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44 @param ext: the datatype extension for the resulting file
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45 """
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46
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47 itemname = itemurl.split('/')[-1]
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48 fname = FNPAT % {'designation': itemname, 'ext': ext}
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49
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50 return fname
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51
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52
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53 def build_bpf(ortho_trans, lexicon):
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54 """ Given an orthographic transcript, generate a BPF-format phonetic
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55 transcription for passing to MAUS, using the specified lexicon.
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56
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57 @type ortho_trans: C{String}
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58 @param ortho_trans: the (space-separated) orthographic transcript
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59 @type lex: C{Dict}
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60 @param lex: the lexicon to use to translate words to phonetic sybmols
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61
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62 @rtype: C{String}
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63 @returns: the BPF-formatted transcript
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64
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65 @raises IncompleteLexiconError: if there is a word appearing in the
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66 orthographic transcript that is not covered by the lexicon
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67
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68 """
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69
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70 spl = re.compile(r'[\s.,!?"\-]')
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71 words = [w.lower() for w in spl.split(ortho_trans) if w]
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72 ort = []
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73 kan = []
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74
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75 for n, word in enumerate(words):
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76 try:
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77 ort.append("ORT: %d %s" % (n, word))
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78 kan.append("KAN: %d %s" % (n, lexicon[word]))
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79 except KeyError:
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80 raise IncompleteLexiconError("'" + word +
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81 "' not present in lexicon")
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82
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83 nl = u"\n"
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84 return nl.join(ort) + nl + nl.join(kan)
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85
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86
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87 def load_lexicon(lexiconfile):
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88 """ Load the given file as a lexicon dictionary.
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89 Should be a tsv file with two columns, first column
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90 is orthography, second is phonetic transcription.
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91
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92 @type lexiconfile: C{String}
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93 @param lexiconfile: the filename of the lexicon file
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94
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95 @rtype: C{Dict}
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96 @returns: the lexicon, as a dictionary with orthographic entries as keys
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97
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98 """
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99 lex = {}
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100
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101 with open(lexiconfile) as f:
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102 for line in f:
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103 orth, pron = line.split('\t')
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104 lex[orth] = pron
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105
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106 return lex
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107
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108
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109 def list_to_bpf(item_list, lexicon, output_path):
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110 """
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111 Generate a BPF file for each item in this item list.
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112 Items consist of (prompt, ItemURL). URL is used to generate output
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113 file name.
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114
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115 :type documents: list of pyalveo.Document
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116 :param documents: Documents to download
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117
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118 :type output_path: String
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119 :param output_path: directory to download to the documents to
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120 """
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121 if not os.path.exists(output_path):
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122 os.makedirs(output_path)
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123
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124 for prompt, itemURL in item_list:
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125
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126 fname = galaxy_name(itemURL, 'par')
d4c27fdc928b planemo upload commit 7b5663b41b2dc11f9e375b8f386bc31855800bcf-dirty
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127 bpftext = build_bpf(prompt, lexicon)
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128 with open(os.path.join(output_path, fname), 'w') as out:
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129 out.write(bpftext)
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130
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131
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132 def main():
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133 args = parser()
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134 item_list = read_item_list(args.item_list)
d4c27fdc928b planemo upload commit 7b5663b41b2dc11f9e375b8f386bc31855800bcf-dirty
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135 lexicon = load_lexicon(args.lexicon)
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136 list_to_bpf(item_list, lexicon, args.output_path)
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137
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138
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139 if __name__ == '__main__':
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140 main()