Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

annotate scripts/ReMatCh/modules/seqFromWebTaxon.py @ 3:0cbed1c0a762 draft default tip

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Tue, 28 Jan 2020 10:42:31 -0500
parents 965517909457
children
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3
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1 #!/usr/bin/env python3
0
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2
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3 # -*- coding: utf-8 -*-
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4
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5 '''
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6 Adapted from:
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7 https://github.com/mickaelsilva/pythonscripts/blob/master/SeqOfWeb/SeqFromWebTaxon.py
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8 mickaelsilva
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9 '''
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10
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11 import sys
3
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12 import urllib.request
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13 import urllib.parse
0
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14 import xml.etree.ElementTree as ET
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15 import time
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16 import argparse
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17 import os
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18
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19
3
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20 def run_seq_from_web_taxon(taxonname, outputfile, getmachine, getOmicsDataType, getLibraryType, print_True):
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21 print('\n' + 'Searching RunIDs for ' + taxonname)
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22
3
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23 taxonname = urllib.parse.quote(taxonname)
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24 url = "http://www.ebi.ac.uk/ena/data/view/Taxon%3A" + taxonname + "&display=xml"
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25 try:
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26 content = urllib.request.urlopen(url)
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27 xml = content.read()
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28 tree = ET.fromstring(xml)
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29 taxonid = ''
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30 except:
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31 print("Ooops!There might be a problem with the ena service, try later or check if the xml is well formated"
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32 " at " + url)
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33 raise
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34 for child in tree:
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35 taxonid = child.get('taxId')
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36 if (taxonid):
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37 print("\n" + "Taxon ID found: " + taxonid)
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38 url = "http://www.ebi.ac.uk/ena/data/warehouse/search?query=%22tax_tree%28" + \
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39 taxonid + \
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40 "%29%22&result=read_run&display=xml"
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41
3
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42 content = urllib.request.urlopen(url)
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43 xml = content.read()
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44 tree = ET.fromstring(xml)
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45
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46 runid = ''
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47 n = 0
3
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48 with open(outputfile, "wt") as f:
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49 f.write('#' + str(time.strftime("%d/%m/%Y")) + "\n")
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50 model = ''
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51 prjid = ''
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52 length_line = 0
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53 omics = ''
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54 libraryType = ''
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55 for child in tree:
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56 runid = child.get('accession')
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57
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58 n += 1
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59
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60 if getmachine is True or getOmicsDataType is True or getLibraryType is True:
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61 for child2 in child:
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62 if child2.tag == 'EXPERIMENT_REF':
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63 expid = child2.get('accession')
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64 url2 = "http://www.ebi.ac.uk/ena/data/view/" + expid + "&display=xml"
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65 content = urllib.request.urlopen(url2)
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66 xml = content.read()
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67 tree2 = ET.fromstring(xml)
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68 try:
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69 for child3 in tree2:
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70 for child4 in child3:
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71 if child4.tag == 'PLATFORM':
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72 for child5 in child4:
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73 for child6 in child5:
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74 if child6.tag == 'INSTRUMENT_MODEL':
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75 model = child6.text
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76 elif child4.tag == 'STUDY_REF':
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77 prjid = child4.get('accession')
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78 elif child4.tag == 'DESIGN':
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79 if getOmicsDataType is True or getLibraryType is True:
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80 for child5 in child4:
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81 if child5.tag == 'LIBRARY_DESCRIPTOR':
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82 for child6 in child5:
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83 if child6.tag == 'LIBRARY_SOURCE' and getOmicsDataType is True:
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84 omics = child6.text
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85 elif child6.tag == 'LIBRARY_LAYOUT' and getLibraryType is True:
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86 libraryType = child6[0].tag
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87 except:
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88 model = 'not found'
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89 omics = 'not found'
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90 libraryType = 'not found'
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91 f.write(str(runid) + "\t" + model + "\t" + prjid + "\t" + omics + "\t" + libraryType + "\n")
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92 if print_True:
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93 line = "run acession %s sequenced on %s from project %s for %s %s end" \
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94 " data" % (runid, model, prjid, omics, libraryType)
0
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95 if length_line < len(line):
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96 length_line = len(line)
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97 sys.stderr.write("\r" + line + str(' ' * (length_line - len(line))))
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98 sys.stderr.flush()
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99 else:
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100 f.write(str(runid) + '\t' * 4 + "\n")
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101 if print_True:
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102 line = "run acession %s" % (runid, prjid)
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103 if length_line < len(line):
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104 length_line = len(line)
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105 sys.stderr.write("\r" + line + str(' ' * (length_line - len(line))))
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106 sys.stderr.flush()
3
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107 print("\n")
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108 print("\n"
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109 "found %s run id's" % n)
0
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110
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111 else:
3
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112 print("taxon name does not exist")
0
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113
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114
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115 def main():
3
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116 parser = argparse.ArgumentParser(description="This program gets a list of sequencing runs and machine were the"
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117 " sequencing was performed, given a taxon name accepted by the"
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118 " European nucleotide Archive")
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119 parser.add_argument('-i', nargs=1, type=str, help='taxon name', metavar='"Streptococcus agalactiae"', required=True)
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120 parser.add_argument('-o', nargs=1, type=str, help='output file name', required=True)
3
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121 parser.add_argument('-g', help='True to include sequencing machine in the output', action='store_true',
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122 required=False)
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123 parser.add_argument('--getOmicsDataType', help='Informs the programme to include OMICS data type'
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124 ' (examples: GENOMIC / TRANSCRIPTOMIC / SYNTHETIC) in the output',
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125 action='store_true')
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126 parser.add_argument('--getLibraryType', help='Informs the programme to include library type'
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127 ' (examples: PAIRED / SINGLE) in the output', action='store_true')
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128
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129 args = parser.parse_args()
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130
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131 getmachine = args.g
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132 taxonname = args.i[0]
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133
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134 outdir = os.path.dirname(os.path.abspath(args.o[0]))
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135 if not os.path.isdir(outdir):
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136 os.makedirs(outdir)
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137 outputfile = os.path.abspath(args.o[0])
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138
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139 getOmicsDataType = args.getOmicsDataType
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140 getLibraryType = args.getLibraryType
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141
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142 run_seq_from_web_taxon(taxonname, outputfile, getmachine, getOmicsDataType, getLibraryType, True)
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143
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144
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145 if __name__ == "__main__":
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146 main()