Mercurial > repos > iss > eurl_vtec_wgs_pt
annotate scripts/ReMatCh/modules/seqFromWebTaxon.py @ 5:fd9093b9368f draft
planemo upload commit 9af296d380b81335353ebfb8bb6de831e1fbebe1
author | iss |
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date | Thu, 19 Oct 2023 20:27:22 +0000 |
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1 #!/usr/bin/env python3 |
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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 |
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12 import urllib.request |
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13 import urllib.parse |
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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 |
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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 |
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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 |
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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 |
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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) |
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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() |
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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) |
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110 |
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111 else: |
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112 print("taxon name does not exist") |
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113 |
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114 |
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115 def main(): |
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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) |
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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() |