annotate uniprot.py @ 9:468c71dac78a draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
author bgruening
date Wed, 22 May 2024 21:18:15 +0000
parents af5eccf83605
children 95fb5712344f
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cd2a41c65447 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit fb201f32a92466c2bd8086e91bbf777401f1b489
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1 import argparse
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2 import json
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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3 import re
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cd2a41c65447 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit fb201f32a92466c2bd8086e91bbf777401f1b489
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4 import sys
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5 import time
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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6 import zlib
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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7 from urllib.parse import (
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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8 parse_qs,
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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9 urlencode,
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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10 urlparse,
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11 )
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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12 from xml.etree import ElementTree
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14 import requests
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15 from requests.adapters import (
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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16 HTTPAdapter,
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17 Retry,
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18 )
0
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21 POLLING_INTERVAL = 3
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22 API_URL = "https://rest.uniprot.org"
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25 retries = Retry(total=5, backoff_factor=0.25, status_forcelist=[500, 502, 503, 504])
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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26 session = requests.Session()
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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27 session.mount("https://", HTTPAdapter(max_retries=retries))
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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30 def check_response(response):
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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31 try:
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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32 response.raise_for_status()
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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33 except requests.HTTPError:
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34 print(response.json())
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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35 raise
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38 def submit_id_mapping(from_db, to_db, ids):
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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39 print(f"{from_db} {to_db}")
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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40 request = requests.post(
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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41 f"{API_URL}/idmapping/run",
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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42 data={"from": from_db, "to": to_db, "ids": ",".join(ids)},
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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43 )
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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44 check_response(request)
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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45 return request.json()["jobId"]
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48 def get_next_link(headers):
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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49 re_next_link = re.compile(r'<(.+)>; rel="next"')
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50 if "Link" in headers:
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51 match = re_next_link.match(headers["Link"])
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52 if match:
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53 return match.group(1)
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54
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55
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56 def check_id_mapping_results_ready(job_id):
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57 while True:
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58 request = session.get(f"{API_URL}/idmapping/status/{job_id}")
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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59 check_response(request)
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60 j = request.json()
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61 if "jobStatus" in j:
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62 if j["jobStatus"] == "RUNNING":
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63 print(f"Retrying in {POLLING_INTERVAL}s")
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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64 time.sleep(POLLING_INTERVAL)
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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65 else:
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66 raise Exception(j["jobStatus"])
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67 else:
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68 return bool(j["results"] or j["failedIds"])
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69
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70
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71 def get_batch(batch_response, file_format, compressed):
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72 batch_url = get_next_link(batch_response.headers)
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73 while batch_url:
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74 batch_response = session.get(batch_url)
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75 batch_response.raise_for_status()
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76 yield decode_results(batch_response, file_format, compressed)
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77 batch_url = get_next_link(batch_response.headers)
0
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78
9
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80 def combine_batches(all_results, batch_results, file_format):
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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81 if file_format == "json":
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82 for key in ("results", "failedIds"):
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83 if key in batch_results and batch_results[key]:
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84 all_results[key] += batch_results[key]
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85 elif file_format == "tsv":
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86 return all_results + batch_results[1:]
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87 else:
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88 return all_results + batch_results
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89 return all_results
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90
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91
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92 def get_id_mapping_results_link(job_id):
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93 url = f"{API_URL}/idmapping/details/{job_id}"
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94 request = session.get(url)
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95 check_response(request)
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96 return request.json()["redirectURL"]
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97
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98
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99 def decode_results(response, file_format, compressed):
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100 if compressed:
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101 decompressed = zlib.decompress(response.content, 16 + zlib.MAX_WBITS)
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102 if file_format == "json":
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103 j = json.loads(decompressed.decode("utf-8"))
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104 return j
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105 elif file_format == "tsv":
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106 return [line for line in decompressed.decode("utf-8").split("\n") if line]
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107 elif file_format == "xlsx":
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108 return [decompressed]
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109 elif file_format == "xml":
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110 return [decompressed.decode("utf-8")]
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111 else:
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112 return decompressed.decode("utf-8")
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113 elif file_format == "json":
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114 return response.json()
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115 elif file_format == "tsv":
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116 return [line for line in response.text.split("\n") if line]
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117 elif file_format == "xlsx":
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118 return [response.content]
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119 elif file_format == "xml":
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120 return [response.text]
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121 return response.text
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122
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123
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124 def get_xml_namespace(element):
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125 m = re.match(r"\{(.*)\}", element.tag)
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126 return m.groups()[0] if m else ""
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127
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128
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129 def merge_xml_results(xml_results):
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130 merged_root = ElementTree.fromstring(xml_results[0])
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131 for result in xml_results[1:]:
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132 root = ElementTree.fromstring(result)
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133 for child in root.findall("{http://uniprot.org/uniprot}entry"):
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134 merged_root.insert(-1, child)
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135 ElementTree.register_namespace("", get_xml_namespace(merged_root[0]))
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136 return ElementTree.tostring(merged_root, encoding="utf-8", xml_declaration=True)
0
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137
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138
9
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139 def print_progress_batches(batch_index, size, total):
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140 n_fetched = min((batch_index + 1) * size, total)
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141 print(f"Fetched: {n_fetched} / {total}")
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142
0
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143
9
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144 def get_id_mapping_results_search(url):
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145 parsed = urlparse(url)
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146 query = parse_qs(parsed.query)
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147 file_format = query["format"][0] if "format" in query else "json"
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148 if "size" in query:
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149 size = int(query["size"][0])
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150 else:
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151 size = 500
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152 query["size"] = size
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153 compressed = (
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154 query["compressed"][0].lower() == "true" if "compressed" in query else False
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155 )
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156 parsed = parsed._replace(query=urlencode(query, doseq=True))
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157 url = parsed.geturl()
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158 request = session.get(url)
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159 check_response(request)
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160 results = decode_results(request, file_format, compressed)
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161 total = int(request.headers["x-total-results"])
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162 print_progress_batches(0, size, total)
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163 for i, batch in enumerate(get_batch(request, file_format, compressed), 1):
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164 results = combine_batches(results, batch, file_format)
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165 print_progress_batches(i, size, total)
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166 if file_format == "xml":
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167 return merge_xml_results(results)
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168 return results
0
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169
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170
9
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171 # print(results)
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172 # {'results': [{'from': 'P05067', 'to': 'CHEMBL2487'}], 'failedIds': ['P12345']}
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173
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174 if __name__ == "__main__":
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175 parser = argparse.ArgumentParser(description="retrieve uniprot mapping")
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176 subparsers = parser.add_subparsers(dest="tool")
0
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177
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178 mapping = subparsers.add_parser("map")
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179 mapping.add_argument("f", help="from")
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180 mapping.add_argument("t", help="to")
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181 mapping.add_argument(
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182 "inp",
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183 nargs="?",
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184 type=argparse.FileType("r"),
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185 default=sys.stdin,
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186 help="input file (default: stdin)",
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187 )
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188 mapping.add_argument(
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189 "out",
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190 nargs="?",
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191 type=argparse.FileType("w"),
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192 default=sys.stdout,
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193 help="output file (default: stdout)",
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194 )
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195 mapping.add_argument("--format", default="tab", help="output format")
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196
9
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197 retrieve = subparsers.add_parser("retrieve")
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198 retrieve.add_argument(
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199 "inp",
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200 metavar="in",
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201 nargs="?",
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202 type=argparse.FileType("r"),
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203 default=sys.stdin,
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204 help="input file (default: stdin)",
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205 )
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206 retrieve.add_argument(
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207 "out",
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208 nargs="?",
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209 type=argparse.FileType("w"),
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210 default=sys.stdout,
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211 help="output file (default: stdout)",
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212 )
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213 retrieve.add_argument("-f", "--format", help="specify output format", default="txt")
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214 mapping = subparsers.add_parser("menu")
0
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215
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216 args = parser.parse_args()
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217
9
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218 # code for auto generating the from - to conditional
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219 if args.tool == "menu":
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220 from lxml import etree
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221
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222 request = session.get("https://rest.uniprot.org/configure/idmapping/fields")
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223 check_response(request)
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224 fields = request.json()
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225
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226 tos = dict()
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227 from_cond = etree.Element("conditional", name="from_cond")
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228 from_select = etree.SubElement(
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229 from_cond, "param", name="from", type="select", label="Source database:"
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230 )
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231
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232 rules = dict()
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233 for rule in fields["rules"]:
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234 rules[rule["ruleId"]] = rule["tos"]
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235
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236 for group in fields["groups"]:
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237 group_name = group["groupName"]
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238 group_name = group_name.replace("databases", "DBs")
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239 for item in group["items"]:
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240 if item["to"]:
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241 tos[item["name"]] = f"{group_name} - {item['displayName']}"
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242
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243 for group in fields["groups"]:
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244 group_name = group["groupName"]
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245 group_name = group_name.replace("databases", "DBs")
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246 for item in group["items"]:
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247 if not item["from"]:
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248 continue
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249 option = etree.SubElement(from_select, "option", value=item["name"])
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250 option.text = f"{group_name} - {item['displayName']}"
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251 when = etree.SubElement(from_cond, "when", value=item["name"])
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252
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253 to_select = etree.SubElement(
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254 when, "param", name="to", type="select", label="Target database:"
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255 )
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256 ruleId = item["ruleId"]
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257 for to in rules[ruleId]:
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258 option = etree.SubElement(to_select, "option", value=to)
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259 option.text = tos[to]
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260 etree.indent(from_cond, space=" ")
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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261 print(etree.tostring(from_cond, pretty_print=True, encoding="unicode"))
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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262 sys.exit(0)
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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263
7
bfdc6a7ffd3a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit ddbed5f0b0879b4a001d2da6a521b0c9a39c1e7b"
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264 # get the IDs from the file as sorted list
bfdc6a7ffd3a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit ddbed5f0b0879b4a001d2da6a521b0c9a39c1e7b"
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265 # (sorted is convenient for testing)
bfdc6a7ffd3a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit ddbed5f0b0879b4a001d2da6a521b0c9a39c1e7b"
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266 query = set()
bfdc6a7ffd3a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit ddbed5f0b0879b4a001d2da6a521b0c9a39c1e7b"
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267 for line in args.inp:
bfdc6a7ffd3a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit ddbed5f0b0879b4a001d2da6a521b0c9a39c1e7b"
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268 query.add(line.strip())
bfdc6a7ffd3a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit ddbed5f0b0879b4a001d2da6a521b0c9a39c1e7b"
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269 query = sorted(query)
0
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270
9
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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271 if args.tool == "map":
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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272 job_id = submit_id_mapping(from_db=args.f, to_db=args.t, ids=query)
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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273 elif args.tool == "retrieve":
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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274 job_id = submit_id_mapping(
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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275 from_db="UniProtKB_AC-ID", to_db="UniProtKB", ids=query
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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276 )
0
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277
9
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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278 if check_id_mapping_results_ready(job_id):
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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279 link = get_id_mapping_results_link(job_id)
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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280 link = f"{link}?format={args.format}"
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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281 print(link)
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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282 results = get_id_mapping_results_search(link)
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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283
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284 if not isinstance(results, str):
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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285 results = "\n".join(results)
468c71dac78a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
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286 args.out.write(f"{results}\n")