Mercurial > repos > bgruening > uniprot_rest_interface

annotate uniprot.py @ 9:f31d8d59ffb6 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
author bgruening
date Tue, 06 Aug 2024 14:49:34 +0000
parents d2ad6e2c55d1
children
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357dc1f016f5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit fb201f32a92466c2bd8086e91bbf777401f1b489
bgruening
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1 import argparse
9
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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2 import json
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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3 import re
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357dc1f016f5 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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f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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5 import time
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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6 import zlib
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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7 from time import sleep
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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8 from urllib.parse import (
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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9 parse_qs,
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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10 urlencode,
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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11 urlparse,
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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12 )
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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13 from xml.etree import ElementTree
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15 import requests
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f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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16 from requests.adapters import (
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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17 HTTPAdapter,
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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18 Retry,
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19 )
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22 BATCH_SIZE = 50000 # Limit at UniProt is 100k
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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23 POLLING_INTERVAL = 5
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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24 API_URL = "https://rest.uniprot.org"
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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27 retries = Retry(total=5, backoff_factor=0.25, status_forcelist=[500, 502, 503, 504])
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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28 session = requests.Session()
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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29 session.mount("https://", HTTPAdapter(max_retries=retries))
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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32 def check_response(response):
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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33 try:
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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34 response.raise_for_status()
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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35 except requests.HTTPError:
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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36 raise
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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39 def submit_id_mapping(from_db, to_db, ids):
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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40 print(f"{from_db} {to_db}")
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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41 request = requests.post(
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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42 f"{API_URL}/idmapping/run",
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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43 data={"from": from_db, "to": to_db, "ids": ",".join(ids)},
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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44 )
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45 check_response(request)
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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46 return request.json()["jobId"]
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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47
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48
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49 def get_next_link(headers):
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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50 re_next_link = re.compile(r'<(.+)>; rel="next"')
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51 if "Link" in headers:
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52 match = re_next_link.match(headers["Link"])
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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53 if match:
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54 return match.group(1)
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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57 def check_id_mapping_results_ready(job_id):
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58 while True:
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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59 request = session.get(f"{API_URL}/idmapping/status/{job_id}")
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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60 check_response(request)
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61 j = request.json()
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62 if "jobStatus" in j:
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63 if j["jobStatus"] in ["NEW", "RUNNING"]:
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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64 print(f"Retrying in {POLLING_INTERVAL}s")
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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65 time.sleep(POLLING_INTERVAL)
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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66 else:
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67 raise Exception(j["jobStatus"])
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68 else:
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69 return bool(j["results"] or j["failedIds"])
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70
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71
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72 def get_batch(batch_response, file_format, compressed):
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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73 batch_url = get_next_link(batch_response.headers)
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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74 while batch_url:
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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75 batch_response = session.get(batch_url)
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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76 batch_response.raise_for_status()
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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77 yield decode_results(batch_response, file_format, compressed)
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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78 batch_url = get_next_link(batch_response.headers)
0
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79
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81 def combine_batches(all_results, batch_results, file_format):
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82 if file_format == "json":
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83 for key in ("results", "failedIds"):
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84 if key in batch_results and batch_results[key]:
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85 all_results[key] += batch_results[key]
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86 elif file_format == "tsv":
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87 return all_results + batch_results[1:]
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88 else:
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89 return all_results + batch_results
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90 return all_results
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91
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92
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93 def get_id_mapping_results_link(job_id):
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94 url = f"{API_URL}/idmapping/details/{job_id}"
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95 request = session.get(url)
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96 check_response(request)
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97 return request.json()["redirectURL"]
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98
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99
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100 def decode_results(response, file_format, compressed):
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101 if compressed:
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102 decompressed = zlib.decompress(response.content, 16 + zlib.MAX_WBITS)
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103 if file_format == "json":
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104 j = json.loads(decompressed.decode("utf-8"))
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105 return j
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106 elif file_format in ["tsv", "gff"]:
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107 return [line for line in decompressed.decode("utf-8").split("\n") if line]
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108 elif file_format == "xlsx":
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109 return [decompressed]
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110 elif file_format == "xml":
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111 return [decompressed.decode("utf-8")]
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112 else:
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113 return decompressed.decode("utf-8")
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114 elif file_format == "json":
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115 return response.json()
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116 elif file_format in ["tsv", "gff"]:
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117 return [line for line in response.text.split("\n") if line]
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118 elif file_format == "xlsx":
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119 return [response.content]
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120 elif file_format == "xml":
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121 return [response.text]
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122 return response.text
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123
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124
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125 def get_xml_namespace(element):
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126 m = re.match(r"\{(.*)\}", element.tag)
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127 return m.groups()[0] if m else ""
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128
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129
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130 def merge_xml_results(xml_results):
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131 merged_root = ElementTree.fromstring(xml_results[0])
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132 for result in xml_results[1:]:
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133 root = ElementTree.fromstring(result)
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134 for child in root.findall("{http://uniprot.org/uniprot}entry"):
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135 merged_root.insert(-1, child)
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136 ElementTree.register_namespace("", get_xml_namespace(merged_root[0]))
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137 return ElementTree.tostring(merged_root, encoding="utf-8", xml_declaration=True)
0
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138
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139
9
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140 def print_progress_batches(batch_index, size, total):
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141 n_fetched = min((batch_index + 1) * size, total)
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142 print(f"Fetched: {n_fetched} / {total}")
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143
0
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144
9
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145 def get_id_mapping_results_search(url, first):
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146 parsed = urlparse(url)
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147 query = parse_qs(parsed.query)
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148 file_format = query["format"][0] if "format" in query else "json"
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149 if "size" in query:
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150 size = int(query["size"][0])
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151 else:
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152 size = 500
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153 query["size"] = size
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154 compressed = (
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155 query["compressed"][0].lower() == "true" if "compressed" in query else False
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156 )
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157 parsed = parsed._replace(query=urlencode(query, doseq=True))
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158 url = parsed.geturl()
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159 request = session.get(url)
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160 check_response(request)
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161 results = decode_results(request, file_format, compressed)
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162 total = int(request.headers["x-total-results"])
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163 print_progress_batches(0, size, total)
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164 for i, batch in enumerate(get_batch(request, file_format, compressed), 1):
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165 results = combine_batches(results, batch, file_format)
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166 print_progress_batches(i, size, total)
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167 if len(results) > 1 and file_format == "tsv" and not first:
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168 results = results[1:]
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169 if file_format == "xml":
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170 return merge_xml_results(results)
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171 return results
0
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172
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173
9
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174 # print(results)
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175 # {'results': [{'from': 'P05067', 'to': 'CHEMBL2487'}], 'failedIds': ['P12345']}
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176
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177 if __name__ == "__main__":
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178 parser = argparse.ArgumentParser(description="retrieve uniprot mapping")
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179 subparsers = parser.add_subparsers(dest="tool")
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180
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181 mapping = subparsers.add_parser("map")
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182 mapping.add_argument("f", help="from")
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183 mapping.add_argument("t", help="to")
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184 mapping.add_argument(
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185 "inp",
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186 nargs="?",
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187 type=argparse.FileType("r"),
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188 default=sys.stdin,
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189 help="input file (default: stdin)",
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190 )
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191 mapping.add_argument(
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192 "out",
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193 nargs="?",
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194 type=argparse.FileType("w"),
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195 default=sys.stdout,
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196 help="output file (default: stdout)",
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197 )
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198 mapping.add_argument("--format", default="tab", help="output format")
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199
9
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200 retrieve = subparsers.add_parser("retrieve")
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201 retrieve.add_argument(
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202 "inp",
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203 metavar="in",
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204 nargs="?",
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205 type=argparse.FileType("r"),
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206 default=sys.stdin,
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207 help="input file (default: stdin)",
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208 )
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209 retrieve.add_argument(
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210 "out",
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211 nargs="?",
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212 type=argparse.FileType("w"),
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213 default=sys.stdout,
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214 help="output file (default: stdout)",
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215 )
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216 retrieve.add_argument("-f", "--format", help="specify output format", default="txt")
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217 mapping = subparsers.add_parser("menu")
0
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218
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219 args = parser.parse_args()
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220
9
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221 # code for auto generating the from - to conditional
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222 if args.tool == "menu":
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223 from lxml import etree
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224
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225 request = session.get("https://rest.uniprot.org/configure/idmapping/fields")
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226 check_response(request)
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227 fields = request.json()
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228
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229 tos = dict()
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230 from_cond = etree.Element("conditional", name="from_cond")
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231 from_select = etree.SubElement(
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232 from_cond, "param", name="from", type="select", label="Source database:"
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233 )
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234
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235 rules = dict()
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236 for rule in fields["rules"]:
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237 rules[rule["ruleId"]] = rule["tos"]
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238
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239 for group in fields["groups"]:
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240 group_name = group["groupName"]
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241 group_name = group_name.replace("databases", "DBs")
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242 for item in group["items"]:
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243 if item["to"]:
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244 tos[item["name"]] = f"{group_name} - {item['displayName']}"
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245
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246 for group in fields["groups"]:
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247 group_name = group["groupName"]
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248 group_name = group_name.replace("databases", "DBs")
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249 for item in group["items"]:
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250 if not item["from"]:
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251 continue
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252 option = etree.SubElement(from_select, "option", value=item["name"])
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253 option.text = f"{group_name} - {item['displayName']}"
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254 when = etree.SubElement(from_cond, "when", value=item["name"])
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255
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256 to_select = etree.SubElement(
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257 when, "param", name="to", type="select", label="Target database:"
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258 )
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259 ruleId = item["ruleId"]
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260 for to in rules[ruleId]:
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261 option = etree.SubElement(to_select, "option", value=to)
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262 option.text = tos[to]
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263 etree.indent(from_cond, space=" ")
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264 print(etree.tostring(from_cond, pretty_print=True, encoding="unicode"))
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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265 sys.exit(0)
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266
7
b1cc2c5bde0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit ddbed5f0b0879b4a001d2da6a521b0c9a39c1e7b"
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267 # get the IDs from the file as sorted list
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268 # (sorted is convenient for testing)
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269 query = set()
b1cc2c5bde0e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit ddbed5f0b0879b4a001d2da6a521b0c9a39c1e7b"
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270 for line in args.inp:
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271 query.add(line.strip())
9
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272 query = list(query)
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273 results = []
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274 first = True # if False the header is removed
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275 while len(query) > 0:
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276 batch = query[:BATCH_SIZE]
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277 query = query[BATCH_SIZE:]
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278 print(f"processing {len(batch)} left {len(query)}")
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279 if args.tool == "map":
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280 job_id = submit_id_mapping(from_db=args.f, to_db=args.t, ids=batch)
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281 elif args.tool == "retrieve":
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282 job_id = submit_id_mapping(from_db="UniProtKB_AC-ID", to_db="UniProtKB", ids=batch)
0
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283
9
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284 if check_id_mapping_results_ready(job_id):
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285 link = get_id_mapping_results_link(job_id)
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286 link = f"{link}?format={args.format}"
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287 print(link)
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288 results.extend(get_id_mapping_results_search(link, first))
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289 first = False
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290 print(f"got {len(results)} results so far")
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291 if len(query):
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292 sleep(5)
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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293
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294 if not isinstance(results, str):
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295 results = "\n".join(results)
f31d8d59ffb6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 1c020106d4d7f957c9f1ec0d9885bbb2d56e70e7
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296 args.out.write(f"{results}\n")