Mercurial > repos > earlhaminst > ensembl_get_sequences

annotate get_feature_info.py @ 7:c79ce2342f1e draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
author earlhaminst
date Mon, 17 Feb 2025 14:49:24 +0000
parents 7af66c2b3831
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
parents:
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1 # A simple tool to connect to the Ensembl server and retrieve feature
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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2 # information using the Ensembl REST API.
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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3 import json
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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4 import optparse
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3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
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5 from itertools import islice
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c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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6 from urllib.parse import urljoin
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earlhaminst
parents:
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e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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8 import requests
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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10 parser = optparse.OptionParser()
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c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
parents: 6
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11 parser.add_option("-i", "--input", help="List of Ensembl IDs")
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
parents: 6
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12 parser.add_option(
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
parents: 6
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13 "-e",
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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14 "--expand",
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
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15 type="choice",
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
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16 choices=["0", "1"],
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
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17 default="0",
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
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18 help="Expands the search to include any connected features. e.g. If the object is a gene, its transcripts, translations and exons will be returned as well.",
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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19 )
1
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20
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c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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21 parser.add_option(
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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22 "-f",
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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23 "--format",
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
parents: 6
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24 type="choice",
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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25 choices=["full", "condensed"],
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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26 default="full",
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
parents: 6
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27 help="Specify the formats to emit from this endpoint",
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
parents: 6
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28 )
1
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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29 options, args = parser.parse_args()
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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30 if options.input is None:
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c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
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31 raise Exception("-i option must be specified")
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33
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34 server = "https://rest.ensembl.org"
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
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35 ext = "lookup/id"
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36
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earlhaminst
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37 headers = {"Content-Type": "application/json", "Accept": "application/json"}
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
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38 params = {k: getattr(options, k) for k in ("format", "expand")}
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3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
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40 first = True
3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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41
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earlhaminst
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42 print("{")
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3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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1
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44 with open(options.input) as f:
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3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
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45 while True:
3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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46 ids = [line.strip() for line in islice(f, 50)]
3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
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47 if not ids:
3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
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48 break
3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
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49 if not first:
3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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50 print(",")
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c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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51 data = {"ids": ids}
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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52 r = requests.post(
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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53 urljoin(server, ext),
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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54 params=params,
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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55 headers=headers,
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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56 data=json.dumps(data),
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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57 allow_redirects=False,
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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58 )
1
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59
4
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60 if not r.ok:
3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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61 r.raise_for_status()
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62
4
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earlhaminst
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63 print(r.text[1:-1])
3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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64
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65 first = False
3b686142e9c2 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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66
7
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67 print("}")