Mercurial > repos > earlhaminst > ensembl_get_sequences

annotate get_genetree.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
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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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1 # A simple tool to connect to the Ensembl server and retrieve genetree using
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 # the Ensembl REST API.
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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3 import optparse
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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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4 from urllib.parse import urljoin
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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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6 import requests
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7
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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8 parser = optparse.OptionParser()
7
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9 parser.add_option(
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10 "--id_type",
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11 type="choice",
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12 default="gene_id",
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13 choices=["gene_id", "gene_tree_id"],
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14 help="Input type",
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15 )
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16 parser.add_option("--species", help="Species name/alias")
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17 parser.add_option("-i", "--input", help="Ensembl ID")
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18 parser.add_option(
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19 "--format",
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20 type="choice",
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21 choices=["json", "orthoxml", "phyloxml", "nh"],
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22 default="json",
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23 help="Output format",
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24 )
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25 parser.add_option(
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26 "-s",
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27 "--sequence",
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28 type="choice",
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29 choices=["protein", "cdna", "none"],
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30 default="protein",
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31 help="The type of sequence to bring back. Setting it to none results in no sequence being returned",
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32 )
1
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33
7
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34 parser.add_option(
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35 "-a",
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36 "--aligned",
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37 type="choice",
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38 choices=["0", "1"],
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39 default="0",
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40 help="Return the aligned string if true. Otherwise, return the original sequence (no insertions)",
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41 )
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42 parser.add_option(
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43 "-c",
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44 "--cigar_line",
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45 type="choice",
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46 choices=["0", "1"],
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47 default="0",
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48 help="Return the aligned sequence encoded in CIGAR format",
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49 )
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50 parser.add_option(
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51 "--nh_format",
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52 type="choice",
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53 choices=[
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54 "full",
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55 "display_label_composite",
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56 "simple",
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57 "species",
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58 "species_short_name",
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59 "ncbi_taxon",
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60 "ncbi_name",
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61 "njtree",
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62 "phylip",
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63 ],
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64 default="simple",
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65 help="The format of a NH (New Hampshire) request",
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66 )
1
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67 options, args = parser.parse_args()
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68 if options.input is None:
7
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69 raise Exception("-i option must be specified")
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70
7
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71 server = "https://rest.ensembl.org"
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72
7
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73 if options.id_type == "gene_id":
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74 ext = f"genetree/member/id/{options.species}/{options.input}"
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75 elif options.id_type == "gene_tree_id":
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76 ext = f"genetree/id/{options.input}"
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77
7
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78 if options.format == "json":
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79 content_type = "application/json"
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80 elif options.format == "orthoxml":
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81 content_type = "text/x-orthoxml+xml"
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82 elif options.format == "phyloxml":
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83 content_type = "text/x-phyloxml+xml"
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84 elif options.format == "nh":
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85 content_type = "text/x-nh"
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
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diff changeset
86 headers = {"Content-Type": content_type}
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
parents: 6
diff changeset
87 params = {
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
parents: 6
diff changeset
88 k: getattr(options, k) for k in ("sequence", "aligned", "cigar_line", "nh_format")
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
parents: 6
diff changeset
89 }
c79ce2342f1e planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
earlhaminst
parents: 6
diff changeset
90 r = requests.get(urljoin(server, ext), params=params, headers=headers)
1
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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parents:
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91
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
parents:
diff changeset
92 if not r.ok:
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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93 r.raise_for_status()
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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94
2
4b7261f484bb planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 099d38157cec200f0a343579ca9babcd8acb266f
earlhaminst
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95 print(r.text)