planemo upload commit bce663a3ac9d4b5f86a3becf93c7639221ee01ea
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jpayne |
| date |
Thu, 20 Dec 2018 11:04:53 -0500 |
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02ac32a00e25 |
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556cac4fb538 |
| rev |
line source |
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jpayne@0
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1 #! /usr/bin/env python3
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2
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3 "Grab SRR numbers from BioProjects via the EMBL-ENA REST API's."
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4
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5 import requests
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6 import sys
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7
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8 sra_exp_query = "http://www.ebi.ac.uk/ebisearch/ws/rest/sra-experiment?query={bioproject}"
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9
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10 sample = """{
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11 "hitCount": 2,
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12 "entries": [
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13 {
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14 "id": "SRX377510",
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15 "source": "sra-experiment"
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16 },
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17 {
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18 "id": "SRX583279",
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19 "source": "sra-experiment"
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20 }
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21 ],
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22 "facets": []
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23 }"""
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24
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25 sra_run_query = "http://www.ebi.ac.uk/ebisearch/ws/rest/sra-run?query={experiment}"
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26
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27 sample = """{
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28 "hitCount": 1,
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29 "entries": [
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30 {
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31 "id": "SRR1029665",
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32 "source": "sra-run"
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33 }
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34 ],
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35 "facets": []
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36 }"""
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37
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38 if __name__ == "__main__":
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39 try:
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40 bioproject = sys.argv[1]
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41 b_result = requests.get(sra_exp_query.format(bioproject=bioproject), headers=dict(Accept="application/json"))
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42 b_result.raise_for_status()
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43 if b_result.json()['entries']:
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44 for experiment in [d['id'] for d in b_result.json()['entries']]:
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45 r_result = requests.get(sra_run_query.format(experiment=experiment), headers=dict(Accept="application/json"))
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46 r_result.raise_for_status()
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47 for run in [d['id'] for d in r_result.json()['entries']]:
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48 print(run)
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49 else:
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50 print(f"No results found for '{bioproject}'.", file=sys.stderr)
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51 quit(1)
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52 except IndexError:
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53 raise ValueError("Please provide an NCBI BioProject, NCBI BioSample, EMBL Project, or EMBL Study accession.")
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54 except KeyError as e:
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55 raise ValueError() from e
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56
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57
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58
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