Mercurial > repos > jpayne > bioproject_to_srr
annotate bio2srr.py @ 0:bbf3b6e6a026 tip
planemo upload commit b'4aa8338dc8bcd7f6c0fb675044ea9d0c045ee7f3\n'
| author | jpayne |
|---|---|
| date | Tue, 05 Dec 2017 11:42:47 -0500 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@0 | 1 #! /usr/bin/env python3 |
| jpayne@0 | 2 |
| jpayne@0 | 3 "Grab SRR numbers from BioProjects via the EMBL-ENA REST API's." |
| jpayne@0 | 4 |
| jpayne@0 | 5 import requests |
| jpayne@0 | 6 import sys |
| jpayne@0 | 7 |
| jpayne@0 | 8 sra_exp_query = "http://www.ebi.ac.uk/ebisearch/ws/rest/sra-experiment?query={bioproject}" |
| jpayne@0 | 9 |
| jpayne@0 | 10 sample = """{ |
| jpayne@0 | 11 "hitCount": 2, |
| jpayne@0 | 12 "entries": [ |
| jpayne@0 | 13 { |
| jpayne@0 | 14 "id": "SRX377510", |
| jpayne@0 | 15 "source": "sra-experiment" |
| jpayne@0 | 16 }, |
| jpayne@0 | 17 { |
| jpayne@0 | 18 "id": "SRX583279", |
| jpayne@0 | 19 "source": "sra-experiment" |
| jpayne@0 | 20 } |
| jpayne@0 | 21 ], |
| jpayne@0 | 22 "facets": [] |
| jpayne@0 | 23 }""" |
| jpayne@0 | 24 |
| jpayne@0 | 25 sra_run_query = "http://www.ebi.ac.uk/ebisearch/ws/rest/sra-run?query={experiment}" |
| jpayne@0 | 26 |
| jpayne@0 | 27 sample = """{ |
| jpayne@0 | 28 "hitCount": 1, |
| jpayne@0 | 29 "entries": [ |
| jpayne@0 | 30 { |
| jpayne@0 | 31 "id": "SRR1029665", |
| jpayne@0 | 32 "source": "sra-run" |
| jpayne@0 | 33 } |
| jpayne@0 | 34 ], |
| jpayne@0 | 35 "facets": [] |
| jpayne@0 | 36 }""" |
| jpayne@0 | 37 |
| jpayne@0 | 38 if __name__ == "__main__": |
| jpayne@0 | 39 try: |
| jpayne@0 | 40 bioproject = sys.argv[1] |
| jpayne@0 | 41 b_result = requests.get(sra_exp_query.format(bioproject=bioproject), headers=dict(Accept="application/json")) |
| jpayne@0 | 42 b_result.raise_for_status() |
| jpayne@0 | 43 if b_result.json()['entries']: |
| jpayne@0 | 44 for experiment in [d['id'] for d in b_result.json()['entries']]: |
| jpayne@0 | 45 r_result = requests.get(sra_run_query.format(experiment=experiment), headers=dict(Accept="application/json")) |
| jpayne@0 | 46 r_result.raise_for_status() |
| jpayne@0 | 47 for run in [d['id'] for d in r_result.json()['entries']]: |
| jpayne@0 | 48 print(run) |
| jpayne@0 | 49 else: |
| jpayne@0 | 50 print(f"No results found for '{bioproject}'.", file=sys.stderr) |
| jpayne@0 | 51 quit(1) |
| jpayne@0 | 52 except IndexError: |
| jpayne@0 | 53 raise ValueError("Please provide an NCBI BioProject, NCBI BioSample, EMBL Project, or EMBL Study accession.") |
| jpayne@0 | 54 except KeyError as e: |
| jpayne@0 | 55 raise ValueError() from e |
| jpayne@0 | 56 |
| jpayne@0 | 57 |
| jpayne@0 | 58 |