Mercurial > repos > jpayne > bioproject_to_srr
changeset 0:bbf3b6e6a026 tip
planemo upload commit b'4aa8338dc8bcd7f6c0fb675044ea9d0c045ee7f3\n'
| author | jpayne |
|---|---|
| date | Tue, 05 Dec 2017 11:42:47 -0500 |
| parents | |
| children | |
| files | bio2srr.py bio2srr.xml test-data/test.txt |
| diffstat | 3 files changed, 99 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bio2srr.py Tue Dec 05 11:42:47 2017 -0500 @@ -0,0 +1,58 @@ +#! /usr/bin/env python3 + +"Grab SRR numbers from BioProjects via the EMBL-ENA REST API's." + +import requests +import sys + +sra_exp_query = "http://www.ebi.ac.uk/ebisearch/ws/rest/sra-experiment?query={bioproject}" + +sample = """{ + "hitCount": 2, + "entries": [ + { + "id": "SRX377510", + "source": "sra-experiment" + }, + { + "id": "SRX583279", + "source": "sra-experiment" + } + ], + "facets": [] +}""" + +sra_run_query = "http://www.ebi.ac.uk/ebisearch/ws/rest/sra-run?query={experiment}" + +sample = """{ + "hitCount": 1, + "entries": [ + { + "id": "SRR1029665", + "source": "sra-run" + } + ], + "facets": [] +}""" + +if __name__ == "__main__": + try: + bioproject = sys.argv[1] + b_result = requests.get(sra_exp_query.format(bioproject=bioproject), headers=dict(Accept="application/json")) + b_result.raise_for_status() + if b_result.json()['entries']: + for experiment in [d['id'] for d in b_result.json()['entries']]: + r_result = requests.get(sra_run_query.format(experiment=experiment), headers=dict(Accept="application/json")) + r_result.raise_for_status() + for run in [d['id'] for d in r_result.json()['entries']]: + print(run) + else: + print(f"No results found for '{bioproject}'.", file=sys.stderr) + quit(1) + except IndexError: + raise ValueError("Please provide an NCBI BioProject, NCBI BioSample, EMBL Project, or EMBL Study accession.") + except KeyError as e: + raise ValueError() from e + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bio2srr.xml Tue Dec 05 11:42:47 2017 -0500 @@ -0,0 +1,26 @@ +<tool id="bio2srr" name="Bioproject to SRR" version="0.1.0"> + <description>Retrieve SRR accessions from BioProject or BioSample.</description> + <requirements> + <requirement type="package" version="2.18.4">requests</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + $__tool_directory__/bio2srr.py "$input1" > "$output" + ]]></command> + <inputs> + <param type="text" name="input1" label="BioProject or BioSample" /> + </inputs> + <outputs> + <data format="txt" name="output" /> + </outputs> + <tests> + <test> + <param name="input1" value="NOTHING" /> + <output name="output" file="test.txt" /> + </test> + </tests> + <help><![CDATA[ + Retrieve SRR accessions by BioSample or BioProject. + ]]></help> + <citations> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.txt Tue Dec 05 11:42:47 2017 -0500 @@ -0,0 +1,15 @@ +ERR2130609 +ERR2130611 +ERR2130613 +ERR2130497 +ERR2130499 +ERR2130502 +ERR2130503 +ERR2130506 +ERR2130508 +ERR2130510 +ERR2130512 +ERR2130517 +ERR2130520 +ERR2130521 +ERR2130523 \ No newline at end of file