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Merge pull request #146 from sanger-tol/dev
Release 2.0.0
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| Original file line number | Diff line number | Diff line change |
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@@ -20,3 +20,4 @@ lint: | |
| multiqc_config: | ||
| - report_comment | ||
| actions_ci: false | ||
| template_strings: False | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| #File_source,File_type,Url,Output_type | ||
| ENA,Assembly,https://www.ebi.ac.uk/ena/browser/api/xml/ASSEMBLY_ACCESSION,xml | ||
| ENA,Bioproject,https://www.ebi.ac.uk/ena/browser/api/xml/BIOPROJECT_ACCESSION,xml | ||
| ENA,Biosample,https://www.ebi.ac.uk/ena/browser/api/xml/BIOSAMPLE_ACCESSION,xml | ||
| ENA,Taxonomy,https://www.ebi.ac.uk/ena/browser/api/xml/TAXONOMY_ID,xml | ||
| NCBI,Assembly,https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/ASSEMBLY_ACCESSION/dataset_report?filters.exclude_atypical=false&filters.assembly_version=current&chromosomes=1&chromosomes=2&chromosomes=3&chromosomes=X&chromosomes=Y&chromosomes=M,json | ||
| NCBI,Taxonomy,https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=TAXONOMY_ID,xml | ||
| GOAT,Assembly,http://goat.genomehubs.org/api/v2/record?recordId=ASSEMBLY_ACCESSION&result=assembly&taxonomy=ncbi,json | ||
| COPO,Biosample,https://copo-project.org/api/sample/biosampleAccession/BIOSAMPLE_ACCESSION?standard=tol&return_type=json,json |
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| <?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article> | ||
| <article> | ||
| <body> | ||
| <sec> | ||
| <title>Species taxonomy</title> | ||
| <p>{{ TAX_STRING }}; | ||
| <italic>{{ GENUS }}</italic>; | ||
| <italic>{{ GENUS_SPECIES }}</italic> ($TAXONOMY_AUTHORITY) (NCBI:txid{{ NCBI_TAXID }}) {{ TEST_NOT_REPLACED }}. | ||
| </p> | ||
| </sec> | ||
| <sec> | ||
| <table> | ||
| <thead> | ||
| <tr> | ||
| <th align="center" valign="top">INSDC accession</th> | ||
| <th align="center" valign="top">Chromosome</th> | ||
| <th align="center" valign="top">Length (Mb)</th> | ||
| <th align="center" valign="top">GC%</th> | ||
| </tr> | ||
| </thead> | ||
| <tbody> | ||
| {% for chromosome in CHR_TABLE %} | ||
| <tr> | ||
| <td align="left" valign="top">{{ chromosome.get('Accession') }}</td> | ||
| <td align="center" valign="top">{{ chromosome.get('Chromosome') }}</td> | ||
| <td align="center" valign="top">{{ chromosome.get('Length') }}</td> | ||
| <td align="center" valign="top">{{ chromosome.get('GC') }}</td> | ||
| </tr> | ||
| {% endfor %} | ||
| </tbody> | ||
| </table> | ||
| </sec> | ||
| </body> | ||
| </article> |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,5 +1,4 @@ | ||
| sample,datatype,datafile | ||
| uoEpiScrs1,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Epithemia_sp._CRS-2021b/genomic_data/uoEpiScrs1/pacbio/m64228e_220617_134154.ccs.bc1015_BAK8B_OA--bc1015_BAK8B_OA.rmdup.subset.bam | ||
| uoEpiScrs1,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Epithemia_sp._CRS-2021b/genomic_data/uoEpiScrs1/pacbio/m64016e_220621_193126.ccs.bc1008_BAK8A_OA--bc1008_BAK8A_OA.rmdup.subset.bam | ||
| uoEpiScrs1c,hic,https://tolit.cog.sanger.ac.uk/test-data/Epithemia_sp._CRS-2021b/analysis/uoEpiScrs1.1/read_mapping/hic/GCA_946965045.1.unmasked.hic.uoEpiScrs1.subsampled.cram | ||
| uoEpiScrs1b,hic,https://tolit.cog.sanger.ac.uk/test-data/Epithemia_sp._CRS-2021b/analysis/uoEpiScrs1.1/read_mapping/hic/GCA_946965045.1.unmasked.hic.uoEpiScrs1.subsampled.bam | ||
| ilCerPisi1,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Ceramica_pisi/genomic_data/ilCerPisi1/pacbio/m84047_230817_174414_s3.ccs.bc2048.subsampled.bam | ||
| ilCerPisi1,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Ceramica_pisi/genomic_data/ilCerPisi1/pacbio/m64097e_230309_154741.ccs.bc1012_BAK8A_OA--bc1012_BAK8A_OA.subsampled.bam | ||
| ilCerPisi1,hic,https://tolit.cog.sanger.ac.uk/test-data/Ceramica_pisi/analysis/ilCerPisi1.1/read_mapping/hic/GCA_963859965.1.unmasked.hic.ilCerPisi2.subsampled.cram |
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| #!/usr/bin/env python3 | ||
|
|
||
| import os | ||
| import sys | ||
| import requests | ||
| import argparse | ||
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| def parse_args(args=None): | ||
| Description = "Use the genome assembly accession to fetch additional infromation on genome from ENA" | ||
| Epilog = "Example usage: python check_parameters.py --assembly --wgs_biosample --output" | ||
|
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| parser = argparse.ArgumentParser(description=Description, epilog=Epilog) | ||
| parser.add_argument("--assembly", required=True, help="The INSDC accession for the assembly") | ||
| parser.add_argument("--wgs_biosample", required=True, help="The biosample accession for the WGS data") | ||
| parser.add_argument("--hic_biosample", required=False, help="The biosample accession for the Hi-C data") | ||
| parser.add_argument("--rna_biosample", required=False, help="The biosample accession for the RNASeq data") | ||
| parser.add_argument("--output", required=True, help="Output file path") | ||
| return parser.parse_args() | ||
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| def make_dir(path): | ||
| if len(path) > 0: | ||
| os.makedirs(path, exist_ok=True) | ||
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| def fetch_assembly_data(assembly, wgs_biosample, hic_biosample, rna_biosample, output_file): | ||
| url = f"https://www.ebi.ac.uk/ena/portal/api/search?query=assembly_set_accession%3D%22{assembly}%22&result=assembly&fields=assembly_set_accession%2Ctax_id%2Cscientific_name%2Cstudy_accession&limit=0&download=true&format=json" | ||
| response = requests.get(url) | ||
|
|
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| if response.status_code == 200: | ||
| assembly_data = response.json() | ||
| taxon_id = assembly_data[0].get("tax_id", None) | ||
| species = assembly_data[0].get("scientific_name", None).replace(" ", "_") | ||
| study = assembly_data[0].get("study_accession", None) | ||
| params = [assembly, species, taxon_id] | ||
| header = ["assembly", "species", "taxon_id"] | ||
|
|
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| if study: | ||
| study_url = f"https://www.ebi.ac.uk/ena/portal/api/search?query=study_accession%3D%22{study}%22&result=study&fields=parent_study_accession&limit=0&download=true&format=json" | ||
| study_response = requests.get(study_url) | ||
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| if study_response.status_code == 200: | ||
| study_data = study_response.json() | ||
| studies = study_data[0].get("parent_study_accession").split(";") | ||
| params.append(studies[0]) | ||
| header.append("bioproject") | ||
|
|
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| else: | ||
| raise AssertionError(f"Could not determine the Bioproject linked to this assembly {assembly}\n") | ||
| else: | ||
| raise AssertionError(f"Could not determine the Bioproject linked to this assembly {assembly}\n") | ||
|
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| # Validate wgs_biosample | ||
| wgs_url = f"https://www.ebi.ac.uk/ena/portal/api/search?query=sample_accession%3D%22{wgs_biosample}%22&result=sample&fields=sample_accession%2Ctax_id&limit=0&download=true&format=json" | ||
| wgs_response = requests.get(wgs_url) | ||
|
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| if wgs_response.status_code == 200: | ||
| wgs_data = wgs_response.json() | ||
| tax_id = wgs_data[0].get("tax_id") | ||
|
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| if tax_id != taxon_id: | ||
| raise AssertionError( | ||
| f"The WGS biosample taxon id: {tax_id} does not match the assembly taxon id: {taxon_id}\n" | ||
| ) | ||
| else: | ||
| params.append(wgs_biosample) | ||
| header.append("wgs_biosample") | ||
|
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| else: | ||
| raise AssertionError(f"The WGS biosample id: {wgs_biosample} could not retrieved from ENA\n") | ||
|
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| # Validate hic_biosample | ||
| if hic_biosample and hic_biosample != "null": | ||
| print(hic_biosample) | ||
| hic_url = f"https://www.ebi.ac.uk/ena/portal/api/search?query=sample_accession%3D%22{hic_biosample}%22&result=sample&fields=sample_accession%2Ctax_id&limit=0&download=true&format=json" | ||
| hic_response = requests.get(hic_url) | ||
|
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| if hic_response.status_code == 200: | ||
| hic_data = hic_response.json() | ||
| hic_tax_id = hic_data[0].get("tax_id") | ||
|
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| if hic_tax_id != taxon_id: | ||
| raise AssertionError( | ||
| f"The Hi-C biosample taxon id: {hic_tax_id} does not match the assembly taxon id: {taxon_id}\n" | ||
| ) | ||
| else: | ||
| header.append("hic_biosample") | ||
| params.append(hic_biosample) | ||
|
|
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| else: | ||
| raise AssertionError(f"The Hi-C biosample id: {hic_biosample} could not retrieved from ENA\n") | ||
| else: | ||
| header.append("hic_biosample") | ||
| params.append("null") | ||
|
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| # Validate rna_biosample | ||
| if rna_biosample and rna_biosample != "null": | ||
| rna_url = f"https://www.ebi.ac.uk/ena/portal/api/search?query=sample_accession%3D%22{rna_biosample}%22&result=sample&fields=sample_accession%2Ctax_id&limit=0&download=true&format=json" | ||
| rna_response = requests.get(rna_url) | ||
|
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| if rna_response.status_code == 200: | ||
| rna_data = rna_response.json() | ||
| rna_tax_id = rna_data[0].get("tax_id") | ||
|
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| if rna_tax_id != taxon_id: | ||
| raise AssertionError( | ||
| f"The RNASeq biosample taxon id: {rna_tax_id} does not match the assembly taxon id: {taxon_id}\n" | ||
| ) | ||
| else: | ||
| header.append("rna_biosample") | ||
| params.append(rna_biosample) | ||
|
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| else: | ||
| raise AssertionError(f"The RNASeq biosample id: {rna_biosample} could not retrieved from ENA\n") | ||
|
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| else: | ||
| header.append("rna_biosample") | ||
| params.append("null") | ||
|
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| with open(output_file, "w") as fout: | ||
| # Write header | ||
| fout.write(",".join(header) + "\n") | ||
| fout.write(",".join(params) + "\n") | ||
|
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| return output_file | ||
| else: | ||
| raise AssertionError(f"The assemby accession: {assembly} was not found\n") | ||
|
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| def main(args=None): | ||
| args = parse_args(args) | ||
| hic_biosample = args.hic_biosample | ||
| rna_biosample = args.rna_biosample | ||
| fetch_assembly_data( | ||
| args.assembly, | ||
| args.wgs_biosample, | ||
| hic_biosample, | ||
| rna_biosample, | ||
| args.output, | ||
| ) | ||
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| if __name__ == "__main__": | ||
| sys.exit(main()) |
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