インストール

Pythonのツールなのでpipでインストールする。

pip intall ffq

ヘルプ

ffq -h

とくに難しいオプションはない。

ffq 0.0.2: Fetch run information from the European Nucleotide Archive (ENA).

positional arguments:
  IDs         Can be a SRA / ENA Run Accessions or Study Accessions, GEO Study
              Accessions, DOIs or paper titles.

optional arguments:
  -h, --help  Show this help message and exit
  -o OUT      Path to JSON file to write run information. If `--split` is
              used, path to directory in which to place JSON files. (default:
              standard out)
  -t TYPE     The type of term used to query data. Can be one of SRR, ERR,
              DRR, SRP, ERP, DRP, GSE, DOI (default: SRR)
  --split     Split runs into their own files.
  --verbose   Print debugging information

SRR を検索してみる

ffq SRR1000000

出力はJSON形式である。

{
    "SRR1000000": {
        "accession": "SRR1000000",
        "experiment": {
            "accession": "SRX357886",
            "title": "Illumina HiSeq 2000 paired end sequencing",
            "platform": "ILLUMINA",
            "instrument": "Illumina HiSeq 2000"
        },
        "study": {
            "accession": "SRP056282",
            "title": "Allelic Spectrum in Common Disease:Sequence from participants in the FUSION study",
            "abstract": "This study is part of a re-sequencing project to identify variants associated with metabolic syndrome traits in a Finnish cohort. Metabolic syndrome (MetS) increases the risk of cardiovascular disease and diabetes, and prevalence is estimated to be as high as 25% in the United States. MetS is characterized via measure of triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), systolic blood pressure (SBP), diastolic blood pressure (DBP), fasting plasma glucose (FG), body mass index (BMI) and waist-to-hip ratio (WHR). Closely related traits include low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), fasting plasma insulin (FI) and height (HT).  Seventeen loci associated with TG, HDL-C, LDL-C, TC, FG, and FI (Kathiresan et al. 2008, Willer et al. 2008, Sabatti et al. 2009, Dupuis et al. 2010, Teslovich et al. 2010) were prioritized for sequencing. At each locus, protein-coding regions and 5'' and 3'' untranslated regions of genes... (for more see dbGaP study page.)"
        },
        "sample": {
            "accession": "SRS485766",
            "title": "DNA sample from a human female participant in the dbGaP study \"Sequence Data From Participants in the FUSION Study\"",
            "organism": "Homo sapiens",
            "attributes": {
                "gap_accession": "phs000702",
                "gap_parent_phs": "phs000867",
                "submitter handle": "NIDDK",
                "biospecimen repository": "NIDDK",
                "study name": "Sequence Data From Participants in the FUSION Study",
                "study design": "Case-Control",
                "biospecimen repository sample id": "FU04357",
                "submitted sample id": "FU04357",
                "submitted subject id": "656230",
                "gap_sample_id": "894937",
                "gap_subject_id": "237778",
                "sex": "female",
                "analyte type": "DNA",
                "gap_consent_code": "1",
                "gap_consent_short_name": "GRU-IRB",
                "ENA-FIRST-PUBLIC": "2013-10-01",
                "ENA-LAST-UPDATE": "2018-04-12"
            }
        },
        "title": "Illumina HiSeq 2000 paired end sequencing",
        "files": []
    }
}

生JSONファイルだと、情報量が多くてわかりにくいと思われる場合は、jqコマンドを用いて情報を整理すると良いと思う。

ffq SRR1000000 | jq '.SRR1000000.study.title'
# "Allelic Spectrum in Common Disease:Sequence from participants in the FUSION study"

この記事は以上です。

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