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parsing kegg page

I was wondering how I can parse, a page on kegg like this, given the "fpr:FP2_11210"

http://www.kegg.jp/dbget-bin/www_bget?fpr:FP2_11210

I already looked into two Bioconductor packages "pathway" and "Kegg Graph" but didn't find something relevant. I was hoping somebody already might have some script in his toolbox. Thank you

kegg
• 2,721 views • link
written by Quak Quak

Do you know about KEGG REST API?

What exactly you want to do? The page you linked doesn't seem to be intended as parseable, rather, it is meant for human consumption.

• 0 views • link
written by h.mon h.mon

2 answers

use TOGOWS: http://togows.dbcls.jp/

$ wget -q -O - "http://togows.org/entry/kegg-genes/fpr:FP2_11210.json" | python -m json.tool
[
    {
        "aafasta": ">FP2_11210 (GenBank) hypothetical protein\nMDRKLYPTAQKRHQNSKILFKSFPFYITQKVSKMQGFAQKISNKFGDLPDGIDVKFWYNSLAFTEKCLSYDKQSNDKTAVLRASGYHLGGKHA",
        "aalen": 93,
        "aaseq": "MDRKLYPTAQKRHQNSKILFKSFPFYITQKVSKMQGFAQKISNKFGDLPDGIDVKFWYNSLAFTEKCLSYDKQSNDKTAVLRASGYHLGGKHA",
        "chromosome": null,
        "classes": [],
        "codon_usage": {
            "aaa": null,
            "aac": null,
            "aag": null,
            "aat": null,
            "aca": null,
            "acc": null,
            "acg": null,
            "act": null,
            "aga": null,
            "agc": null,
            "agg": null,
            "agt": null,
            "ata": null,
            "atc": null,
            "atg": null,
            "att": null,
            "caa": null,
            "cac": null,
            "cag": null,
            "cat": null,
            "cca": null,
            "ccc": null,
            "ccg": null,
            "cct": null,
            "cga": null,
            "cgc": null,
            "cgg": null,
            "cgt": null,
            "cta": null,
            "ctc": null,
            "ctg": null,
            "ctt": null,
            "gaa": null,
            "gac": null,
            "gag": null,
            "gat": null,
            "gca": null,
            "gcc": null,
            "gcg": null,
            "gct": null,
            "gga": null,
            "ggc": null,
            "ggg": null,
            "ggt": null,
            "gta": null,
            "gtc": null,
            "gtg": null,
            "gtt": null,
            "taa": null,
            "tac": null,
            "tag": null,
            "tat": null,
            "tca": null,
            "tcc": null,
            "tcg": null,
            "tct": null,
            "tga": null,
            "tgc": null,
            "tgg": null,
            "tgt": null,
            "tta": null,
            "ttc": null,
            "ttg": null,
            "ttt": null
        },
        "dblinks": {
            "NCBI-ProteinID": [
                "CBK98661"
            ],
            "UniProt": [
                "D4JXB2"
            ]
        },
        "definition": "(GenBank) hypothetical protein",
        "division": "CDS",
        "eclinks": [],
        "entry_id": "FP2_11210",
        "gbposition": "complement(1100614..1100895)",
        "genes_id": "fpr:FP2_11210",
        "modules": {},
        "motifs": {
            "Pfam": [
                "Nod1"
            ]
        },
        "nafasta": ">FP2_11210 (GenBank) hypothetical protein\natggatagaaagttgtatccaactgcccaaaaacggcatcagaactcgaaaatcctcttcaaatctttcccattttatattacccaaaaagtgagtaaaatgcaagggtttgcacaaaaaatatcaaacaaattcggtgatttgcccgatggaatagacgtgaaattttggtataatagtttagcattcacagagaaatgtttatcgtatgacaagcagagcaacgataagaccgccgtgcttcgcgccagcggctaccatttgggaggtaaacacgcatga",
        "nalen": 282,
        "name": "",
        "names": [],
        "naseq": "atggatagaaagttgtatccaactgcccaaaaacggcatcagaactcgaaaatcctcttcaaatctttcccattttatattacccaaaaagtgagtaaaatgcaagggtttgcacaaaaaatatcaaacaaattcggtgatttgcccgatggaatagacgtgaaattttggtataatagtttagcattcacagagaaatgtttatcgtatgacaagcagagcaacgataagaccgccgtgcttcgcgccagcggctaccatttgggaggtaaacacgcatga",
        "ntfasta": ">FP2_11210 (GenBank) hypothetical protein\natggatagaaagttgtatccaactgcccaaaaacggcatcagaactcgaaaatcctcttcaaatctttcccattttatattacccaaaaagtgagtaaaatgcaagggtttgcacaaaaaatatcaaacaaattcggtgatttgcccgatggaatagacgtgaaattttggtataatagtttagcattcacagagaaatgtttatcgtatgacaagcagagcaacgataagaccgccgtgcttcgcgccagcggctaccatttgggaggtaaacacgcatga",
        "ntlen": 282,
        "ntseq": "atggatagaaagttgtatccaactgcccaaaaacggcatcagaactcgaaaatcctcttcaaatctttcccattttatattacccaaaaagtgagtaaaatgcaagggtttgcacaaaaaatatcaaacaaattcggtgatttgcccgatggaatagacgtgaaattttggtataatagtttagcattcacagagaaatgtttatcgtatgacaagcagagcaacgataagaccgccgtgcttcgcgccagcggctaccatttgggaggtaaacacgcatga",
        "organism": "Faecalibacterium prausnitzii L2-6",
        "organism_code": "fpr",
        "organism_id": "T02591",
        "orthologs": {},
        "pathways": {},
        "position": "complement(1100614..1100895)",
        "structure": []
    }
]
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

KEGGREST package is the wrench https://bioconductor.org/packages/release/bioc/vignettes/KEGGREST/inst/doc/KEGGREST-vignette.html

• 0 views • link
written by Quak Quak

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