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Sourcecode: python-biopython version File versions

DBXRef.py

class DBXRef:
    def __init__(self, dbname, dbid, reftype = None, negate = 0):
        self.dbname = dbname
        self.dbid = dbid
        self.reftype = reftype
        self.negate = negate

    def __str__(self):
        if self.reftype is None:
            reftype = ""
        else:
            reftype = self.reftype + "="
        s = "%s/%s%s" % (self.dbname, reftype, self.dbid)
        if self.negate:
            s = "not(%s)" % s
        return s
    __repr__ = __str__

class BioformatDBName:
    def __getitem__(self, name):
        return name
class UnknownDBName:
    def __getitem__(self, name):
        return "x-unknown-" + name.lower()

dbname_conversions = {
    "bioformat": BioformatDBName(),
    "unknown": UnknownDBName(),
    "sp": {"AARHUS/GHENT-2DPAGE": "x-aarhus-ghent-2dpage",
           "CARBBANK": "x-carbbank",
           "DICTYDB": "x-dictydb",
           "ECO2DBASE": "x-eco2dbase",
           "ECOGENE": "x-ecogene",
           "EMBL": "embl",     # EMBL (in GO)
           "FLYBASE": "fb",    # Flybase (in GO)
           "GCRDB": "x-gcrdb",
           "HIV": "x-hiv",
           "HSC-2DPAGE": "x-hsc",
           "HSSP": "x-hssp",
           "MAIZE-2DPAGE": "x-maize",
           "MAIZEDB": "x-maizedb",
           "MENDEL": "x-mendel",
           "MGD": "mgd",       # (in GO)
           "MIM": "x-mim",
           "PDB": "x-pdb",       # Protein Data Bank
           "PFAM": "x-pfam",
           "PIR": "pir", # GO
           "PROSITE": "x-prosite",
           "REBASE": "x-rebase",
           "SGD": "sgd", # GO
           "STYGENE": "x-stygene",
           "SUBTILIST": "x-subtilist",
           "SWISS-2DPAGE": "x-swiss",
           "TIGR": "tigr", # GO
           "TRANSFAC": "x-transfac",
           "WORMPEP": "x-wormpep",
           "YEPD": "x-yepd",
           "ZFIN": "x-zfin",
           },
    "go": {"CGEN": "cgen",    # Compugen, Inc.
           "DDB": "ddb",      # DictyBase (Dictyostelium discoideum)
           "DDBJ": "ddbj",    # DNA Database of Japan
           "EC": "ec",        # Enzyme Commission
           "EMBL": "embl",    # EMBL Nucleotide Sequence Data Library
           "ENSEMBL": "ensembl", # ENSEMBL
           "ENZYME": "enzyme",   # ENZYME
           "FB": "fb",        # FlyBase
           "GB": "gb",        # GenBank
           "GO": "go",        # Gene Ontology
           "GXD": "gxd",      # Gene Expression Database (mouse)
           "IPR": "ipr",      # InterPro
           "ISBN": "isbn",    # International Standard Book Number
           "IUBMB": "iubmb",  # International Union of Biochemistry
                              #      and Molecular Biology
           "IUPAC": "iupac",  # International Union of Pure and Applied
                              #      Chemistry
           "MEDLINE": "medline", # MEDLINE
           "MGD": "mgd",     # Mouse Genome Database
           "MGI": "mgi",     # Mouse Genome Informatics
           "NC-IUBMB": "NC-IUBMB",
                             #  Nomenclature Committee of the International
                             #     Union of Biochemistry and Molecular Biology
           "PIR": "pir",     # PIR
           "PMID": "pmid",   # PubMed
           "Pombase": "pombase", # Schizosaccharomyces pombe
           "Pompep": "pompep",   # Schizosaccharomyces pombe Protein
                                 #    Sequence Database
           "RESID": "resid", # RESID (protein post-translational modifications)
           "SGD": "sgd",     # Saccharomyces Genome Database
           "SP": "sp",       # SWISS-PROT
           "SWALL": "swall", # SWISS-PROT + TrEMBL + TrEMBLnew
           "TAIR": "tair",   # The Arabidopsis Information Resource
           "taxonID": "taxonid", # Taxonomy ID
           "TC": "tc",       # Transport Commission
           "TIGR": "tigr",   # The Institute of Genome Research
           "TR": "tr",       # TrEMBL
           "WB": "wb",       # WormBase (Caenorhabditis elegans)
    },
    # http://www.ncbi.nlm.nih.gov/collab/db_xref.html
    "genbank": {
      "ATCC": "x-atcc",  # American Type Culture Collection database
                         #    /db_xref="ATCC:123456"
      "ATCC(in host)": "x-atcc-host", # See above
      "ATCC(dna)": "x-atcc-dna",      # See above

      "BDGP_EST": "x-bdgp-est", #  Berkeley Drosophila Genome Project
                                #       EST database
                                #   /db_xref="BDGP_EST:123456"
      
      "BDGP_INS": "x-bdgp-ins", #  Berkeley Drosophila Genome Project
                                #      database -- Insertion
                                #   /db_xref="BDGP_INS:123456"


      "dbEST": "x-dbest",  #  EST database maintained at the NCBI.
                           #  /db_xref="dbEST:123456"

      "dbSNP": "x-dbsnp",  #  Variation database maintained at the NCBI.
                           #  /db_xref="dbSNP:4647"

      "dbSTS": "x-dbsts",  # STS database maintained at the NCBI.
                           # /db_xref="dbSTS:456789"

      "ENSEMBL": "ensembl", #  Database of automatically annotated genomic data
                            # /db_xref="ENSEMBL:HUMAN-Clone-AC005612"
                            # /db_xref="ENSEMBL:HUMAN-Gene-ENSG00000007102" 

      "ESTLIB": "x-estlib", # EBI's EST library identifier  #'
                            # /db_xref="ESTLIB:1200"

      "FANTOM_DB": "x-fantom-db", # Database of Functional Annotation of Mouse
                                  # /db_xref="FANTOM_DB:0610005A07"

      "FLYBASE": "fb", # Database of Genetic and molecular data of Drosophila.
                       # /db_xref="FLYBASE:FBgn0000024"

      "GDB": "x-gdb",  # Human Genome Database accession numbers.
                       # /db_xref="GDB:G00-128-600"

      "GI": "x-gi",    # GenInfo identifier, used as a unique sequence
                       # identifier for nucleotide and proteins.
                       # /db_xref="GI:1234567890"

      "GO": "go",      # Gene Ontology Database identifier
                       # /db_xref="GO:123"

      "IMGT/LIGM": "x-imgt-ligm", #  Immunogenetics database, immunoglobulins
                                  #  and T-cell receptors
                                  # /db_xref="IMGT/LIGM:U03895"

      "IMGT/HLA": "x-imgt-hla",   # Immunogenetics database, human MHC
                                  # /db_xref="IMGT/HLA:HLA00031"


      "LocusID": "x-locus-id", # NCBI LocusLink ID.
                               # /db_xref="LocusID:51199"

      "MaizeDB": "x-maizedb",  # Maize Genome Database unique identifiers.
                               # /db_xref="MaizeDB:Probe/79847"

      "MGD": "mgd",  # Mouse Genome Database accession numbers.
                     # /db_xref="MGD:123456"

      "MGI": "mgi",  # Medicago Genome Initiative
                     # /db_xref="MGI:S:20819"

      "MIM": "x-mim", # Mendelian Inheritance in Man numbers.
                      # /db_xref="MIM:123456"

      "niaEST": "x-niaEST", # NIA Mouse cDNA Project
                            # /db_xref="niaEST:L0304H12-3"

      "PIR": "pir", # Protein Information Resource accession numbers.
                    # /db_xref="PIR:S12345"

      "PSEUDO": "x-pseudo-embl", #  EMBL pseudo protein identifier
                                 # /db_xref="PSEUDO:CAC44644.1"

      "RATMAP": "x-ratmap", #  Rat Genome Database 
                            # /db_xref="RATMAP:5"

      "RiceGenes": "x-ricegenes", #  Rice database accession numbers.
                                  # /db_xref="RiceGenes:AA231856"

      "REMTREMBL": "x-remtrembl",
              # Computer-annotated protein sequence database containing
              # the translations of those codings sequences (CDS) present
              # in the EMBL Nucleotide Sequence Database that won't be  '
              # included in SWISS-PROT. These include: immunoglobulins and
              # T-cell receptors, synthetic sequences, patent application
              # sequences, small fragments, CDS not coding for real 
              # proteins and truncated proteins.
              # example:      /db_xref="REMTREMBL:CAC01666"

      "RZPD": "x-rzpd", # Resource Centre Primary Database Clone Identifiers
                        # /db_xref="RZPD:IMAGp998I142450Q6"

      "SGD": "sgd",  # Saccharomyces Genome Database accession numbers.
                     # /db_xref="SGD:L0000470"

      "SoyBase": "x-soybase", #  Glycine max Genome Database 
                              # /db_xref="SoyBase:Satt005"

      "SPTREMBL": "x-sptrembl",  # is this the same as "swall" ?
              # Computer-annotated protein sequence database 
              # supplementing SWISS-PROT and containing the 
              # translations of all coding sequences (CDS) 
              # present in the EMBL Nucleotide Sequence 
              # Database not yet integrated in SWISS-PROT. 
              #   /db_xref="SPTREMBL:Q00177"                    

      "SWISS-PROT": "sp", # Swiss-Prot protein database accession numbers.
                          # /db_xref="SWISS-PROT:P12345"

      "taxon": "taxonid", #  NCBI taxonomic identifier.
                          # /db_xref="taxon:4932"
      },
}

def from_parser(dbname_style, dbname, idtype, dbid, negate):
    try:
        dbname = dbname_conversions[dbname_style][dbname]
    except KeyError:
        dbname = "x-unknown2-%s--%s" % (dbname_style, dbname)
    return DBXRef(dbname, dbid, idtype, negate)

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