Package Bio :: Package UniGene
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Package UniGene

source code

Parse Unigene flat file format files such as the Hs.data file.

Here is an overview of the flat file format that this parser deals with:
   Line types/qualifiers:

       ID           UniGene cluster ID
       TITLE        Title for the cluster
       GENE         Gene symbol
       CYTOBAND     Cytological band
       EXPRESS      Tissues of origin for ESTs in cluster
       RESTR_EXPR   Single tissue or development stage contributes
                    more than half the total EST frequency for this gene.
       GNM_TERMINUS genomic confirmation of presence of a 3' terminus;
                    T if a non-templated polyA tail is found among
                    a cluster's sequences; else
                    I if templated As are found in genomic sequence or
                    S if a canonical polyA signal is found on
                      the genomic sequence
       GENE_ID      Entrez gene identifier associated with at least one
                    sequence in this cluster;
                    to be used instead of LocusLink.
       LOCUSLINK    LocusLink identifier associated with at least one
                    sequence in this cluster;
                    deprecated in favor of GENE_ID
       HOMOL        Homology;
       CHROMOSOME   Chromosome.  For plants, CHROMOSOME refers to mapping
                    on the arabidopsis genome.
       STS          STS
            ACC=         GenBank/EMBL/DDBJ accession number of STS
                         [optional field]
            UNISTS=      identifier in NCBI's UNISTS database
       TXMAP        Transcript map interval
            MARKER=      Marker found on at least one sequence in this
                         cluster
            RHPANEL=     Radiation Hybrid panel used to place marker
       PROTSIM      Protein Similarity data for the sequence with
                    highest-scoring protein similarity in this cluster
            ORG=         Organism
            PROTGI=      Sequence GI of protein
            PROTID=      Sequence ID of protein
            PCT=         Percent alignment
            ALN=         length of aligned region (aa)
       SCOUNT       Number of sequences in the cluster
       SEQUENCE     Sequence
            ACC=         GenBank/EMBL/DDBJ accession number of sequence
            NID=         Unique nucleotide sequence identifier (gi)
            PID=         Unique protein sequence identifier (used for
                         non-ESTs)
            CLONE=       Clone identifier (used for ESTs only)
            END=         End (5'/3') of clone insert read (used for
                         ESTs only)
            LID=         Library ID; see Hs.lib.info for library name
                         and tissue
            MGC=         5' CDS-completeness indicator; if present, the
                         clone associated with this sequence is believed
                         CDS-complete. A value greater than 511 is the gi
                         of the CDS-complete mRNA matched by the EST,
                         otherwise the value is an indicator of the
                         reliability of the test indicating CDS
                         completeness; higher values indicate more
                         reliable CDS-completeness predictions.
           SEQTYPE=      Description of the nucleotide sequence.
                         Possible values are mRNA, EST and HTC.
           TRACE=        The Trace ID of the EST sequence, as provided by
                         NCBI Trace Archive

Submodules [hide private]

Classes [hide private]
  SequenceLine
Store the information for one SEQUENCE line from a Unigene file
  ProtsimLine
Store the information for one PROTSIM line from a Unigene file
  STSLine
Store the information for one STS line from a Unigene file
  Record
Store a Unigene record
Functions [hide private]
 
parse(handle) source code
 
read(handle) source code
 
_read(handle) source code
Variables [hide private]
  __package__ = None
hash(x)