# Bio.UniGene package

## Module contents

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

class Bio.UniGene.SequenceLine(text=None)

  Bases: `object`

  Store the information for one SEQUENCE line from a Unigene file.

  Initialize with the text part of the SEQUENCE line, or nothing.

  Attributes and descriptions (access as LOWER CASE):

    - 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

  __init__(text=None)

    Initialize the class.

  __repr__()

    Return UniGene SequenceLine object as a string.

  __firstlineno__ = 78
  __static_attributes__ = ('acc', 'clone', 'end', 'image', 'is_image', 'lid', 'mgc', 'nid', 'pid', 'seqtype', 'text', 'trace')

class Bio.UniGene.ProtsimLine(text=None)

  Bases: `object`

  Store the information for one PROTSIM line from a Unigene file.

  Initialize with the text part of the PROTSIM line, or nothing.

  Attributes and descriptions (access as LOWER CASE) ORG= Organism PROTGI= Sequence GI of protein PROTID= Sequence ID of protein PCT= Percent alignment ALN= length of aligned region (aa)

  __init__(text=None)

    Initialize the class.

  __repr__()

    Return UniGene ProtsimLine object as a string.

  __firstlineno__ = 137
  __static_attributes__ = ('aln', 'org', 'pct', 'protgi', 'protid', 'text')

class Bio.UniGene.STSLine(text=None)

  Bases: `object`

  Store the information for one STS line from a Unigene file.

  Initialize with the text part of the STS line, or nothing.

  Attributes and descriptions (access as LOWER CASE)

  ACC= GenBank/EMBL/DDBJ accession number of STS [optional field] UNISTS= identifier in NCBI’s UNISTS database

  __init__(text=None)

    Initialize the class.

  __repr__()

    Return UniGene STSLine object as a string.

  __firstlineno__ = 173
  __static_attributes__ = ('acc', 'text', 'unists')

class Bio.UniGene.Record

  Bases: `object`

  Store a Unigene record.

  Here is what is stored:

      self.ID           = ''  # ID line
      self.species      = ''  # Hs, Bt, etc.
      self.title        = ''  # TITLE line
      self.symbol       = ''  # GENE line
      self.cytoband     = ''  # CYTOBAND line
      self.express      = []  # EXPRESS line, parsed on ';'
                              # Will be an array of strings
      self.restr_expr   = ''  # RESTR_EXPR line
      self.gnm_terminus = ''  # GNM_TERMINUS line
      self.gene_id      = ''  # GENE_ID line
      self.locuslink    = ''  # LOCUSLINK line
      self.homol        = ''  # HOMOL line
      self.chromosome   = ''  # CHROMOSOME line
      self.protsim      = []  # PROTSIM entries, array of Protsims
                              # Type ProtsimLine
      self.sequence     = []  # SEQUENCE entries, array of Sequence entries
                              # Type SequenceLine
      self.sts          = []  # STS entries, array of STS entries
                              # Type STSLine
      self.txmap        = []  # TXMAP entries, array of TXMap entries

  __init__()

    Initialize the class.

  __repr__()

    Represent the UniGene Record object as a string for debugging.

  __firstlineno__ = 204
  __static_attributes__ = ('ID', 'chromosome', 'cytoband', 'express', 'gene_id', 'gnm_terminus', 'homol', 'locuslink', 'protsim', 'restr_expr', 'sequence', 'species', 'sts', 'symbol', 'title', 'txmap')

Bio.UniGene.parse(handle)

  Read and load a UniGene records, for files containing multiple records.

Bio.UniGene.read(handle)

  Read and load a UniGene record, one record per file.

Biopython v: 1.85

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