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.

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.

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.

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.

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.