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.