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Bio::GenBank::Record::Record Class Reference

List of all members.


Detailed Description

Hold GenBank information in a format similar to the original record.

The Record class is meant to make data easy to get to when you are
just interested in looking at GenBank data.

Attributes:
o locus - The name specified after the LOCUS keyword in the GenBank
record. This may be the accession number, or a clone id or something else.
o size - The size of the record.
o residue_type - The type of residues making up the sequence in this
record. Normally something like RNA, DNA or PROTEIN, but may be as
esoteric as 'ss-RNA circular'.
o data_file_division - The division this record is stored under in
GenBank (ie. PLN -> plants; PRI -> humans, primates; BCT -> bacteria...)
o date - The date of submission of the record, in a form like '28-JUL-1998'
o accession - list of all accession numbers for the sequence.
o nid - Nucleotide identifier number.
o pid - Proteint identifier number
o version - The accession number + version (ie. AB01234.2)
o db_source - Information about the database the record came from
o gi - The NCBI gi identifier for the record.
o keywords - A list of keywords related to the record.
o segment - If the record is one of a series, this is info about which
segment this record is (something like '1 of 6').
o source - The source of material where the sequence came from.
o organism - The genus and species of the organism (ie. 'Homo sapiens')
o taxonomy - A listing of the taxonomic classification of the organism,
starting general and getting more specific.
o references - A list of Reference objects.
o comment - Text with any kind of comment about the record.
o features - A listing of Features making up the feature table.
o base_counts - A string with the counts of bases for the sequence.
o origin - A string specifying info about the origin of the sequence.
o sequence - A string with the sequence itself.
o contig - A string of location information for a CONTIG in a RefSeq
file.

Definition at line 88 of file Record.py.


Public Member Functions

def __init__
def __str__

Public Attributes

 accession
 base_counts
 comment
 contig
 data_file_division
 date
 db_source
 definition
 features
 gi
 keywords
 locus
 nid
 organism
 origin
 pid
 primary
 references
 residue_type
 segment
 sequence
 size
 source
 taxonomy
 version

Static Public Attributes

string BASE_FEATURE_FORMAT = "%-"
string BASE_FORMAT = "%-"
int GB_BASE_INDENT = 12
int GB_FEATURE_INDENT = 21
int GB_FEATURE_INTERNAL_INDENT = 5
int GB_INTERNAL_INDENT = 2
int GB_LINE_LENGTH = 79
int GB_OTHER_INTERNAL_INDENT = 3
int GB_SEQUENCE_INDENT = 9
string INTERNAL_FEATURE_FORMAT = " "
string INTERNAL_FORMAT = " "
string OTHER_INTERNAL_FORMAT = " "
string SEQUENCE_FORMAT = "%"

Private Member Functions

def _accession_line
def _base_count_line
def _comment_line
def _contig_line
def _db_source_line
def _definition_line
def _features_line
def _keywords_line
def _locus_line
def _nid_line
def _organism_line
def _origin_line
def _pid_line
def _segment_line
def _sequence_line
def _source_line
def _version_line

The documentation for this class was generated from the following file:

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