Package Bio :: Package GenBank :: Module Record :: Class Record
[hide private]
[frames] | no frames]

Class Record

source code

object --+

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.

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
o project - The genome sequencing project numbers
            (will be replaced by the dblink cross-references in 2009).
o dblinks - The genome sequencing project number(s) and other links.
            (will replace the project information in 2009).

Instance Methods [hide private]
x.__init__(...) initializes x; see help(type(x)) for signature
source code
Provide a GenBank formatted output option for a Record.
source code
Provide the output string for the LOCUS line.
source code
Provide output for the DEFINITION line.
source code
Output for the ACCESSION line.
source code
Output for the VERSION line.
source code
_project_line(self) source code
_dblink_line(self) source code
Output for the NID line.
source code
Output for PID line.
source code
Output for the KEYWORDS line.
source code
Output for DBSOURCE line.
source code
Output for the SEGMENT line.
source code
Output for SOURCE line on where the sample came from.
source code
Output for ORGANISM line with taxonomy info.
source code
Output for the COMMENT lines.
source code
Output for the FEATURES line.
source code
Output for the BASE COUNT line with base information.
source code
Output for the ORIGIN line...
source code
Output for all of the sequence.
source code
_wgs_line(self) source code
_wgs_scafld_line(self) source code
Output for CONTIG location information from RefSeq.
source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Class Variables [hide private]
  BASE_FORMAT = '%-12s'
  INTERNAL_FORMAT = ' %-10s'
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]


source code 
x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__
(inherited documentation)

(Informal representation operator)

source code 
Provide a GenBank formatted output option for a Record.

The objective of this is to provide an easy way to read in a GenBank
record, modify it somehow, and then output it in 'GenBank format.'
We are striving to make this work so that a parsed Record that is
output using this function will look exactly like the original

Much of the output is based on format description info at:

Overrides: object.__str__


source code 
Output for the NID line. Use of NID is obsolete in GenBank files.


source code 
Output for PID line. Presumedly, PID usage is also obsolete.


source code 
Output for the ORIGIN line