Bio.GenBank.Record module
Hold GenBank data in a straightforward format.
- Classes:
Record - All of the information in a GenBank record.
Reference - hold reference data for a record.
Feature - Hold the information in a Feature Table.
Qualifier - Qualifiers on a Feature.
- class Bio.GenBank.Record.Record
Bases:
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.
- Attributes:
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.
size - The size of the record.
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’.
data_file_division - The division this record is stored under in GenBank (ie. PLN -> plants; PRI -> humans, primates; BCT -> bacteria…)
date - The date of submission of the record, in a form like ‘28-JUL-1998’
accession - list of all accession numbers for the sequence.
nid - Nucleotide identifier number.
pid - Proteint identifier number
version - The accession number + version (ie. AB01234.2)
db_source - Information about the database the record came from
gi - The NCBI gi identifier for the record.
keywords - A list of keywords related to the record.
segment - If the record is one of a series, this is info about which segment this record is (something like ‘1 of 6’).
source - The source of material where the sequence came from.
organism - The genus and species of the organism (ie. ‘Homo sapiens’)
taxonomy - A listing of the taxonomic classification of the organism, starting general and getting more specific.
references - A list of Reference objects.
comment - Text with any kind of comment about the record.
features - A listing of Features making up the feature table.
base_counts - A string with the counts of bases for the sequence.
origin - A string specifying info about the origin of the sequence.
sequence - A string with the sequence itself.
contig - A string of location information for a CONTIG in a RefSeq file
project - The genome sequencing project numbers (will be replaced by the dblink cross-references in 2009).
dblinks - The genome sequencing project number(s) and other links. (will replace the project information in 2009).
- GB_LINE_LENGTH = 79
- GB_BASE_INDENT = 12
- GB_FEATURE_INDENT = 21
- GB_INTERNAL_INDENT = 2
- GB_OTHER_INTERNAL_INDENT = 3
- GB_FEATURE_INTERNAL_INDENT = 5
- GB_SEQUENCE_INDENT = 9
- BASE_FORMAT = '%-12s'
- INTERNAL_FORMAT = ' %-10s'
- OTHER_INTERNAL_FORMAT = ' %-9s'
- BASE_FEATURE_FORMAT = '%-21s'
- INTERNAL_FEATURE_FORMAT = ' %-16s'
- SEQUENCE_FORMAT = '%9s'
- __init__()
Initialize the class.
- __str__()
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 record.
Much of the output is based on format description info at:
- class Bio.GenBank.Record.Reference
Bases:
object
Hold information from a GenBank reference.
- Attributes:
number - The number of the reference in the listing of references.
bases - The bases in the sequence the reference refers to.
authors - String with all of the authors.
consrtm - Consortium the authors belong to.
title - The title of the reference.
journal - Information about the journal where the reference appeared.
medline_id - The medline id for the reference.
pubmed_id - The pubmed_id for the reference.
remark - Free-form remarks about the reference.
- __init__()
Initialize the class.
- __str__()
Convert the reference to a GenBank format string.
- class Bio.GenBank.Record.Feature(key='', location='')
Bases:
object
Hold information about a Feature in the Feature Table of GenBank record.
- Attributes:
key - The key name of the feature (ie. source)
location - The string specifying the location of the feature.
qualifiers - A list of Qualifier objects in the feature.
- __init__(key='', location='')
Initialize the class.
- __repr__()
Representation of the object for debugging or logging.
- __str__()
Return feature as a GenBank format string.
- class Bio.GenBank.Record.Qualifier(key='', value='')
Bases:
object
Hold information about a qualifier in a GenBank feature.
- Attributes:
key - The key name of the qualifier (ie. /organism=)
value - The value of the qualifier (“Dictyostelium discoideum”).
- __init__(key='', value='')
Initialize the class.
- __repr__()
Representation of the object for debugging or logging.
- __str__()
Return feature qualifier as a GenBank format string.