Package Bio :: Package GenBank :: Module Record :: Class Record
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Class Record

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object --+
         |
        Record

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
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]
 
__init__(self)
x.__init__(...) initializes x; see help(type(x)) for signature
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__str__(self)
Provide a GenBank formatted output option for a Record.
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_locus_line(self)
Provide the output string for the LOCUS line.
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_definition_line(self)
Provide output for the DEFINITION line.
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_accession_line(self)
Output for the ACCESSION line.
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_version_line(self)
Output for the VERSION line.
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_project_line(self) source code
 
_dblink_line(self) source code
 
_nid_line(self)
Output for the NID line.
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_pid_line(self)
Output for PID line.
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_keywords_line(self)
Output for the KEYWORDS line.
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_db_source_line(self)
Output for DBSOURCE line.
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_segment_line(self)
Output for the SEGMENT line.
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_source_line(self)
Output for SOURCE line on where the sample came from.
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_organism_line(self)
Output for ORGANISM line with taxonomy info.
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_comment_line(self)
Output for the COMMENT lines.
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_features_line(self)
Output for the FEATURES line.
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_base_count_line(self)
Output for the BASE COUNT line with base information.
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_origin_line(self)
Output for the ORIGIN line...
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_sequence_line(self)
Output for all of the sequence.
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_wgs_line(self) source code
 
_wgs_scafld_line(self) source code
 
_contig_line(self)
Output for CONTIG location information from RefSeq.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Class Variables [hide private]
  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'
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

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

Overrides: object.__init__
(inherited documentation)

__str__(self)
(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
record.

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

ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt

Overrides: object.__str__

_nid_line(self)

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

_pid_line(self)

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

_origin_line(self)

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Output for the ORIGIN line