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:

Instance Methods [hide private]
 
__init__(self)
x.__init__(...) initializes x; see x.__class__.__doc__ 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 x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

__str__(self)
(Informal representation operator)

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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.