Bio :: GenBank :: _RecordConsumer :: Class _RecordConsumer
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Class _RecordConsumer

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          object --+    
                   |    
_BaseGenBankConsumer --+
                       |
                      _RecordConsumer

Create a GenBank Record object from scanner generated information (PRIVATE).
Instance Methods [hide private]
 
__init__(self)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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wgs(self, content) source code
 
add_wgs_scafld(self, content) source code
 
locus(self, content) source code
 
size(self, content) source code
 
residue_type(self, content) source code
 
data_file_division(self, content) source code
 
date(self, content) source code
 
definition(self, content) source code
 
accession(self, content) source code
 
nid(self, content) source code
 
pid(self, content) source code
 
version(self, content) source code
 
db_source(self, content) source code
 
gi(self, content) source code
 
keywords(self, content) source code
 
project(self, content) source code
 
dblink(self, content) source code
 
segment(self, content) source code
 
source(self, content) source code
 
organism(self, content) source code
 
taxonomy(self, content) source code
 
reference_num(self, content)
Grab the reference number and signal the start of a new reference.
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reference_bases(self, content) source code
 
authors(self, content) source code
 
consrtm(self, content) source code
 
title(self, content) source code
 
journal(self, content) source code
 
medline_id(self, content) source code
 
pubmed_id(self, content) source code
 
remark(self, content) source code
 
comment(self, content) source code
 
primary_ref_line(self, content)
Data for the PRIMARY line
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primary(self, content) source code
 
features_line(self, content)
Get ready for the feature table when we reach the FEATURE line.
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start_feature_table(self)
Signal the start of the feature table.
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feature_key(self, content)
Grab the key of the feature and signal the start of a new feature.
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_add_feature(self)
Utility function to add a feature to the Record.
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location(self, content) source code
 
feature_qualifier(self, key, value) source code
 
feature_qualifier_name(self, content_list)
Deal with qualifier names
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feature_qualifier_description(self, content) source code
 
base_count(self, content) source code
 
origin_name(self, content) source code
 
contig_location(self, content)
Signal that we have contig information to add to the record.
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sequence(self, content)
Add sequence information to a list of sequence strings.
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record_end(self, content)
Signal the end of the record and do any necessary clean-up.
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Inherited from _BaseGenBankConsumer: __getattr__

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

Class Variables [hide private]

Inherited from _BaseGenBankConsumer: remove_space_keys

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)

_add_feature(self)

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Utility function to add a feature to the Record.

This does all of the appropriate checking to make sure we haven't left any info behind, and that we are only adding info if it exists.

feature_qualifier_name(self, content_list)

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Deal with qualifier names

We receive a list of keys, since you can have valueless keys such as /pseudo which would be passed in with the next key (since no other tags separate them in the file)

sequence(self, content)

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Add sequence information to a list of sequence strings.

This removes spaces in the data and uppercases the sequence, and then adds it to a list of sequences. Later on we'll join this list together to make the final sequence. This is faster than adding on the new string every time.