Bio :: GenBank :: _FeatureConsumer :: Class _FeatureConsumer
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Class _FeatureConsumer

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ParserSupport.AbstractConsumer --+    
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              _BaseGenBankConsumer --+
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                                    _FeatureConsumer

Create a SeqRecord object with Features to return.

Attributes: o use_fuzziness - specify whether or not to parse with fuzziness in feature locations. o feature_cleaner - a class that will be used to provide specialized cleaning-up of feature values.

Instance Methods [hide private]
 
__init__(self, use_fuzziness, feature_cleaner=None) source code
 
locus(self, locus_name)
Set the locus name is set as the name of the Sequence.
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size(self, content)
Record the sequence length.
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residue_type(self, type)
Record the sequence type so we can choose an appropriate alphabet.
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data_file_division(self, division) source code
 
date(self, submit_date) source code
 
definition(self, definition)
Set the definition as the description of the sequence.
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accession(self, acc_num)
Set the accession number as the id of the sequence.
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wgs(self, content) source code
 
add_wgs_scafld(self, content) source code
 
nid(self, content) source code
 
pid(self, content) source code
 
version(self, version_id) source code
 
project(self, content)
Handle the information from the PROJECT line as a list of projects.
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dblink(self, content)
Store DBLINK cross references as dbxrefs in our record object.
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version_suffix(self, version)
Set the version to overwrite the id.
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db_source(self, content) source code
 
gi(self, content) source code
 
keywords(self, content) source code
 
segment(self, content) source code
 
source(self, content) source code
 
organism(self, content) source code
 
taxonomy(self, content)
Records (another line of) the taxonomy lineage.
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reference_num(self, content)
Signal the beginning of a new reference object.
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reference_bases(self, content)
Attempt to determine the sequence region the reference entails.
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_split_reference_locations(self, location_string)
Get reference locations out of a string of reference information
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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)
Deal with a reference comment.
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comment(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)
Indicate we've got to the start of the feature table.
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_add_feature(self)
Utility function to add a feature to the SeqRecord.
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feature_key(self, content) source code
 
location(self, content)
Parse out location information from the location string.
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_set_function(self, function, cur_feature)
Set the location information based on a function.
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_set_ordering_info(self, function, cur_feature)
Parse a join or order and all of the information in it.
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_set_location_info(self, parse_info, cur_feature)
Set the location information for a feature from the parse info.
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_set_location(self, location, cur_feature)
Set the location information for a feature.
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_get_location(self, range_info)
Return a (possibly fuzzy) location from a Range object.
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_get_position(self, position)
Return a (possibly fuzzy) position for a single coordinate.
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_add_qualifier(self)
Add a qualifier to the current feature without loss of info.
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feature_qualifier_name(self, content_list)
When we get a qualifier key, use it as a dictionary key.
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feature_qualifier_description(self, content) source code
 
contig_location(self, content)
Deal with CONTIG information.
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origin_name(self, content) source code
 
base_count(self, content) source code
 
base_number(self, content) source code
 
sequence(self, content)
Add up sequence information as we get it.
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record_end(self, content)
Clean up when we've finished the record.
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Inherited from ParserSupport.AbstractConsumer: __getattr__

Class Variables [hide private]

Inherited from _BaseGenBankConsumer: remove_space_keys

Method Details [hide private]

__init__(self, use_fuzziness, feature_cleaner=None)
(Constructor)

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Overrides: _BaseGenBankConsumer.__init__

accession(self, acc_num)

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Set the accession number as the id of the sequence.

If we have multiple accession numbers, the first one passed is used.

project(self, content)

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Handle the information from the PROJECT line as a list of projects.

e.g. PROJECT GenomeProject:28471

or: PROJECT GenomeProject:13543 GenomeProject:99999

This is stored as dbxrefs in the SeqRecord to be consistent with the projected switch of this line to DBLINK in future GenBank versions. Note the NCBI plan to replace "GenomeProject:28471" with the shorter "Project:28471" as part of this transition.

dblink(self, content)

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Store DBLINK cross references as dbxrefs in our record object.

This line type is expected to replace the PROJECT line in 2009. e.g.

During transition:

PROJECT     GenomeProject:28471
DBLINK      Project:28471
            Trace Assembly Archive:123456

Once the project line is dropped:

DBLINK      Project:28471
            Trace Assembly Archive:123456

Note GenomeProject -> Project.

We'll have to see some real examples to be sure, but based on the
above example we can expect one reference per line.

version_suffix(self, version)

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Set the version to overwrite the id.

Since the verison provides the same information as the accession number, plus some extra info, we set this as the id if we have a version.

reference_bases(self, content)

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Attempt to determine the sequence region the reference entails.

Possible types of information we may have to deal with:

(bases 1 to 86436) (sites) (bases 1 to 105654; 110423 to 111122) 1 (residues 1 to 182)

_split_reference_locations(self, location_string)

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Get reference locations out of a string of reference information

The passed string should be of the form:

    1 to 20; 20 to 100

This splits the information out and returns a list of location objects
based on the reference locations.

_add_feature(self)

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Utility function to add a feature to the SeqRecord.

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.

location(self, content)

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Parse out location information from the location string.

This uses a comprehensive but slow spark based parser to do the parsing, and then translates the results of the parse into appropriate Location objects.

_set_function(self, function, cur_feature)

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Set the location information based on a function.

This handles all of the location functions like 'join', 'complement' and 'order'.

Arguments: o function - A LocationParser.Function object specifying the function we are acting on. o cur_feature - The feature to add information to.

_set_ordering_info(self, function, cur_feature)

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Parse a join or order and all of the information in it.

This deals with functions that order a bunch of locations, specifically 'join' and 'order'. The inner locations are added as subfeatures of the top level feature

_set_location_info(self, parse_info, cur_feature)

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Set the location information for a feature from the parse info.

Arguments: o parse_info - The classes generated by the LocationParser. o cur_feature - The feature to add the information to.

_set_location(self, location, cur_feature)

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Set the location information for a feature.

Arguments: o location - An AbsoluteLocation object specifying the info about the location. o cur_feature - The feature to add the information to.

_get_location(self, range_info)

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Return a (possibly fuzzy) location from a Range object.

Arguments: o range_info - A location range (ie. something like 67..100). This may also be a single position (ie 27).

This returns a FeatureLocation object. If parser.use_fuzziness is set at one, the positions for the end points will possibly be fuzzy.

_get_position(self, position)

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Return a (possibly fuzzy) position for a single coordinate.

Arguments: o position - This is a LocationParser.* object that specifies a single coordinate. We will examine the object to determine the fuzziness of the position.

This is used with _get_location to parse out a location of any end_point of arbitrary fuzziness.

_add_qualifier(self)

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Add a qualifier to the current feature without loss of info.

If there are multiple qualifier keys with the same name we would lose some info in the dictionary, so we append a unique number to the end of the name in case of conflicts.

feature_qualifier_name(self, content_list)

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When we get a qualifier key, use it as a dictionary key.

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)

contig_location(self, content)

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Deal with CONTIG information.

Most CONTIG descriptions use a join of other externally referenced sequences. Currently this code tries to use the location parser, and represent this as a SeqFeature with sub-features.

sequence(self, content)

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Add up sequence information as we get it.

To try and make things speedier, this puts all of the strings into a list of strings, and then uses string.join later to put them together. Supposedly, this is a big time savings