AbstractConsumer

_add_feature ( self )

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.

_add_qualifier ( self )

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.

_get_location ( self,  range_info )

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 )

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.

_set_function (
        self,
        function,
        cur_feature,
        )

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_location (
        self,
        location,
        cur_feature,
        )

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.

_set_location_info (
        self,
        parse_info,
        cur_feature,
        )

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_ordering_info (
        self,
        function,
        cur_feature,
        )

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

_split_reference_locations ( self,  location_string )

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.

accession ( self,  acc_num )

Set the accession number as the id of the sequence.

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

contig_location ( self,  content )

Deal with a location of CONTIG information.

definition ( self,  definition )

Set the definition as the description of the sequence.

features_line ( self,  content )

Get ready for the feature table when we reach the FEATURE line.

location ( self,  content )

Parse out location information from the location string.

This uses Andrew's nice spark based parser to do the parsing for us, and translates the results of the parse into appropriate Location objects.

locus ( self,  locus_name )

Set the locus name is set as the name of the Sequence.

qualifier_key ( self,  content )

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

record_end ( self,  content )

Clean up when we've finished the record.

reference_bases ( self,  content )

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)

reference_num ( self,  content )

Signal the beginning of a new reference object.

residue_type ( self,  type )

Record the sequence type so we can choose an appropriate alphabet.

sequence ( self,  content )

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

start_feature_table ( self )

Indicate we've got to the start of the feature table.

version ( self,  version_id )

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.