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Imported modules
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import Martel
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Functions
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_check_attrs
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_check_attrs ( attrs, names )
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Exceptions
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TypeError("attr %r is not allowed here (valid terms: %s)" %( name, names ) )
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_check_gapchar
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_check_gapchar ( s )
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Exceptions
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TypeError("%r not allowed as a gap character" %( s, ) )
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_check_name
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_check_name ( f, text )
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_complain_if_given
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_complain_if_given ( attrs, name )
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Exceptions
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NotImplementedError("Don't yet handle %r" %( name, ) )
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_f
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_f ()
pre- Python 2.2 functions didn't allow attributes
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_must_have
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_must_have ( expr, f )
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Exceptions
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TypeError("group %r not present in the expression but is required" %( tag, ) )
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_must_have_set
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_must_have_set ( expr, sets )
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Exceptions
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TypeError( s )
TypeError("missing required tags (need %s) in expression" % [f.tag for f in sets [ 0 ] ] )
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_must_not_have
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_must_not_have ( expr, f )
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Exceptions
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TypeError("group %r present in the expression but is not allowed" %( tag, ) )
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_set_if_given
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_set_if_given (
attrs,
field,
d,
valid=None,
convert=None,
)
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Exceptions
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TypeError("%s (%r) must be one of %s" %( field, value, valid ) )
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alphabet
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alphabet ( expr, attrs={} )
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application_name
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application_name ( expr, attrs={} )
BLASTN", "BLASTP
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application_version
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application_version ( expr, attrs={} )
0.11", "2.0a19MP-WashU
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database_name
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database_name ( expr, attrs={} )
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database_num_letters
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database_num_letters ( expr, attrs={} )
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database_num_sequences
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database_num_sequences ( expr, attrs={} )
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dbid
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dbid ( expr, attrs={} )
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dbxref
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dbxref ( expr, attrs={} )
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dbxref_dbid
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dbxref_dbid ( expr, attrs={} )
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dbxref_dbname
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dbxref_dbname ( expr, attrs={} )
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dbxref_negate
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dbxref_negate ( expr, attrs={} )
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description
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description ( expr, attrs={} )
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description_block
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description_block ( expr, attrs={} )
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description_line
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description_line ( expr, attrs={} )
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fast_dbxref
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fast_dbxref ( expr, attrs={} )
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feature
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feature ( expr, attrs={} )
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feature_block
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feature_block ( expr, attrs={} )
style determines the namespace for the feature name
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feature_description
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feature_description ( expr, attrs={} )
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feature_location
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feature_location ( expr, attrs={} )
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feature_location_end
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feature_location_end ( expr, attrs={} )
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feature_location_start
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feature_location_start ( expr, attrs={} )
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feature_name
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feature_name ( expr, attrs={} )
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feature_qualifier
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feature_qualifier ( expr, attrs={} )
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feature_qualifier_description
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feature_qualifier_description ( expr, attrs={} )
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feature_qualifier_name
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feature_qualifier_name ( expr, attrs={} )
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hit
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hit ( expr, attrs={} )
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hit_description
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hit_description ( expr, attrs={} )
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hit_length
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hit_length ( expr, attrs={} )
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hsp
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hsp ( expr, attrs={} )
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hsp_frame
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hsp_frame ( expr, attrs={} )
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hsp_seqalign
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hsp_seqalign ( expr, attrs={} )
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hsp_seqalign_homology_seq
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hsp_seqalign_homology_seq ( expr, attrs={} )
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hsp_seqalign_query_end
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hsp_seqalign_query_end ( expr, attrs={} )
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hsp_seqalign_query_leader
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hsp_seqalign_query_leader ( expr, attrs={} )
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hsp_seqalign_query_name
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hsp_seqalign_query_name ( expr, attrs={} )
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hsp_seqalign_query_seq
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hsp_seqalign_query_seq ( expr, attrs={} )
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hsp_seqalign_query_start
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hsp_seqalign_query_start ( expr, attrs={} )
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hsp_seqalign_subject_end
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hsp_seqalign_subject_end ( expr, attrs={} )
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hsp_seqalign_subject_name
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hsp_seqalign_subject_name ( expr, attrs={} )
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hsp_seqalign_subject_seq
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hsp_seqalign_subject_seq ( expr, attrs={} )
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hsp_seqalign_subject_start
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hsp_seqalign_subject_start ( expr, attrs={} )
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hsp_strand
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hsp_strand ( expr, attrs={} )
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hsp_value
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hsp_value ( expr, attrs={} )
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query_description
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query_description ( expr, attrs={} )
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query_description_block
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query_description_block ( expr, attrs={} )
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query_size
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query_size ( expr, attrs={} )
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record
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record ( expr, attrs={} )
identifier, description, and cross-references
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search_header
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search_header ( expr, attrs={} )
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search_parameter
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search_parameter ( expr, attrs={} )
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search_statistic
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search_statistic ( expr, attrs={} )
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search_table
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search_table ( expr, attrs={} )
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search_table_description
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search_table_description ( expr, attrs={} )
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search_table_entry
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search_table_entry ( expr, attrs={} )
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search_table_value
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search_table_value ( expr, attrs={} )
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sequence
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sequence ( expr, attrs={} )
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sequence_block
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sequence_block ( expr, attrs={} )
What about three letter codes?
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