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Bio::expressions::swissprot::sprot38 Namespace Reference

Detailed Description

Parser for the SWISS-PROT 38 format.

You probably want to use the variables 'record' (for a single record)
and 'format' (for a set of records).


def Simple


tuple _to_secondary_end = Martel.Re(r"([^.\R]|(?!.\R)\.)+")
tuple AC
tuple AC_block = Martel.Group("AC_block", Martel.Rep1(AC))
tuple bogus_DR_group
tuple CC
tuple CC_begin
tuple CC_copyright
tuple CC_copyright_begin
tuple CC_copyright_end
tuple comment
tuple database_id
tuple DE
tuple DE_block = Std.description_block(Martel.Group("DE_block", Martel.Rep1(DE)))
tuple DR
tuple DR_block = Martel.Group("DR_block", Martel.Rep1(DR))
tuple DR_embl
tuple DR_general
tuple DR_prosite
tuple DT_ann_update
tuple DT_created
 DT_created = Martel.Group("DT_created", Martel.Re( r"DT (?P<day>)-(?P<month>...)-(?P<year>{4}) \(Rel. "\ r"(?P<release>), Created\)" )).
tuple DT_seq_update
tuple end = Martel.Group("END", Martel.Str("//") + Martel.AnyEol())
tuple exp = Martel.select_names(format, ("entry_name", "sequence"))
tuple fast_DR_embl = Std.fast_dbxref(real_DR_embl, {"style": "sp-embl"})
tuple fast_DR_general
tuple fast_DR_prosite = Std.fast_dbxref(real_DR_prosite, {"style": "sp-prosite"})
tuple feature_block
 feature_block = Martel.Group("feature_block", Martel.Rep1(FT))
tuple format
tuple format_expression
tuple FT
tuple FT_continuation = Martel.Str("FT ")
tuple FT_desc = Std.feature_description(Martel.UntilEol())
tuple FT_end = Std.feature_location_end(Martel.Re(r".{6}"))
tuple FT_name = Std.feature_name(Martel.Re(r".{8}"))
 FT_range = Martel.Group("FT", Martel.Re("FT (?P<ft_name>.{8}) " \ "(?P<ft_from>.{6}) (?P<ft_to>.{6})" \ "( (?P<ft_description>[^\R]*))?\R") ) FT_continuation = Martel.Group("FT_continuation", Martel.Re("FT " \ "(?P<ft_description>[^\R]*)\R") ) FT = Martel.Group("feature", FT_range + Martel.Rep(FT_continuation)).
tuple FT_range = Martel.Str("FT ")
tuple FT_start = Std.feature_location_start(Martel.Re(r".{6}"))
tuple GN = Simple("GN", "gene_names")
tuple GN_block = Martel.Group("GN_block", Martel.Rep1(GN))
tuple ID
tuple KW = Simple("KW", "keyword")
tuple KW_block = Martel.Group("KW_block", Martel.Rep1(KW))
tuple OC = Simple("OC", "organism_classification")
tuple OC_block = Martel.Group("OC_block", Martel.Rep1(OC))
tuple OG = Simple("OG", "organelle")
tuple OG_block = Martel.Group("OG_block", Martel.Rep1(OG))
tuple OS = Simple("OS", "organism_species")
tuple OS_block = Martel.Group("OS_block", Martel.Rep1(OS))
tuple parser = exp.make_parser()
tuple primary_id
tuple RA = Simple("RA", "reference_author")
tuple RA_block = Martel.Group("RA_block", Martel.Rep1(RA))
tuple RC = Simple("RC", "reference_comment")
tuple RC_block = Martel.Group("RC_block", Martel.Rep1(RC))
tuple real_DR_embl
tuple real_DR_general
tuple real_DR_prosite
tuple record
tuple reference
tuple RL = Simple("RL", "reference_location")
tuple RL_block = Martel.Group("RL_block", Martel.Rep1(RL))
tuple RN = Martel.Group("RN", Martel.Re("RN \[(?P<reference_number>\d+)]\R"))
tuple RP = Simple("RP", "reference_position")
tuple RT = Simple("RT", "reference_title")
tuple RT_block = Martel.Group("RT_block", Martel.Rep1(RT))
tuple RX
tuple secondary_id
tuple sequence
 sequence = Martel.Group("sequence_block", Martel.Group("SQ_data_block", SQ + Martel.Rep(SQ_data)))
tuple single_comment
tuple SQ
tuple SQ_data = Martel.Str(" ")
 SQ_data = Martel.Group("SQ_data", Martel.Re(" (?P<sequence>[^\R]*)\R")).

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