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Bio::expressions::embl::embl65 Namespace Reference


Detailed Description

Format from EMBL Nucleotide Sequence Database Release 65, December 2000


Variables

tuple AC_block = Martel.Rep1(AC_line)
tuple AC_line = Martel.Str("AC ")
tuple accession
 AC - accession number (>=1 per entry).
tuple CC_block = Martel.Rep1(CC_line)
tuple CC_line = Martel.Str("CC ")
 CC - comments or notes (>=0 per entry).
tuple date = Time.make_expression("%(day)-%(Jan)-%(year)")
 DT - date (2 per entry).
tuple DE_block
tuple DE_line = Martel.Str("DE ")
 DE - description (>=1 per entry).
tuple divisions
 ID - identification (begins each entry; 1 per entry) ID entryname dataclass; molecule; division; sequencelength BP.
 DR_block = sprot38.DR_block
 DR - database cross-reference (>=0 per entry).
 DT_block = DT_created_line+DT_updated_line
tuple DT_created_line = Martel.Str("DT ")
tuple DT_updated_line = Martel.Str("DT ")
tuple end = Martel.Str("//")
 
  • termination line (ends each entry; 1 per entry)

tuple feature
tuple feature_qualifier
tuple FH_block = Martel.Str("FH Key Location/Qualifiers")
 FH - feature table header (0 or 2 per entry).
tuple format
tuple format_expression
tuple fq_dbxref = Std.feature_qualifier_name(Martel.Str("db_xref"))
 FT - feature table data (>=0 per entry) FT_line = Martel.Str("FT ") + \ Martel.ToEol("ft_data") FT_block = Martel.Rep1(FT_line).
 fq_generic = \
tuple FT_block
tuple ID_line = Martel.Str("ID ")
tuple KW_block = Martel.Rep1(KW_line)
tuple KW_line = Martel.Str("KW ")
 KW - keyword (>=1 per entry).
 OC_block = sprot38.OC_block
 OC - organism classification (>=1 per entry).
 OG_block = sprot38.OG_block
 OG - organelle (0 or 1 per entry).
tuple organism
 OS_block = sprot38.OS_block
 OS - organism species (>=1 per entry).
 RA_block = sprot38.RA_block
 RC_block = sprot38.RC_block
tuple record
tuple reference
 RL_block = sprot38.RL_block
 RN_line = sprot38.RN
 RN - reference number (>=1 per entry) RC - reference comment (>=0 per entry) RP - reference positions (>=1 per entry) RX - reference cross-reference (>=0 per entry) RA - reference author(s) (>=1 per entry) RT - reference title (>=1 per entry) RL - reference location (>=1 per entry).
 RP_line = sprot38.RP
 RT_block = sprot38.RT_block
tuple RX_block = Martel.Group("RX_block", Martel.Rep1(RX_line))
 RX_line = sprot38.RX
tuple SQ_block = Std.sequence_block(SQ_line + Martel.Rep1(SQ_data))
tuple SQ_data = Martel.Str(" ")
 bb - (blanks) sequence data (>=1 per entry)
tuple SQ_line = Martel.Str("SQ Sequence ")
 SQ - sequence header (1 per entry).
tuple SV_line = Martel.Str("SV ")
 SV - sequence version (1 per entry).
tuple whitespace = Martel.Spaces()
tuple XX = Martel.Str("XX")
 XX - spacer line (many per entry).


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