Package Martel :: Package test :: Package testformats :: Module swissprot38
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Module swissprot38

source code

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).

Functions [hide private]
 
Simple(tag, tag_data) source code
Variables [hide private]
  ID = Martel.Group("ID", Martel.Re(r"ID (?P<entry_name>\w+) +...
  AC = Martel.Group("AC", Martel.Re(r"AC (?P<ac_number>\w+);( ...
  AC_block = Martel.Group("AC_block", Martel.Rep1(AC))
  DT_created = Martel.Group("DT_created", Martel.Re(r"DT (?P<d...
  DT_seq_update = Martel.Group("DT_seq_update", Martel.Re(r"DT ...
  DT_ann_update = Martel.Group("DT_ann_update", Martel.Re(r"DT ...
  DE = Simple("DE", "description")
  DE_block = Martel.Group("DE_block", Martel.Rep1(DE))
  GN = Simple("GN", "gene_names")
  GN_block = Martel.Group("GN_block", Martel.Rep1(GN))
  OS = Simple("OS", "organism_species")
  OS_block = Martel.Group("OS_block", Martel.Rep1(OS))
  OG = Simple("OG", "organelle")
  OG_block = Martel.Group("OG_block", Martel.Rep1(OG))
  OC = Simple("OC", "organism_classification")
  OC_block = Martel.Group("OC_block", Martel.Rep1(OC))
  RN = Martel.Group("RN", Martel.Re("RN \[(?P<reference_number...
  RP = Simple("RP", "reference_position")
  RC = Simple("RC", "reference_comment")
  RC_block = Martel.Group("RC_block", Martel.Rep1(RC))
  RX = Martel.Group("RX", Martel.Re("RX (?P<bibliographic_data...
  RA = Simple("RA", "reference_author")
  RA_block = Martel.Group("RA_block", Martel.Rep1(RA))
  RT = Simple("RT", "reference_title")
  RT_block = Martel.Group("RT_block", Martel.Rep1(RT))
  RL = Simple("RL", "reference_location")
  RL_block = Martel.Group("RL_block", Martel.Rep1(RL))
  reference = Martel.Group("reference", RN+ RP+ Martel.Opt(RC_bl...
  CC_begin = Martel.Group("CC", Martel.Re("CC -!- ")+ Martel.T...
  CC = Martel.Group("CC", Martel.Re("CC ")+ Martel.ToEol("...
  single_comment = Martel.Group("comment", CC_begin+ Martel.Rep(...
  CC_copyright_begin = Martel.Group("CC_copyright_begin", Martel...
  CC_copyright = Martel.Group("CC_copyright", Martel.Re("CC (?...
  CC_copyright_end = Martel.Group("CC_copyright_end", Martel.Re(...
  bogus_DR_group = Martel.Group("bogus_DR_block", Martel.Re(r"(?...
  comment = Martel.Group("comment_block", Martel.Rep(single_comm...
  DR_general = Martel.Re("(?P<database_identifier>[^;]+);" "(?P<...
  DR_prosite = Martel.Re("(?P<database_identifier>(PROSITE|PFAM)...
  DR_embl = Martel.Re("(?P<database_identifier>EMBL); " "(?P<pri...
  DR = Martel.Group("DR", Martel.Str("DR ")+ Martel.Group("dat...
  DR_block = Martel.Group("DR_block", Martel.Rep1(DR))
  KW = Simple("KW", "keyword")
  KW_block = Martel.Group("KW_block", Martel.Rep1(KW))
  FT_range = Martel.Group("FT", Martel.Re("FT (?P<ft_name>.{8}...
  FT_continuation = Martel.Group("FT_continuation", Martel.Re("F...
  FT = Martel.Group("feature", FT_range+ Martel.Rep(FT_continuat...
  feature_block = Martel.Group("feature_block", Martel.Rep1(FT))
  SQ = Martel.Group("SQ", Martel.Re("SQ SEQUENCE +(?P<sequence...
  SQ_data = Martel.Group("SQ_data", Martel.Re(" (?P<sequence...
  sequence = Martel.Group("sequence_block", Martel.Group("SQ_dat...
  end = Martel.Group("END", Martel.Str("//")+ Martel.AnyEol())
  record = Martel.Group("swissprot38_record", ID+ AC+ DT_created...
  format_expression = Martel.Group("swissprot38", Martel.Rep1(re...
  format = Martel.ParseRecords("swissprot38", {}, record, Record...
Variables Details [hide private]

ID

Value:
Martel.Group("ID", Martel.Re(r"ID   (?P<entry_name>\w+) +(?P<data_clas\
s_table>\w+); +" r"(?P<molecule_type>\w+); +(?P<sequence_length>\d+) A\
A\.\R"))

AC

Value:
Martel.Group("AC", Martel.Re(r"AC   (?P<ac_number>\w+);( (?P<ac_number\
>\w+);)*\R"))

DT_created

Value:
Martel.Group("DT_created", Martel.Re(r"DT   (?P<day>\d\d)-(?P<month>..\
.)-(?P<year>\d{4}) \(Rel. " r"(?P<release>\d\d), Created\)\R"))

DT_seq_update

Value:
Martel.Group("DT_seq_update", Martel.Re(r"DT   (?P<day>\d\d)-(?P<month\
>...)-(?P<year>\d{4}) \(Rel. " r"(?P<release>\d\d), Last sequence upda\
te\)\R"))

DT_ann_update

Value:
Martel.Group("DT_ann_update", Martel.Re(r"DT   (?P<day>\d\d)-(?P<month\
>...)-(?P<year>\d{4}) \(Rel. " r"(?P<release>\d\d), Last annotation up\
date\)\R"))

RN

Value:
Martel.Group("RN", Martel.Re("RN   \[(?P<reference_number>\d+)]\R"))

RX

Value:
Martel.Group("RX", Martel.Re("RX   (?P<bibliographic_database_name>\w+\
); " "(?P<bibliographic_identifier>\d+)\.\R"))

reference

Value:
Martel.Group("reference", RN+ RP+ Martel.Opt(RC_block)+ Martel.Opt(RX)\
+ RA_block+ Martel.Opt(RT_block)+ RL_block)

CC_begin

Value:
Martel.Group("CC", Martel.Re("CC   -!- ")+ Martel.ToEol("comment_text"\
))

CC

Value:
Martel.Group("CC", Martel.Re("CC       ")+ Martel.ToEol("comment_text"\
))

single_comment

Value:
Martel.Group("comment", CC_begin+ Martel.Rep(CC))

CC_copyright_begin

Value:
Martel.Group("CC_copyright_begin", Martel.Re("CC   -+\R"))

CC_copyright

Value:
Martel.Group("CC_copyright", Martel.Re("CC   (?!-+\R)")+ Martel.ToEol(\
"copyright"))

CC_copyright_end

Value:
Martel.Group("CC_copyright_end", Martel.Re("CC   -+\R"))

bogus_DR_group

Value:
Martel.Group("bogus_DR_block", Martel.Re(r"(?P<DR>DR   (?P<database_id\
entifier>MIM); " r"(?P<primary_identifier>601385); " r"(?P<secondary_i\
dentifier>-).\R)"))

comment

Value:
Martel.Group("comment_block", Martel.Rep(single_comment)+ Martel.Opt(b\
ogus_DR_group)+ Martel.Opt(CC_copyright_begin+ Martel.Rep(CC_copyright\
)+ CC_copyright_end))

DR_general

Value:
Martel.Re("(?P<database_identifier>[^;]+);" "(?P<primary_identifier>[^\
;]+); " "(?P<secondary_identifier>([^.\R]|(?!.\R)\.)+)")

DR_prosite

Value:
Martel.Re("(?P<database_identifier>(PROSITE|PFAM)); " "(?P<primary_ide\
ntifier>[^;]+); " "(?P<secondary_identifier>[^;]+); " "(?P<status_iden\
tifier>[^.]+)")

DR_embl

Value:
Martel.Re("(?P<database_identifier>EMBL); " "(?P<primary_identifier>[^\
;]+); " "(?P<secondary_identifier>[^;]+); " "(?P<status_identifier>[^.\
]+)")

DR

Value:
Martel.Group("DR", Martel.Str("DR   ")+ Martel.Group("database_referen\
ce", Martel.Alt(DR_embl, DR_prosite, DR_general))+ Martel.Str(".")+ Ma\
rtel.AnyEol())

FT_range

Value:
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

Value:
Martel.Group("FT_continuation", Martel.Re("FT                         \
       " "(?P<ft_description>[^\R]*)\R"))

FT

Value:
Martel.Group("feature", FT_range+ Martel.Rep(FT_continuation))

SQ

Value:
Martel.Group("SQ", Martel.Re("SQ   SEQUENCE +(?P<sequence_length>\d+) \
AA;" " +(?P<molecular_weight>\d+) MW;" " +(?P<crc32>\w+) CRC32;\R"))

SQ_data

Value:
Martel.Group("SQ_data", Martel.Re("     (?P<sequence>[^\R]*)\R"))

sequence

Value:
Martel.Group("sequence_block", Martel.Group("SQ_data_block", SQ+ Marte\
l.Rep(SQ_data)))

record

Value:
Martel.Group("swissprot38_record", ID+ AC+ DT_created+ DT_seq_update+ \
DT_ann_update+ Martel.Opt(DE_block)+ Martel.Opt(GN_block)+ Martel.Opt(\
OS_block)+ Martel.Opt(OG_block)+ Martel.Opt(OC_block)+ Martel.Group("r\
eference_block", Martel.Rep(reference))+ comment+ Martel.Opt(DR_block)\
+ Martel.Opt(KW_block)+ Martel.Opt(feature_block)+ sequence+ end)

format_expression

Value:
Martel.Group("swissprot38", Martel.Rep1(record))

format

Value:
Martel.ParseRecords("swissprot38", {}, record, RecordReader.EndsWith, \
("//\n",))