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sprot38.py

00001 """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).

"""
import Martel
from Martel import RecordReader, Time
from Bio import Std

def Simple(tag, tag_data):
    return Martel.Group(tag,
                        Martel.Str(tag + "   ") + \
                        Martel.ToEol(tag_data)
                        )
#--- ID

ID = Martel.Group("ID",
                  Martel.Str("ID   ") + \
                  Std.dbid(Martel.Word("entry_name"), {"type": "primary",
                                                       "dbname": "sp"}) + \
                  Martel.Spaces() + \
                  Martel.Word("data_class_table") + \
                  Martel.Str(";") + Martel.Spaces() + \
                  Martel.Word("molecule_type") + \
                  Martel.Str(";") + Martel.Spaces() + \
                  Martel.Digits("sequence_length") + \
                  Martel.Str(" AA.") + \
                  Martel.AnyEol()
                  )
#--- AC

AC = Martel.Group("AC",
                  Martel.Str("AC   ") + \
                  Std.dbid(Martel.Word("ac_number"),
                           {"type": "accession",
                            "dbname": "sp"}) + \
                  Martel.Str(";") + \
                  Martel.Rep(Martel.Str(" ") + \
                             Std.dbid(Martel.Word("ac_number"),
                                      {"type": "accession"}) + \
                             Martel.Str(";")) + \
                  Martel.AnyEol())

AC_block = Martel.Group("AC_block", Martel.Rep1(AC))


#--- DT

##DT_created = 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"
##    ))
00054 DT_created = Martel.Group("DT_created",
                          Martel.Str("DT   ") + \
                          Time.make_expression("%(DD)-%(Jan)-%(YYYY)") + \
                          Martel.Re(" \(Rel. (?P<release>\d\d), Created\)\R"))
                          

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

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

#--- DE

# Only the last DE is supposed to have a ".", but I don't see why *I*
# need to enforce it.
DE = Martel.Group("DE",
                  Martel.Str("DE   ") + \
                  Std.description(Martel.UntilEol("description")) + \
                  Martel.AnyEol())

DE_block = Std.description_block(Martel.Group("DE_block", Martel.Rep1(DE)))


#--- GN

GN = Simple("GN", "gene_names")
GN_block = Martel.Group("GN_block", Martel.Rep1(GN))

#--- OS

OS = Simple("OS", "organism_species")
OS_block = Martel.Group("OS_block", Martel.Rep1(OS))



#--- OG

OG = Simple("OG", "organelle")
OG_block = Martel.Group("OG_block", Martel.Rep1(OG))


#--- OC

OC = Simple("OC", "organism_classification")
OC_block = Martel.Group("OC_block", Martel.Rep1(OC))

############ Reference section

#--- RN

# occurs once
RN = Martel.Group("RN", Martel.Re("RN   \[(?P<reference_number>\d+)]\R"))

#--- RP

# occurs once
RP = Simple("RP",  "reference_position")


#--- RC

# 0 or more
RC = Simple("RC",  "reference_comment")
RC_block = Martel.Group("RC_block", Martel.Rep1(RC))

#--- RX

# 0 or 1
RX = Martel.Group("RX",
                  Martel.Re("RX   (?P<bibliographic_database_name>\w+); " \
                            "(?P<bibliographic_identifier>\d+)\.\R"))

#--- RA

# 1 or more
RA = Simple("RA",  "reference_author")
RA_block = Martel.Group("RA_block", Martel.Rep1(RA))


#--- RT

# 0 or more
RT = Simple("RT",  "reference_title")
RT_block = Martel.Group("RT_block", Martel.Rep1(RT))


#--- RL

# 1 or more

RL = Simple("RL",  "reference_location")
RL_block = Martel.Group("RL_block", Martel.Rep1(RL))

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


############

#--- CC

CC_begin = Martel.Group("CC",
                        Martel.Re("CC   -!- ") + \
                        Martel.ToEol("comment_text"))
CC =       Martel.Group("CC",
                        Martel.Re("CC       ") + \
                        Martel.ToEol("comment_text"))

single_comment = Martel.Group("comment", 
                              CC_begin +
                              Martel.Rep(CC)
                              )


CC_copyright_begin = Martel.Group("CC_copyright_begin",
                                  Martel.Re("CC   -+\R"))
CC_copyright = Martel.Group("CC_copyright",
                            Martel.Re("CC   (?!-+\R)") + \
                            Martel.ToEol("copyright"))
CC_copyright_end =   Martel.Group("CC_copyright_end",
                                  Martel.Re("CC   -+\R"))

# From N33_HUMAN
bogus_DR_group = Martel.Group("bogus_DR_block",
                       Martel.Re(r"(?P<DR>DR   (?P<database_identifier>MIM); " \
                                 r"(?P<primary_identifier>601385); " \
                                 r"(?P<secondary_identifier>-).\R)")
                       )


comment = Martel.Group("comment_block",
                Martel.Rep(single_comment) + \
                Martel.Opt(bogus_DR_group) + \
                Martel.Opt(CC_copyright_begin + \
                           Martel.Rep(CC_copyright) + \
                           CC_copyright_end \
                           )
                       )

#--- DR

# This is needed for things like
#   DR   MGD; MGI:95401; EPB4.1.
# where I need to scan up to the last "."  That is, I want
# "EPB4.1" to be the secondary identifier, not "EPB4" nor "EPB4.1."

_to_secondary_end = Martel.Re(r"([^.\R]|(?!.\R)\.)+")

database_id = Std.dbxref_dbname(Martel.UntilSep("database_identifier", ";"),
                                {"style": "sp"})

primary_id = Std.dbxref_dbid(Martel.UntilSep("primary_identifier", ";"),
                             {"type": "primary"})

secondary_id = Std.dbxref_dbid(Martel.Group("secondary_identifier",
                                            _to_secondary_end),
                               {"type": "accession"})

# used in StdHandler for fast dxbref - don't rename!
real_DR_general = Std.dbxref(database_id + Martel.Str("; ") + \
                        primary_id + Martel.Str("; ") + \
                        secondary_id,
                        )
fast_DR_general = Std.fast_dbxref(real_DR_general,
                             {"style": "sp-general"})

DR_general = Martel.FastFeature(fast_DR_general, "fast-sp-dbxref",
                                real_DR_general.group_names() )


# used in StdHandler for fast dxbref - don't rename!
real_DR_prosite = Std.dbxref(
    Std.dbxref_dbname(Martel.Group("database_identifier",
                                   Martel.Str("PROSITE", "PFAM")),
                      {"style": "sp"}) +
    Martel.Str("; ") + 
    primary_id +
    Martel.Str("; ") +
    Std.dbxref_dbid(Martel.UntilSep(sep = ";"), {"type": "accession"}) +
    Martel.Str("; ") +
    Martel.UntilSep("status_identifier", "."),
    )

# used in StdHandler for fast dxbref - don't rename!
fast_DR_prosite = Std.fast_dbxref(real_DR_prosite, {"style": "sp-prosite"})

DR_prosite = Martel.FastFeature(fast_DR_prosite, "fast-sp-dbxref",
                                real_DR_prosite.group_names())

real_DR_embl = Std.dbxref(
    Std.dbxref_dbname(Martel.Group("database_identifier",
                                   Martel.Str("EMBL")),
                      {"style": "sp"}) +
    Martel.Str("; ") +
    primary_id +
    Martel.Str("; ") +
    Std.dbxref_dbid(Martel.UntilSep("secondary_identifier", ";"),
                    {"type": "accession"}) +
    Martel.Str("; ") +
    Martel.UntilSep("status_identifier", "."),
    )

fast_DR_embl = Std.fast_dbxref(real_DR_embl, {"style": "sp-embl"})
DR_embl = Martel.FastFeature(fast_DR_embl, "fast-sp-dbxref",
                             real_DR_embl.group_names())

DR = Martel.Group("DR", Martel.Str("DR   ") + \
                  Martel.Group("database_reference",
                               DR_embl | DR_prosite | DR_general) + \
                  Martel.Str(".") + Martel.AnyEol())

DR_block = Martel.Group("DR_block", Martel.Rep1(DR))



#--- KW

KW = Simple("KW", "keyword")
KW_block = Martel.Group("KW_block", Martel.Rep1(KW))


#--- FT

# FT   DOMAIN       77     88       ASP/GLU-RICH (ACIDIC).
# 123456789012345678901234567890123456789012345678901234567890123456789012345
#          1         2         3         4         5         6         7
# FT   ........ ...... ......       .........................................
# FT   12345678 123456 123456       12345678901234567890123456789012345678901
# FT   .{8}     .{6}   .{6}         [^\R]*
#              1      1      1234567

# "FT   " + ".{8}" + " " + ".{6}" + " " + ".{6}" + "       " + "[^\R]*" + "\R"
# "FT   .{8} .{6} .{6}       [^\R]*\R"

##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))

00311 FT_name = Std.feature_name(Martel.Re(r".{8}"))
FT_start = Std.feature_location_start(Martel.Re(r".{6}"))
FT_end = Std.feature_location_end(Martel.Re(r".{6}"))
FT_desc = Std.feature_description(Martel.UntilEol())

FT_range = Martel.Str("FT   ") + \
           FT_name + \
           Martel.Str(" ") + \
           FT_start + \
           Martel.Str(" ") + \
           FT_end + \
           Martel.Opt(Martel.Str("       ") + \
                      FT_desc) + \
           Martel.AnyEol()

FT_continuation = Martel.Str("FT                                ") + \
                  FT_desc + \
                  Martel.AnyEol()

FT = Std.feature(FT_range + Martel.Rep(FT_continuation),
                 {"location-style": "sp"})


##feature_block = Martel.Group("feature_block", Martel.Rep1(FT))
00335 feature_block = Std.feature_block(Martel.Rep1(FT),
                                  {"style": "swissprot"})


#--- SQ

# SQ   SEQUENCE  XXXX AA; XXXXX MW;  XXXXX CRC32;
# (Those X's don't really indicate the size)

SQ = Martel.Group("SQ",
   Martel.Re("SQ   SEQUENCE +(?P<sequence_length>\d+) AA;" \
             " +(?P<molecular_weight>\d+) MW;" \
             " +(?P<crc?type=32>\w+) CRC32;\R")
                  )
##SQ_data = Martel.Group("SQ_data",
##                       Martel.Re("     (?P<sequence>[^\R]*)\R"))
00351 SQ_data = Martel.Str("     ") + \
          Std.sequence(Martel.UntilEol()) + \
          Martel.AnyEol()


##sequence = Martel.Group("sequence_block", Martel.Group("SQ_data_block",
##                                                 SQ + Martel.Rep(SQ_data)))
00358 sequence = Std.sequence_block(SQ + Martel.Rep(SQ_data),
                              {"alphabet": "iupac-ambiguous-protein"})

#--- //

end = Martel.Group("END", Martel.Str("//") + Martel.AnyEol())

####################### put it all together

record = Std.record(
    ID +
    AC_block +
    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("OX_block", Martel.NullOp()) +
    Martel.Group("reference_block", Martel.Rep(reference)) +
    comment +
    Martel.Opt(DR_block) +
    Martel.Opt(KW_block) +
    Martel.Opt(feature_block) +
    sequence +
    end,
                      {"format": "swissprot/38"})


format_expression = Martel.Group("dataset", Martel.Rep1(record),
                                 {"format": "swissprot/38"})

format = Martel.ParseRecords("dataset", {"format": "swissprot/38"},
                             record, RecordReader.EndsWith, ("//\n",) )
                             
if __name__ == "__main__":
    exp = Martel.select_names(format, ("entry_name", "sequence"))
    parser = exp.make_parser()
    parser.parseFile(open("/home/dalke/ftps/swissprot/sprot38.dat"))

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