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genbank.py

00001 """Martel based parser to read GenBank formatted files.

This is a huge regular regular expression for GenBank, built using
the 'regular expressions on steroids' capabilities of Martel.

Documentation for GenBank format that I found:

o GenBank/EMBL feature tables are described at:
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html

o There are also descriptions of different GenBank lines at:
http://www.ibc.wustl.edu/standards/gbrel.txt
"""

import warnings
warnings.warn("Bio.expressions was deprecated, as it does not work with recent versions of mxTextTools. If you want to continue to use this module, please get in contact with the Biopython developers at biopython-dev@biopython.org to avoid permanent removal of this module from Biopython", DeprecationWarning)


# Martel
import Martel
from Martel import RecordReader

# identify certain items as important for format converters
from Bio import Std

# --- first set up some helper constants and functions

# - useful constants for dealing with the blank space in GenBank documents
# this is useful since blank space can be significant in GenBank flat files.
INDENT = 12
FEATURE_KEY_INDENT = 5
FEATURE_QUALIFIER_INDENT = 21

blank_space = Martel.Spaces()
small_indent_space = Martel.Str(" " * 2)
big_indent_space = Martel.Str(" " * FEATURE_KEY_INDENT)
qualifier_space = Martel.Str(" " * FEATURE_QUALIFIER_INDENT) | \
                  Martel.Str("\t" + " " * (FEATURE_QUALIFIER_INDENT - 8))

# - useful functions
00041 def define_block(identifier, block_tag, block_data, std_block_tag = None,
                 std_tag = None):
    """Define a Martel grouping which can parse a block of text.

    Many of the GenBank lines we'll want to process are grouped into
    a block like:

    IDENTIFIER   Blah blah blah

    Where blah blah blah can wrap for multiple lines. This function makes
    it easy to consistently define a definition for these blocks.

    Arguments:
    o identifier - The identifier that begins the block (like DEFINITION).
    o block_tag - A callback tag for the entire block.
    o block_data - A callback tag for the data in the block (ie. the
    stuff you are interested in).
    o std_block_tag - A Bio.Std Martel tag used to register the entire
    block as having being a "standard" type of information.
    o std_tag - A Bio.Std Martel tag used to register just the information
    in the block as being "standard"
    """
    diff = INDENT - len(identifier)
    assert diff > 0, diff
   
    # if no std_tag info is defined, just make std_tag a no-op function
    if std_tag is None:
        def do_nothing(martel_info):
            return martel_info
        std_tag = do_nothing

    identifier_and_text = Martel.Str(identifier) + \
                          Martel.Rep(Martel.Str(" ")) + \
                          std_tag(Martel.UntilEol(block_data)) + \
                          Martel.AnyEol()
    indented_text = Martel.Str(" "*INDENT) + \
                    std_tag(Martel.UntilEol(block_data)) + \
                    Martel.AnyEol()
    block_info = Martel.Group(
        block_tag,
        identifier_and_text +
        Martel.Rep(Martel.Alt(Martel.AnyEol(), indented_text))
        )
    # tag the info as some standard Martel element if specified
    if std_block_tag is not None:
        block_info = std_block_tag(block_info)

    return block_info


# first line
# LOCUS       AC007323    86436 bp    DNA             PLN       19-JAN-2000
locus = Martel.Group("locus",
                     Martel.Re(r"[\w\-]+"))
size = Martel.Group("size",
                    Martel.Rep1(Martel.Integer()))

# deal with the different kinds of residues we can have
valid_residue_prefixes = ["ss-", "ds-", "ms-"]
valid_residue_types = ["DNA", "RNA", "mRNA", "tRNA", "rRNA", "uRNA",
                       "scRNA", "snRNA", "snoRNA", "PROTEIN"]

residue_prefixes = map(Martel.Str, valid_residue_prefixes)
residue_types = map(Martel.Str, valid_residue_types)

residue_type = Martel.Group("residue_type",
                            Martel.Opt(Martel.Alt(*residue_prefixes)) +
                            Martel.Opt(Martel.Alt(*residue_types)) +
                            Martel.Opt(Martel.Opt(blank_space) +
                                       Martel.Alt(Martel.Str("circular"),
                                                  Martel.Str("linear"))))

date = Martel.Group("date",
                    Martel.Re("[-\w]+"))

# the PLN, etc stuff indicates data file divisions
valid_divisions = ["PRI", "ROD", "MAM", "VRT", "INV", "PLN", "BCT", "RNA",
                   "VRL", "PHG", "SYN", "UNA", "EST", "PAT", "STS", "GSS",
                   "HTG", "HTC", "CON", "ENV"]
divisions = map(Martel.Str, valid_divisions)
data_file_division = Martel.Group("data_file_division",
                                  Martel.Alt(*divisions))

locus_line = Martel.Group("locus_line",
                          Martel.Str("LOCUS") +
                          blank_space +
                          locus +
                          blank_space +
                          size +
                          blank_space +
                          Martel.Re("bp|aa") +
                          blank_space +
                          Martel.Opt(residue_type +
                                     blank_space) +
                          data_file_division +
                          blank_space +
                          date +
                          Martel.AnyEol())

# definition line
# DEFINITION  Genomic sequence for Arabidopsis thaliana BAC T25K16 from
#             chromosome I, complete sequence.
definition_block = define_block("DEFINITION", "definition_block",
                                "definition", Std.description_block,
                                Std.description)

# accession line
# ACCESSION   AC007323
# or
# ACCESSION   NC_004353 REGION: 1..1281640
accession = Martel.Group("accession",
                         Martel.Re("[\w]+"))

region = Martel.Group("region",
                      Martel.Re("[\d]+..[\d]+"))

accession_block = Martel.Group("accession_block",
                               Martel.Str("ACCESSION") +
                               Martel.Rep1(blank_space +
                                   Martel.Rep1(accession +
                                       Martel.Opt(
                                           Martel.Opt(Martel.Str(" ")) +
                                           Martel.Str("REGION:") +
                                           Martel.Opt(Martel.Str(" ")) +
                                           region) +
                                       Martel.Opt(Martel.Str(" "))) +
                                   Martel.AnyEol()))


# accession_block = define_block("ACCESSION", "accession_block", "accession")

# NID         g44010
nid = Martel.Group("nid",
                   Martel.Re("[\w\d]+"))
nid_line = Martel.Group("nid_line",
                        Martel.Str("NID") +
                        blank_space +
                        nid +
                        Martel.AnyEol())

# PID         g6754304
pid = Martel.Group("pid",
                   Martel.Re("[\w\d]+"))
pid_line = Martel.Group("pid_line",
                        Martel.Str("PID") +
                        blank_space +
                        pid +
                        Martel.AnyEol())

# version and GI line
# VERSION     AC007323.5  GI:6587720
version = Martel.Group("version",
                       Std.dbid(Martel.Re("[\w\d\.]+"),
                                {"type" : "primary", "dbname" : "genbank"}))

gi = Martel.Group("gi",
                  Std.dbid(Martel.Re("[\d]+"),
                           {"type" : "secondary", "dbname" : "genbank"}))

version_line = Martel.Group("version_line",
                            Martel.Str("VERSION") +
                            blank_space +
                            version +
                            Martel.Opt(blank_space +
                                       Martel.Str("GI:") +
                                       gi) +
                            Martel.AnyEol())

# DBSOURCE    REFSEQ: accession NM_010510.1
db_source_block = define_block("DBSOURCE", "db_source_block", "db_source")

# keywords line
# KEYWORDS    antifreeze protein homology; cold-regulated gene; cor6.6 gene;
#             KIN1 homology.
keywords_block = define_block("KEYWORDS", "keywords_block", "keywords")

# SEGMENT     1 of 6
segment = Martel.Group("segment",
                       Martel.Integer("segment_num") + \
                       Martel.Str(" of ") + \
                       Martel.Integer("segment_total"))
segment_line = Martel.Group("segment_line",
                            Martel.Str("SEGMENT     ") + segment + \
                            Martel.AnyEol())

# SOURCE      thale cress.
source_block = define_block("SOURCE", "source_block", "source")

# ORGANISM  Arabidopsis thaliana
#           Eukaryota; Viridiplantae; Embryophyta; Tracheophyta; Spermatophyta;
#           Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II;
#            Brassicales; Brassicaceae; Arabidopsis.
organism = Martel.Group("organism",
                        Martel.ToEol())

taxonomy = Martel.Group("taxonomy",
                        Martel.Rep1(blank_space +
                                    Martel.ToEol()))

organism_block = Martel.Group("organism_block",
                              Martel.Str("  ORGANISM") +
                              blank_space +
                              organism +
                              taxonomy)

# REFERENCE   1  (bases 1 to 86436)
#   AUTHORS   Thomashow,M.F.
#   TITLE     Direct Submission
#   JOURNAL   Submitted (01-FEB-1991) M.F. Thomashow, Dept. Crop and Soil
#             Sciences, Dept. Microbiology, Michigan State University, East
#             Lansing, Michigan 48824, USA
reference_num = Martel.Group("reference_num",
                             Martel.Re("[\d]+"))

# can have normal references, like that shown above, or references like:
# REFERENCE   1  (sites)
# with no base information or even:
# REFERENCE   2  (bases 1 to 105654; 110423 to 111122)
reference_bases = Martel.Group("reference_bases",
                               Martel.Str("(") +
                               Martel.Re("[;\w\d \R]+") +
                               Martel.Str(")"))
reference_line = Martel.Group("reference_line",
                              Martel.Str("REFERENCE") +
                              blank_space +
                              reference_num +
                              Martel.Opt(blank_space +
                                         reference_bases) +
                              Martel.AnyEol())

authors_block = define_block("  AUTHORS", "authors_block", "authors")
consrtm_block = define_block("  CONSRTM", "consrtm_block", "consrtm")
title_block   = define_block("  TITLE",   "title_block",   "title")
journal_block = define_block("  JOURNAL", "journal_block", "journal")

#  MEDLINE   92119220
medline_line = Martel.Group("medline_line",
                            Martel.Str("  MEDLINE   ") +
                            Martel.Integer("medline_id") +
                            Martel.AnyEol())

# PUBMED   10617197
pubmed_line = Martel.Group("pubmed_line",
                           Martel.Str("   PUBMED   ") +
                           Martel.Integer("pubmed_id") +
                           Martel.AnyEol())

# REMARK    This sequence is of BAC F10O3 from Arabidopsis thaliana chromosome
remark_block = define_block("  REMARK", "remark_block", "remark")

# an entire reference for the sequence
reference = Martel.Group("reference",
                         reference_line +
                         Martel.Opt(authors_block) +
                         Martel.Opt(consrtm_block) +
                         Martel.Opt(title_block) +
                         journal_block +
                         Martel.Opt(medline_line) +
                         Martel.Opt(pubmed_line) +
                         Martel.Opt(remark_block))

# COMMENT     On Dec 16, 1999 this sequence version replaced gi:5729683.
comment_block = define_block("COMMENT", "comment_block", "comment")
# PRIMARY
primary_line = Martel.Group("primary_line",
                            Martel.Str("PRIMARY") +
                            blank_space +
                            Martel.Str("TPA_SPAN") +
                            blank_space +
                            Martel.Str("PRIMARY_IDENTIFIER") +
                            blank_space +
                            Martel.Str("PRIMARY_SPAN") +
                            blank_space +
                            Martel.Str("COMP") +
                            Martel.ToEol())

primary_ref_line =Martel.Group("primary_ref_line",
                               blank_space +
                               Martel.Re(r"\d+\-\d+") +
                               blank_space +
                               Martel.Re("[\S]+") +
                               blank_space +
                               Martel.Re("\d+\-\d+")+
                               Martel.Opt(blank_space +  Martel.Str("c"))+
                               Martel.ToEol())
                              
primary =  Martel.Group("primary",primary_line +
                        Martel.Rep1(primary_ref_line))
                                       
# start on the feature table. Eeek -- This is the part I was afraid of
# most!

# the header, so that we know we are heading into some features
# FEATURES             Location/Qualifiers
features_line = Martel.Group("features_line",
                             Martel.Str("FEATURES") +
                             blank_space +
                             Martel.Str("Location/Qualifiers") +
                             Martel.AnyEol())

# feature key names are basically words, but sometimes have additional
# characters ("-10_signal", "3'UTR"...)
feature_key = Martel.Group("feature_key",
                            Martel.Re("[\w'-]+"))
"""
location = Martel.Group("location",
                      Martel.ToEol("feature_location") + \
                      Martel.Rep(qualifier_space + \
                                 Martel.Re("(?!/)") + \
                                 Martel.ToEol("feature_location")))
"""

location = Martel.Group("location",
                        Std.feature_location(Martel.UntilEol()) +
                        Martel.AnyEol() +
                        Martel.Rep(qualifier_space +
                                   Martel.AssertNot(Martel.Str("/")) +
                                   Std.feature_location(Martel.UntilEol()) +
                                   Martel.AnyEol())
                        )

feature_key_line = Martel.Group("feature_key_line",
                                big_indent_space +
                                Std.feature_name(feature_key) +
                                location)

# qualifiers escape quotes using double quotes
quote = Martel.Str('"')
quoted_chars = Std.feature_qualifier_description(Martel.Re(r'([^"\R]|"")*'))

quoted_string = (quote + quoted_chars +
                 Martel.Rep(Martel.AnyEol() + qualifier_space + quoted_chars) +
                 quote + Martel.AnyEol())

unquoted_string = Martel.AssertNot(quote) + \
                  Std.feature_qualifier_description(Martel.UntilEol()) + \
                  Martel.AnyEol()

qualifier = Std.feature_qualifier(
    qualifier_space +
    Martel.Str("/") +
    Std.feature_qualifier_name(Martel.Word("feature_qualifier_name")) +
    (Martel.AnyEol() | #  '/pseudo'
     (Martel.Str("=") +
     Martel.Group("feature_qualifier_description",
      (unquoted_string |  #  '/evidence=experimental'
       quoted_string))))   #  '/translation="AAAAAAAA....
                          #   AAAAAAAAAAAAAAAAAAAA'
    )

feature = Std.feature(feature_key_line +
                      Martel.Rep(qualifier))

feature_block = Std.feature_block(Martel.Rep1(feature),
                            {"location-style" : "genbank"})

# BASE COUNT    28300 a  15069 c  15360 g  27707 t
base_count = Martel.Group("base_count",
                          Martel.Re("[\w\d ]+"))
base_count_line = Martel.Group("base_count_line",
                               Martel.Str("BASE COUNT") +
                               blank_space +
                               base_count +
                               Martel.AnyEol())

# ORIGIN      
#       1 ggacaaggcc aaggatgctg ctgctgcagc tggagcttcc gcgcaacaag taaacagata
origin_line = Martel.Group("origin_line",
                           Martel.Str("ORIGIN") +
                           (Martel.ToEol("origin_name") |
                            Martel.AnyEol()))

base_number = Martel.Group("base_number",
                           Martel.Re("[\d]+"))
sequence = Std.sequence(Martel.Group("sequence",
                        Martel.Re("[\w]+")))
sequence_plus_spaces = Martel.Group("sequence_plus_spaces",
                                    Martel.Rep1(Martel.Str(" ") +
                                    Martel.Opt(sequence)) +
                                    Martel.Opt(Martel.Str(" ")))
sequence_line = Martel.Group("sequence_line",
                             blank_space +
                             Martel.Opt(base_number) +
                             sequence_plus_spaces +
                             Martel.AnyEol())

sequence_entry = Std.sequence_block(Martel.Group("sequence_entry",
                                    origin_line +
                                    Martel.Rep1(sequence_line)))

# CONTIG
# this is the contig information for RefSeq records

contig_location = Martel.Group("contig_location",
                    Martel.ToEol("feature_location") + \
                    Martel.Rep(Martel.Str(" " * INDENT) + \
                               Martel.Re("(?!/)") + \
                               Martel.ToEol("feature_location")))

contig_block = Martel.Group("contig_block",
                            Martel.Str("CONTIG") +
                            blank_space +
                            contig_location)

# all done!
# //
record_end = Martel.Group("record_end",
                          Martel.Str("//") +
                          Martel.Rep1(Martel.AnyEol()))

record = Std.record(Martel.Group("genbank_record",
                      locus_line + \
                      definition_block + \
                      accession_block + \
                      Martel.Opt(nid_line) + \
                      Martel.Opt(pid_line) + \
                      Martel.Opt(version_line) + \
                      Martel.Opt(db_source_block) + \
                      keywords_block + \
                      Martel.Opt(segment_line) + \
                      source_block + \
                      organism_block + \
                      Martel.Rep(reference) + \
                      Martel.Opt(primary) +\
                      Martel.Opt(comment_block) + \
                      features_line + \
                      feature_block + \
                      Martel.Alt(Martel.Opt(base_count_line) +
                                 sequence_entry,
                                 contig_block) + \
                      record_end))

# if you download a big mess of GenBank files, it'll have a header
# in that case you should be using 'ncbi_format' instead of the standard
# 'format'
header = Martel.Re("""\
(?P<filename>[^ ]+) +Genetic Sequence Data Bank
 *(?P<release_day>\d+) (?P<release_month>\w+) (?P<release_year>\d+)

 *(?P<data_bank_name>[^\R]+)

 *(?P<data_bank_name>[^\R]+)

 *(?P<num_loci>\d+) loci, *(?P<num_bases>\d+) bases, from *(?P<num_reports>\d+) reported sequences


""")

ncbi_format = Martel.HeaderFooter("genbank", {"format" : "ncbi_genbank"},
                             header, RecordReader.CountLines, (10,),
                             record, RecordReader.EndsWith, ("//",),
                             None, None, None,
                             )

format = Martel.ParseRecords("genbank", {"format" : "genbank"},
                             record, RecordReader.StartsWith, ("LOCUS ",))

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