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"""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
"""
# 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
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 +
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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