forked from biopython/biopython
/
Scanner.py
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/
Scanner.py
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# Copyright 2007-2017 by Peter Cock. All rights reserved.
# Revisions copyright 2010 by Uri Laserson. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Internal code for parsing GenBank and EMBL files (PRIVATE).
This code is NOT intended for direct use. It provides a basic scanner
(for use with a event consumer such as Bio.GenBank._FeatureConsumer)
to parse a GenBank or EMBL file (with their shared INSDC feature table).
It is used by Bio.GenBank to parse GenBank files
It is also used by Bio.SeqIO to parse GenBank and EMBL files
Feature Table Documentation:
- http://www.insdc.org/files/feature_table.html
- http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
- ftp://ftp.ncbi.nih.gov/genbank/docs/
"""
# 17-MAR-2009: added wgs, wgs_scafld for GenBank whole genome shotgun master records.
# These are GenBank files that summarize the content of a project, and provide lists of
# scaffold and contig files in the project. These will be in annotations['wgs'] and
# annotations['wgs_scafld']. These GenBank files do not have sequences. See
# http://groups.google.com/group/bionet.molbio.genbank/browse_thread/thread/51fb88bf39e7dc36
# http://is.gd/nNgk
# for more details of this format, and an example.
# Added by Ying Huang & Iddo Friedberg
import warnings
import re
import sys
from collections import defaultdict
from Bio.File import as_handle
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio import BiopythonParserWarning
class InsdcScanner:
"""Basic functions for breaking up a GenBank/EMBL file into sub sections.
The International Nucleotide Sequence Database Collaboration (INSDC)
between the DDBJ, EMBL, and GenBank. These organisations all use the
same "Feature Table" layout in their plain text flat file formats.
However, the header and sequence sections of an EMBL file are very
different in layout to those produced by GenBank/DDBJ.
"""
# These constants get redefined with sensible values in the sub classes:
RECORD_START = "XXX" # "LOCUS " or "ID "
HEADER_WIDTH = 3 # 12 or 5
FEATURE_START_MARKERS = ["XXX***FEATURES***XXX"]
FEATURE_END_MARKERS = ["XXX***END FEATURES***XXX"]
FEATURE_QUALIFIER_INDENT = 0
FEATURE_QUALIFIER_SPACER = ""
SEQUENCE_HEADERS = ["XXX"] # with right hand side spaces removed
def __init__(self, debug=0):
"""Initialize the class."""
assert len(self.RECORD_START) == self.HEADER_WIDTH
for marker in self.SEQUENCE_HEADERS:
assert marker == marker.rstrip()
assert len(self.FEATURE_QUALIFIER_SPACER) == self.FEATURE_QUALIFIER_INDENT
self.debug = debug
self.handle = None
self.line = None
def set_handle(self, handle):
"""Set the handle attribute."""
self.handle = handle
self.line = ""
def find_start(self):
"""Read in lines until find the ID/LOCUS line, which is returned.
Any preamble (such as the header used by the NCBI on ``*.seq.gz`` archives)
will we ignored.
"""
while True:
if self.line:
line = self.line
self.line = ""
else:
line = self.handle.readline()
if not line:
if self.debug:
print("End of file")
return None
if isinstance(line[0], int):
# Same exception as for FASTQ files
raise ValueError("Is this handle in binary mode not text mode?")
if line[: self.HEADER_WIDTH] == self.RECORD_START:
if self.debug > 1:
print("Found the start of a record:\n" + line)
break
line = line.rstrip()
if line == "//":
if self.debug > 1:
print("Skipping // marking end of last record")
elif line == "":
if self.debug > 1:
print("Skipping blank line before record")
else:
# Ignore any header before the first ID/LOCUS line.
if self.debug > 1:
print("Skipping header line before record:\n" + line)
self.line = line
return line
def parse_header(self):
"""Return list of strings making up the header.
New line characters are removed.
Assumes you have just read in the ID/LOCUS line.
"""
if self.line[: self.HEADER_WIDTH] != self.RECORD_START:
raise ValueError("Not at start of record")
header_lines = []
while True:
line = self.handle.readline()
if not line:
raise ValueError("Premature end of line during sequence data")
line = line.rstrip()
if line in self.FEATURE_START_MARKERS:
if self.debug:
print("Found feature table")
break
# if line[:self.HEADER_WIDTH]==self.FEATURE_START_MARKER[:self.HEADER_WIDTH]:
# if self.debug : print("Found header table (?)")
# break
if line[: self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS:
if self.debug:
print("Found start of sequence")
break
if line == "//":
raise ValueError("Premature end of sequence data marker '//' found")
header_lines.append(line)
self.line = line
return header_lines
def parse_features(self, skip=False):
"""Return list of tuples for the features (if present).
Each feature is returned as a tuple (key, location, qualifiers)
where key and location are strings (e.g. "CDS" and
"complement(join(490883..490885,1..879))") while qualifiers
is a list of two string tuples (feature qualifier keys and values).
Assumes you have already read to the start of the features table.
"""
if self.line.rstrip() not in self.FEATURE_START_MARKERS:
if self.debug:
print("Didn't find any feature table")
return []
while self.line.rstrip() in self.FEATURE_START_MARKERS:
self.line = self.handle.readline()
features = []
line = self.line
while True:
if not line:
raise ValueError("Premature end of line during features table")
if line[: self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS:
if self.debug:
print("Found start of sequence")
break
line = line.rstrip()
if line == "//":
raise ValueError("Premature end of features table, marker '//' found")
if line in self.FEATURE_END_MARKERS:
if self.debug:
print("Found end of features")
line = self.handle.readline()
break
if line[2 : self.FEATURE_QUALIFIER_INDENT].strip() == "":
# This is an empty feature line between qualifiers. Empty
# feature lines within qualifiers are handled below (ignored).
line = self.handle.readline()
continue
if len(line) < self.FEATURE_QUALIFIER_INDENT:
warnings.warn(
"line too short to contain a feature: %r" % line,
BiopythonParserWarning,
)
line = self.handle.readline()
continue
if skip:
line = self.handle.readline()
while (
line[: self.FEATURE_QUALIFIER_INDENT]
== self.FEATURE_QUALIFIER_SPACER
):
line = self.handle.readline()
else:
# Build up a list of the lines making up this feature:
if (
line[self.FEATURE_QUALIFIER_INDENT] != " "
and " " in line[self.FEATURE_QUALIFIER_INDENT :]
):
# The feature table design enforces a length limit on the feature keys.
# Some third party files (e.g. IGMT's EMBL like files) solve this by
# over indenting the location and qualifiers.
feature_key, line = line[2:].strip().split(None, 1)
feature_lines = [line]
warnings.warn(
"Over indented %s feature?" % feature_key,
BiopythonParserWarning,
)
else:
feature_key = line[2 : self.FEATURE_QUALIFIER_INDENT].strip()
feature_lines = [line[self.FEATURE_QUALIFIER_INDENT :]]
line = self.handle.readline()
while line[
: self.FEATURE_QUALIFIER_INDENT
] == self.FEATURE_QUALIFIER_SPACER or (
line != "" and line.rstrip() == ""
): # cope with blank lines in the midst of a feature
# Use strip to remove any harmless trailing white space AND and leading
# white space (e.g. out of spec files with too much indentation)
feature_lines.append(line[self.FEATURE_QUALIFIER_INDENT :].strip())
line = self.handle.readline()
features.append(self.parse_feature(feature_key, feature_lines))
self.line = line
return features
def parse_feature(self, feature_key, lines):
r"""Parse a feature given as a list of strings into a tuple.
Expects a feature as a list of strings, returns a tuple (key, location,
qualifiers)
For example given this GenBank feature::
CDS complement(join(490883..490885,1..879))
/locus_tag="NEQ001"
/note="conserved hypothetical [Methanococcus jannaschii];
COG1583:Uncharacterized ACR; IPR001472:Bipartite nuclear
localization signal; IPR002743: Protein of unknown
function DUF57"
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="NP_963295.1"
/db_xref="GI:41614797"
/db_xref="GeneID:2732620"
/translation="MRLLLELKALNSIDKKQLSNYLIQGFIYNILKNTEYSWLHNWKK
EKYFNFTLIPKKDIIENKRYYLIISSPDKRFIEVLHNKIKDLDIITIGLAQFQLRKTK
KFDPKLRFPWVTITPIVLREGKIVILKGDKYYKVFVKRLEELKKYNLIKKKEPILEEP
IEISLNQIKDGWKIIDVKDRYYDFRNKSFSAFSNWLRDLKEQSLRKYNNFCGKNFYFE
EAIFEGFTFYKTVSIRIRINRGEAVYIGTLWKELNVYRKLDKEEREFYKFLYDCGLGS
LNSMGFGFVNTKKNSAR"
Then should give input key="CDS" and the rest of the data as a list of strings
lines=["complement(join(490883..490885,1..879))", ..., "LNSMGFGFVNTKKNSAR"]
where the leading spaces and trailing newlines have been removed.
Returns tuple containing: (key as string, location string, qualifiers as list)
as follows for this example:
key = "CDS", string
location = "complement(join(490883..490885,1..879))", string
qualifiers = list of string tuples:
[('locus_tag', '"NEQ001"'),
('note', '"conserved hypothetical [Methanococcus jannaschii];\nCOG1583:..."'),
('codon_start', '1'),
('transl_table', '11'),
('product', '"hypothetical protein"'),
('protein_id', '"NP_963295.1"'),
('db_xref', '"GI:41614797"'),
('db_xref', '"GeneID:2732620"'),
('translation', '"MRLLLELKALNSIDKKQLSNYLIQGFIYNILKNTEYSWLHNWKK\nEKYFNFT..."')]
In the above example, the "note" and "translation" were edited for compactness,
and they would contain multiple new line characters (displayed above as \n)
If a qualifier is quoted (in this case, everything except codon_start and
transl_table) then the quotes are NOT removed.
Note that no whitespace is removed.
"""
# Skip any blank lines
iterator = (x for x in lines if x)
try:
line = next(iterator)
feature_location = line.strip()
while feature_location[-1:] == ",":
# Multiline location, still more to come!
line = next(iterator)
feature_location += line.strip()
if feature_location.count("(") > feature_location.count(")"):
# Including the prev line in warning would be more explicit,
# but this way get one-and-only-one warning shown by default:
warnings.warn(
"Non-standard feature line wrapping (didn't break on comma)?",
BiopythonParserWarning,
)
while feature_location[-1:] == "," or feature_location.count(
"("
) > feature_location.count(")"):
line = next(iterator)
feature_location += line.strip()
qualifiers = []
for line_number, line in enumerate(iterator):
# check for extra wrapping of the location closing parentheses
if line_number == 0 and line.startswith(")"):
feature_location += line.strip()
elif line[0] == "/":
# New qualifier
i = line.find("=")
key = line[1:i] # does not work if i==-1
value = line[i + 1 :] # we ignore 'value' if i==-1
if i and value.startswith(" ") and value.lstrip().startswith('"'):
warnings.warn(
"White space after equals in qualifier",
BiopythonParserWarning,
)
value = value.lstrip()
if i == -1:
# Qualifier with no key, e.g. /pseudo
key = line[1:]
qualifiers.append((key, None))
elif not value:
# ApE can output /note=
qualifiers.append((key, ""))
elif value == '"':
# One single quote
if self.debug:
print("Single quote %s:%s" % (key, value))
# DO NOT remove the quote...
qualifiers.append((key, value))
elif value[0] == '"':
# Quoted...
value_list = [value]
while value_list[-1][-1] != '"':
value_list.append(next(iterator))
value = "\n".join(value_list)
# DO NOT remove the quotes...
qualifiers.append((key, value))
else:
# Unquoted
# if debug : print("Unquoted line %s:%s" % (key,value))
qualifiers.append((key, value))
else:
# Unquoted continuation
assert len(qualifiers) > 0
assert key == qualifiers[-1][0]
# if debug : print("Unquoted Cont %s:%s" % (key, line))
if qualifiers[-1][1] is None:
raise StopIteration
qualifiers[-1] = (key, qualifiers[-1][1] + "\n" + line)
return feature_key, feature_location, qualifiers
except StopIteration:
# Bummer
raise ValueError(
"Problem with '%s' feature:\n%s" % (feature_key, "\n".join(lines))
) from None
def parse_footer(self):
"""Return a tuple containing a list of any misc strings, and the sequence."""
# This is a basic bit of code to scan and discard the sequence,
# which was useful when developing the sub classes.
if self.line in self.FEATURE_END_MARKERS:
while self.line[: self.HEADER_WIDTH].rstrip() not in self.SEQUENCE_HEADERS:
self.line = self.handle.readline()
if not self.line:
raise ValueError("Premature end of file")
self.line = self.line.rstrip()
if self.line[: self.HEADER_WIDTH].rstrip() not in self.SEQUENCE_HEADERS:
raise ValueError("Not at start of sequence")
while True:
line = self.handle.readline()
if not line:
raise ValueError("Premature end of line during sequence data")
line = line.rstrip()
if line == "//":
break
self.line = line
return [], "" # Dummy values!
def _feed_first_line(self, consumer, line):
"""Handle the LOCUS/ID line, passing data to the comsumer (PRIVATE).
This should be implemented by the EMBL / GenBank specific subclass
Used by the parse_records() and parse() methods.
"""
pass
def _feed_header_lines(self, consumer, lines):
"""Handle the header lines (list of strings), passing data to the comsumer (PRIVATE).
This should be implemented by the EMBL / GenBank specific subclass
Used by the parse_records() and parse() methods.
"""
pass
@staticmethod
def _feed_feature_table(consumer, feature_tuples):
"""Handle the feature table (list of tuples), passing data to the comsumer (PRIVATE).
Used by the parse_records() and parse() methods.
"""
consumer.start_feature_table()
for feature_key, location_string, qualifiers in feature_tuples:
consumer.feature_key(feature_key)
consumer.location(location_string)
for q_key, q_value in qualifiers:
if q_value is None:
consumer.feature_qualifier(q_key, q_value)
else:
consumer.feature_qualifier(q_key, q_value.replace("\n", " "))
def _feed_misc_lines(self, consumer, lines):
"""Handle any lines between features and sequence (list of strings), passing data to the consumer (PRIVATE).
This should be implemented by the EMBL / GenBank specific subclass
Used by the parse_records() and parse() methods.
"""
pass
def feed(self, handle, consumer, do_features=True):
"""Feed a set of data into the consumer.
This method is intended for use with the "old" code in Bio.GenBank
Arguments:
- handle - A handle with the information to parse.
- consumer - The consumer that should be informed of events.
- do_features - Boolean, should the features be parsed?
Skipping the features can be much faster.
Return values:
- true - Passed a record
- false - Did not find a record
"""
# Should work with both EMBL and GenBank files provided the
# equivalent Bio.GenBank._FeatureConsumer methods are called...
self.set_handle(handle)
if not self.find_start():
# Could not find (another) record
consumer.data = None
return False
# We use the above class methods to parse the file into a simplified format.
# The first line, header lines and any misc lines after the features will be
# dealt with by GenBank / EMBL specific derived classes.
# First line and header:
self._feed_first_line(consumer, self.line)
self._feed_header_lines(consumer, self.parse_header())
# Features (common to both EMBL and GenBank):
if do_features:
self._feed_feature_table(consumer, self.parse_features(skip=False))
else:
self.parse_features(skip=True) # ignore the data
# Footer and sequence
misc_lines, sequence_string = self.parse_footer()
self._feed_misc_lines(consumer, misc_lines)
consumer.sequence(sequence_string)
# Calls to consumer.base_number() do nothing anyway
consumer.record_end("//")
assert self.line == "//"
# And we are done
return True
def parse(self, handle, do_features=True):
"""Return a SeqRecord (with SeqFeatures if do_features=True).
See also the method parse_records() for use on multi-record files.
"""
from Bio.GenBank import _FeatureConsumer
from Bio.GenBank.utils import FeatureValueCleaner
consumer = _FeatureConsumer(
use_fuzziness=1, feature_cleaner=FeatureValueCleaner()
)
if self.feed(handle, consumer, do_features):
return consumer.data
else:
return None
def parse_records(self, handle, do_features=True):
"""Parse records, return a SeqRecord object iterator.
Each record (from the ID/LOCUS line to the // line) becomes a SeqRecord
The SeqRecord objects include SeqFeatures if do_features=True
This method is intended for use in Bio.SeqIO
"""
# This is a generator function
with as_handle(handle) as handle:
while True:
record = self.parse(handle, do_features)
if record is None:
break
if record.id is None:
raise ValueError(
"Failed to parse the record's ID. Invalid ID line?"
)
if record.name == "<unknown name>":
raise ValueError(
"Failed to parse the record's name. Invalid ID line?"
)
if record.description == "<unknown description>":
raise ValueError("Failed to parse the record's description")
yield record
def parse_cds_features(
self, handle, alphabet=None, tags2id=("protein_id", "locus_tag", "product")
):
"""Parse CDS features, return SeqRecord object iterator.
Each CDS feature becomes a SeqRecord.
Arguments:
- alphabet - Obsolete, should be left as None.
- tags2id - Tupple of three strings, the feature keys to use
for the record id, name and description,
This method is intended for use in Bio.SeqIO
"""
if alphabet is not None:
raise ValueError("The alphabet argument is no longer supported")
with as_handle(handle) as handle:
self.set_handle(handle)
while self.find_start():
# Got an EMBL or GenBank record...
self.parse_header() # ignore header lines!
feature_tuples = self.parse_features()
# self.parse_footer() # ignore footer lines!
while True:
line = self.handle.readline()
if not line:
break
if line[:2] == "//":
break
self.line = line.rstrip()
# Now go though those features...
for key, location_string, qualifiers in feature_tuples:
if key == "CDS":
# Create SeqRecord
# ================
# SeqRecord objects cannot be created with annotations, they
# must be added afterwards. So create an empty record and
# then populate it:
record = SeqRecord(seq=None)
annotations = record.annotations
annotations["molecule_type"] = "protein"
# Should we add a location object to the annotations?
# I *think* that only makes sense for SeqFeatures with their
# sub features...
annotations["raw_location"] = location_string.replace(" ", "")
for (qualifier_name, qualifier_data) in qualifiers:
if (
qualifier_data is not None
and qualifier_data[0] == '"'
and qualifier_data[-1] == '"'
):
# Remove quotes
qualifier_data = qualifier_data[1:-1]
# Append the data to the annotation qualifier...
if qualifier_name == "translation":
assert record.seq is None, "Multiple translations!"
record.seq = Seq(qualifier_data.replace("\n", ""))
elif qualifier_name == "db_xref":
# its a list, possibly empty. Its safe to extend
record.dbxrefs.append(qualifier_data)
else:
if qualifier_data is not None:
qualifier_data = qualifier_data.replace(
"\n", " "
).replace(" ", " ")
try:
annotations[qualifier_name] += " " + qualifier_data
except KeyError:
# Not an addition to existing data, its the first bit
annotations[qualifier_name] = qualifier_data
# Fill in the ID, Name, Description
# =================================
try:
record.id = annotations[tags2id[0]]
except KeyError:
pass
try:
record.name = annotations[tags2id[1]]
except KeyError:
pass
try:
record.description = annotations[tags2id[2]]
except KeyError:
pass
yield record
class EmblScanner(InsdcScanner):
"""For extracting chunks of information in EMBL files."""
RECORD_START = "ID "
HEADER_WIDTH = 5
FEATURE_START_MARKERS = ["FH Key Location/Qualifiers", "FH"]
FEATURE_END_MARKERS = ["XX"] # XX can also mark the end of many things!
FEATURE_QUALIFIER_INDENT = 21
FEATURE_QUALIFIER_SPACER = "FT" + " " * (FEATURE_QUALIFIER_INDENT - 2)
SEQUENCE_HEADERS = ["SQ", "CO"] # Remove trailing spaces
EMBL_INDENT = HEADER_WIDTH
EMBL_SPACER = " " * EMBL_INDENT
def parse_footer(self):
"""Return a tuple containing a list of any misc strings, and the sequence."""
if self.line[: self.HEADER_WIDTH].rstrip() not in self.SEQUENCE_HEADERS:
raise ValueError("Footer format unexpected: '%s'" % self.line)
# Note that the SQ line can be split into several lines...
misc_lines = []
while self.line[: self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS:
misc_lines.append(self.line)
self.line = self.handle.readline()
if not self.line:
raise ValueError("Premature end of file")
self.line = self.line.rstrip()
if not (
self.line[: self.HEADER_WIDTH] == " " * self.HEADER_WIDTH
or self.line.strip() == "//"
):
raise ValueError("Unexpected content after SQ or CO line: %r" % self.line)
seq_lines = []
line = self.line
while True:
if not line:
raise ValueError("Premature end of file in sequence data")
line = line.strip()
if not line:
raise ValueError("Blank line in sequence data")
if line == "//":
break
if self.line[: self.HEADER_WIDTH] != (" " * self.HEADER_WIDTH):
raise ValueError(
"Problem with characters in header line, "
" or incorrect header width: " + self.line
)
# Remove tailing number now, remove spaces later
linersplit = line.rsplit(None, 1)
if len(linersplit) == 2 and linersplit[1].isdigit():
seq_lines.append(linersplit[0])
elif line.isdigit():
# Special case of final blank line with no bases
# just the sequence coordinate
pass
else:
warnings.warn(
"EMBL sequence line missing coordinates", BiopythonParserWarning
)
seq_lines.append(line)
line = self.handle.readline()
self.line = line
return misc_lines, "".join(seq_lines).replace(" ", "")
def _feed_first_line(self, consumer, line):
assert line[: self.HEADER_WIDTH].rstrip() == "ID"
if line[self.HEADER_WIDTH :].count(";") == 6:
# Looks like the semi colon separated style introduced in 2006
self._feed_first_line_new(consumer, line)
elif line[self.HEADER_WIDTH :].count(";") == 3:
if line.rstrip().endswith(" SQ"):
# EMBL-bank patent data
self._feed_first_line_patents(consumer, line)
else:
# Looks like the pre 2006 style
self._feed_first_line_old(consumer, line)
elif line[self.HEADER_WIDTH :].count(";") == 2:
# Looks like KIKO patent data
self._feed_first_line_patents_kipo(consumer, line)
else:
raise ValueError("Did not recognise the ID line layout:\n" + line)
def _feed_first_line_patents(self, consumer, line):
# Old style EMBL patent records where ID line ended SQ
# Not 100% sure that PRT here is really molecule type and
# not the data file division...
#
# Either Non-Redundant Level 1 database records,
# ID <accession>; <molecule type>; <non-redundant level 1>; <cluster size L1>
# e.g. ID NRP_AX000635; PRT; NR1; 15 SQ
#
# Or, Non-Redundant Level 2 database records:
# ID <L2-accession>; <molecule type>; <non-redundant level 2>; <cluster size L2>
# e.g. ID NRP0000016E; PRT; NR2; 5 SQ
# e.g. ID NRP_AX000635; PRT; NR1; 15 SQ
fields = [
data.strip() for data in line[self.HEADER_WIDTH :].strip()[:-3].split(";")
]
assert len(fields) == 4
consumer.locus(fields[0])
consumer.residue_type(fields[1]) # semi-redundant
consumer.data_file_division(fields[2])
# TODO - Record cluster size?
def _feed_first_line_patents_kipo(self, consumer, line):
# EMBL format patent sequence from KIPO, e.g.
# ftp://ftp.ebi.ac.uk/pub/databases/patentdata/kipo_prt.dat.gz
#
# e.g. ID DI500001 STANDARD; PRT; 111 AA.
#
# This follows the style of _feed_first_line_old
assert line[: self.HEADER_WIDTH].rstrip() == "ID"
fields = [line[self.HEADER_WIDTH :].split(None, 1)[0]]
fields.extend(line[self.HEADER_WIDTH :].split(None, 1)[1].split(";"))
fields = [entry.strip() for entry in fields]
"""
The tokens represent:
0. Primary accession number
(space sep)
1. ??? (e.g. standard)
(semi-colon)
2. Molecule type (protein)? Division? Always 'PRT'
3. Sequence length (e.g. '111 AA.')
"""
consumer.locus(fields[0]) # Should we also call the accession consumer?
# consumer.molecule_type(fields[2])
self._feed_seq_length(consumer, fields[3])
def _feed_first_line_old(self, consumer, line):
# Expects an ID line in the style before 2006, e.g.
# ID SC10H5 standard; DNA; PRO; 4870 BP.
# ID BSUB9999 standard; circular DNA; PRO; 4214630 BP.
assert line[: self.HEADER_WIDTH].rstrip() == "ID"
fields = [line[self.HEADER_WIDTH :].split(None, 1)[0]]
fields.extend(line[self.HEADER_WIDTH :].split(None, 1)[1].split(";"))
fields = [entry.strip() for entry in fields]
"""
The tokens represent:
0. Primary accession number
(space sep)
1. ??? (e.g. standard)
(semi-colon)
2. Topology and/or Molecule type (e.g. 'circular DNA' or 'DNA')
3. Taxonomic division (e.g. 'PRO')
4. Sequence length (e.g. '4639675 BP.')
"""
consumer.locus(fields[0]) # Should we also call the accession consumer?
consumer.residue_type(fields[2])
if "circular" in fields[2]:
consumer.topology("circular")
consumer.molecule_type(fields[2].replace("circular", "").strip())
elif "linear" in fields[2]:
consumer.topology("linear")
consumer.molecule_type(fields[2].replace("linear", "").strip())
else:
consumer.molecule_type(fields[2].strip())
consumer.data_file_division(fields[3])
self._feed_seq_length(consumer, fields[4])
def _feed_first_line_new(self, consumer, line):
# Expects an ID line in the style introduced in 2006, e.g.
# ID X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP.
# ID CD789012; SV 4; linear; genomic DNA; HTG; MAM; 500 BP.
assert line[: self.HEADER_WIDTH].rstrip() == "ID"
fields = [data.strip() for data in line[self.HEADER_WIDTH :].strip().split(";")]
assert len(fields) == 7
"""
The tokens represent:
0. Primary accession number
1. Sequence version number
2. Topology: 'circular' or 'linear'
3. Molecule type (e.g. 'genomic DNA')
4. Data class (e.g. 'STD')
5. Taxonomic division (e.g. 'PRO')
6. Sequence length (e.g. '4639675 BP.')
"""
consumer.locus(fields[0])
# Call the accession consumer now, to make sure we record
# something as the record.id, in case there is no AC line
consumer.accession(fields[0])
# TODO - How to deal with the version field? At the moment the consumer
# will try and use this for the ID which isn't ideal for EMBL files.
version_parts = fields[1].split()
if (
len(version_parts) == 2
and version_parts[0] == "SV"
and version_parts[1].isdigit()
):
consumer.version_suffix(version_parts[1])
# Based on how the old GenBank parser worked, merge these two:
consumer.residue_type(" ".join(fields[2:4])) # Semi-obsolete
consumer.topology(fields[2])
consumer.molecule_type(fields[3])
# consumer.xxx(fields[4]) # TODO - What should we do with the data class?
consumer.data_file_division(fields[5])
self._feed_seq_length(consumer, fields[6])
@staticmethod
def _feed_seq_length(consumer, text):
length_parts = text.split()
assert len(length_parts) == 2, "Invalid sequence length string %r" % text
assert length_parts[1].upper() in ["BP", "BP.", "AA", "AA."]
consumer.size(length_parts[0])
def _feed_header_lines(self, consumer, lines):
consumer_dict = {
"AC": "accession",
"SV": "version", # SV line removed in June 2006, now part of ID line
"DE": "definition",
# 'RN' : 'reference_num',
# 'RC' : reference comment... TODO
# 'RP' : 'reference_bases',
# 'RX' : reference cross reference... DOI or Pubmed
"RG": "consrtm", # optional consortium
# 'RA' : 'authors',
# 'RT' : 'title',
"RL": "journal",
"OS": "organism",
"OC": "taxonomy",
# 'DR' : data reference
"CC": "comment",
# 'XX' : splitter
}
# We have to handle the following specially:
# RX (depending on reference type...)
for line in lines:
line_type = line[: self.EMBL_INDENT].strip()
data = line[self.EMBL_INDENT :].strip()
if line_type == "XX":
pass
elif line_type == "RN":
# Reformat reference numbers for the GenBank based consumer
# e.g. '[1]' becomes '1'
if data[0] == "[" and data[-1] == "]":
data = data[1:-1]
consumer.reference_num(data)
elif line_type == "RP":
if data.strip() == "[-]":
# Patent EMBL files from KIPO just use: RN [-]
pass
else:
# Reformat reference numbers for the GenBank based consumer
# e.g. '1-4639675' becomes '(bases 1 to 4639675)'
# and '160-550, 904-1055' becomes '(bases 160 to 550; 904 to 1055)'
# Note could be multi-line, and end with a comma
parts = [
bases.replace("-", " to ").strip()
for bases in data.split(",")
if bases.strip()
]
consumer.reference_bases("(bases %s)" % "; ".join(parts))
elif line_type == "RT":
# Remove the enclosing quotes and trailing semi colon.
# Note the title can be split over multiple lines.
if data.startswith('"'):
data = data[1:]
if data.endswith('";'):
data = data[:-2]
consumer.title(data)
elif line_type == "RX":
# EMBL support three reference types at the moment:
# - PUBMED PUBMED bibliographic database (NLM)
# - DOI Digital Object Identifier (International DOI Foundation)
# - AGRICOLA US National Agriculture Library (NAL) of the US Department
# of Agriculture (USDA)
#
# Format:
# RX resource_identifier; identifier.
#
# e.g.
# RX DOI; 10.1016/0024-3205(83)90010-3.
# RX PUBMED; 264242.
#
# Currently our reference object only supports PUBMED and MEDLINE
# (as these were in GenBank files?).
key, value = data.split(";", 1)
if value.endswith("."):
value = value[:-1]
value = value.strip()
if key == "PUBMED":
consumer.pubmed_id(value)
# TODO - Handle other reference types (here and in BioSQL bindings)
elif line_type == "CC":
# Have to pass a list of strings for this one (not just a string)
consumer.comment([data])
elif line_type == "DR":
# Database Cross-reference, format:
# DR database_identifier; primary_identifier; secondary_identifier.
#
# e.g.
# DR MGI; 98599; Tcrb-V4.
#
# TODO - How should we store any secondary identifier?
parts = data.rstrip(".").split(";")
# Turn it into "database_identifier:primary_identifier" to
# mimic the GenBank parser. e.g. "MGI:98599"
if len(parts) == 1:
warnings.warn(
"Malformed DR line in EMBL file.", BiopythonParserWarning
)
else:
consumer.dblink("%s:%s" % (parts[0].strip(), parts[1].strip()))
elif line_type == "RA":
# Remove trailing ; at end of authors list
consumer.authors(data.rstrip(";"))
elif line_type == "PR":
# In the EMBL patent files, this is a PR (PRiority) line which
# provides the earliest active priority within the family.
# The priority number comes first, followed by the priority date.
#
# e.g.
# PR JP19990377484 16-DEC-1999
#
# However, in most EMBL files this is a PR (PRoject) line which
# gives the BioProject reference number.
#
# e.g.
# PR Project:PRJNA60715;
#
# In GenBank files this corresponds to the old PROJECT line
# which was later replaced with the DBLINK line.
if data.startswith("Project:"):
# Remove trailing ; at end of the project reference
consumer.project(data.rstrip(";"))
elif line_type == "KW":
consumer.keywords(data.rstrip(";"))
elif line_type in consumer_dict:
# Its a semi-automatic entry!
getattr(consumer, consumer_dict[line_type])(data)
else:
if self.debug:
print("Ignoring EMBL header line:\n%s" % line)
def _feed_misc_lines(self, consumer, lines):
# TODO - Should we do something with the information on the SQ line(s)?
lines.append("")
line_iter = iter(lines)
try:
for line in line_iter:
if line.startswith("CO "):
line = line[5:].strip()
contig_location = line
while True:
line = next(line_iter)
if not line:
break
elif line.startswith("CO "):
# Don't need to preseve the whitespace here.
contig_location += line[5:].strip()
else:
raise ValueError(
"Expected CO (contig) continuation line, got:\n" + line
)
consumer.contig_location(contig_location)
if line.startswith("SQ Sequence "):
# e.g.
# SQ Sequence 219 BP; 82 A; 48 C; 33 G; 45 T; 11 other;
#
# Or, EMBL-bank patent, e.g.
# SQ Sequence 465 AA; 3963407aa91d3a0d622fec679a4524e0; MD5;
self._feed_seq_length(
consumer, line[14:].rstrip().rstrip(";").split(";", 1)[0]
)