# Copyright 2000 by Jeffrey Chang, Brad Chapman. All rights reserved. # Copyright 2006-2017 by Peter Cock. 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. """Code to work with GenBank formatted files. Rather than using Bio.GenBank, you are now encouraged to use Bio.SeqIO with the "genbank" or "embl" format names to parse GenBank or EMBL files into SeqRecord and SeqFeature objects (see the Biopython tutorial for details). Using Bio.GenBank directly to parse GenBank files is only useful if you want to obtain GenBank-specific Record objects, which is a much closer representation to the raw file contents than the SeqRecord alternative from the FeatureParser (used in Bio.SeqIO). To use the Bio.GenBank parser, there are two helper functions: - read Parse a handle containing a single GenBank record as Bio.GenBank specific Record objects. - parse Iterate over a handle containing multiple GenBank records as Bio.GenBank specific Record objects. The following internal classes are not intended for direct use and may be deprecated in a future release. Classes: - Iterator Iterate through a file of GenBank entries - ErrorFeatureParser Catch errors caused during parsing. - FeatureParser Parse GenBank data in SeqRecord and SeqFeature objects. - RecordParser Parse GenBank data into a Record object. Exceptions: - ParserFailureError Exception indicating a failure in the parser (ie. scanner or consumer) - LocationParserError Exception indicating a problem with the spark based location parser. """ import re import warnings from Bio import BiopythonParserWarning from Bio.Seq import Seq, UnknownSeq from Bio import SeqFeature # other Bio.GenBank stuff from .utils import FeatureValueCleaner from .Scanner import GenBankScanner # Constants used to parse GenBank header lines GENBANK_INDENT = 12 GENBANK_SPACER = " " * GENBANK_INDENT # Constants for parsing GenBank feature lines FEATURE_KEY_INDENT = 5 FEATURE_QUALIFIER_INDENT = 21 FEATURE_KEY_SPACER = " " * FEATURE_KEY_INDENT FEATURE_QUALIFIER_SPACER = " " * FEATURE_QUALIFIER_INDENT # Regular expressions for location parsing _solo_location = r"[<>]?\d+" _pair_location = r"[<>]?\d+\.\.[<>]?\d+" _between_location = r"\d+\^\d+" _within_position = r"\(\d+\.\d+\)" _re_within_position = re.compile(_within_position) _within_location = r"([<>]?\d+|%s)\.\.([<>]?\d+|%s)" % ( _within_position, _within_position, ) assert _re_within_position.match("(3.9)") assert re.compile(_within_location).match("(3.9)..10") assert re.compile(_within_location).match("26..(30.33)") assert re.compile(_within_location).match("(13.19)..(20.28)") _oneof_position = r"one\-of\(\d+(,\d+)+\)" _re_oneof_position = re.compile(_oneof_position) _oneof_location = r"([<>]?\d+|%s)\.\.([<>]?\d+|%s)" % (_oneof_position, _oneof_position) assert _re_oneof_position.match("one-of(6,9)") assert re.compile(_oneof_location).match("one-of(6,9)..101") assert re.compile(_oneof_location).match("one-of(6,9)..one-of(101,104)") assert re.compile(_oneof_location).match("6..one-of(101,104)") assert not _re_oneof_position.match("one-of(3)") assert _re_oneof_position.match("one-of(3,6)") assert _re_oneof_position.match("one-of(3,6,9)") _simple_location = r"\d+\.\.\d+" _re_simple_location = re.compile(r"^%s$" % _simple_location) _re_simple_compound = re.compile( r"^(join|order|bond)\(%s(,%s)*\)$" % (_simple_location, _simple_location) ) _complex_location = r"([a-zA-Z][a-zA-Z0-9_\.\|]*[a-zA-Z0-9]?\:)?(%s|%s|%s|%s|%s)" % ( _pair_location, _solo_location, _between_location, _within_location, _oneof_location, ) _re_complex_location = re.compile(r"^%s$" % _complex_location) _possibly_complemented_complex_location = r"(%s|complement\(%s\))" % ( _complex_location, _complex_location, ) _re_complex_compound = re.compile( r"^(join|order|bond)\(%s(,%s)*\)$" % (_possibly_complemented_complex_location, _possibly_complemented_complex_location) ) assert _re_simple_location.match("104..160") assert not _re_simple_location.match("68451760..68452073^68452074") assert not _re_simple_location.match("<104..>160") assert not _re_simple_location.match("104") assert not _re_simple_location.match("<1") assert not _re_simple_location.match(">99999") assert not _re_simple_location.match("join(104..160,320..390,504..579)") assert not _re_simple_compound.match("bond(12,63)") assert _re_simple_compound.match("join(104..160,320..390,504..579)") assert _re_simple_compound.match("order(1..69,1308..1465)") assert not _re_simple_compound.match("order(1..69,1308..1465,1524)") assert not _re_simple_compound.match("join(<1..442,992..1228,1524..>1983)") assert not _re_simple_compound.match("join(<1..181,254..336,422..497,574..>590)") assert not _re_simple_compound.match( "join(1475..1577,2841..2986,3074..3193,3314..3481,4126..>4215)" ) assert not _re_simple_compound.match("test(1..69,1308..1465)") assert not _re_simple_compound.match("complement(1..69)") assert not _re_simple_compound.match("(1..69)") assert _re_complex_location.match("(3.9)..10") assert _re_complex_location.match("26..(30.33)") assert _re_complex_location.match("(13.19)..(20.28)") assert _re_complex_location.match("41^42") # between assert _re_complex_location.match("AL121804:41^42") assert _re_complex_location.match("AL121804:41..610") assert _re_complex_location.match("AL121804.2:41..610") assert _re_complex_location.match( "AL358792.24.1.166931:3274..3461" ) # lots of dots in external reference assert _re_complex_location.match("one-of(3,6)..101") assert _re_complex_compound.match( "join(153490..154269,AL121804.2:41..610,AL121804.2:672..1487)" ) assert not _re_simple_compound.match( "join(153490..154269,AL121804.2:41..610,AL121804.2:672..1487)" ) assert _re_complex_compound.match("join(complement(69611..69724),139856..140650)") assert _re_complex_compound.match( "join(complement(AL354868.10.1.164018:80837..81016),complement(AL354868.10.1.164018:80539..80835))" ) # Trans-spliced example from NC_016406, note underscore in reference name: assert _re_complex_location.match("NC_016402.1:6618..6676") assert _re_complex_location.match("181647..181905") assert _re_complex_compound.match( "join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)" ) assert not _re_complex_location.match( "join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)" ) assert not _re_simple_compound.match( "join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)" ) assert not _re_complex_location.match( "join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)" ) assert not _re_simple_location.match( "join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)" ) _solo_bond = re.compile(r"bond\(%s\)" % _solo_location) assert _solo_bond.match("bond(196)") assert _solo_bond.search("bond(196)") assert _solo_bond.search("join(bond(284),bond(305),bond(309),bond(305))") def _pos(pos_str, offset=0): """Build a Position object (PRIVATE). For an end position, leave offset as zero (default): >>> _pos("5") ExactPosition(5) For a start position, set offset to minus one (for Python counting): >>> _pos("5", -1) ExactPosition(4) This also covers fuzzy positions: >>> p = _pos("<5") >>> p BeforePosition(5) >>> print(p) <5 >>> int(p) 5 >>> _pos(">5") AfterPosition(5) By default assumes an end position, so note the integer behaviour: >>> p = _pos("one-of(5,8,11)") >>> p OneOfPosition(11, choices=[ExactPosition(5), ExactPosition(8), ExactPosition(11)]) >>> print(p) one-of(5,8,11) >>> int(p) 11 >>> _pos("(8.10)") WithinPosition(10, left=8, right=10) Fuzzy start positions: >>> p = _pos("<5", -1) >>> p BeforePosition(4) >>> print(p) <4 >>> int(p) 4 Notice how the integer behaviour changes too! >>> p = _pos("one-of(5,8,11)", -1) >>> p OneOfPosition(4, choices=[ExactPosition(4), ExactPosition(7), ExactPosition(10)]) >>> print(p) one-of(4,7,10) >>> int(p) 4 """ if pos_str.startswith("<"): return SeqFeature.BeforePosition(int(pos_str[1:]) + offset) elif pos_str.startswith(">"): return SeqFeature.AfterPosition(int(pos_str[1:]) + offset) elif _re_within_position.match(pos_str): s, e = pos_str[1:-1].split(".") s = int(s) + offset e = int(e) + offset if offset == -1: default = s else: default = e return SeqFeature.WithinPosition(default, left=s, right=e) elif _re_oneof_position.match(pos_str): assert pos_str.startswith("one-of(") assert pos_str[-1] == ")" parts = [ SeqFeature.ExactPosition(int(pos) + offset) for pos in pos_str[7:-1].split(",") ] if offset == -1: default = min(int(pos) for pos in parts) else: default = max(int(pos) for pos in parts) return SeqFeature.OneOfPosition(default, choices=parts) else: return SeqFeature.ExactPosition(int(pos_str) + offset) def _loc(loc_str, expected_seq_length, strand, seq_type=None): """Make FeatureLocation from non-compound non-complement location (PRIVATE). This is also invoked to 'automatically' fix ambiguous formatting of features that span the origin of a circular sequence. Simple examples, >>> _loc("123..456", 1000, +1) FeatureLocation(ExactPosition(122), ExactPosition(456), strand=1) >>> _loc("<123..>456", 1000, strand = -1) FeatureLocation(BeforePosition(122), AfterPosition(456), strand=-1) A more complex location using within positions, >>> _loc("(9.10)..(20.25)", 1000, 1) FeatureLocation(WithinPosition(8, left=8, right=9), WithinPosition(25, left=20, right=25), strand=1) Notice how that will act as though it has overall start 8 and end 25. Zero length between feature, >>> _loc("123^124", 1000, 0) FeatureLocation(ExactPosition(123), ExactPosition(123), strand=0) The expected sequence length is needed for a special case, a between position at the start/end of a circular genome: >>> _loc("1000^1", 1000, 1) FeatureLocation(ExactPosition(1000), ExactPosition(1000), strand=1) Apart from this special case, between positions P^Q must have P+1==Q, >>> _loc("123^456", 1000, 1) Traceback (most recent call last): ... ValueError: Invalid between location '123^456' You can optionally provide a reference name: >>> _loc("AL391218.9:105173..108462", 2000000, 1) FeatureLocation(ExactPosition(105172), ExactPosition(108462), strand=1, ref='AL391218.9') >>> _loc("<2644..159", 2868, 1, "circular") CompoundLocation([FeatureLocation(BeforePosition(2643), ExactPosition(2868), strand=1), FeatureLocation(ExactPosition(0), ExactPosition(159), strand=1)], 'join') """ if ":" in loc_str: ref, loc_str = loc_str.split(":") else: ref = None try: s, e = loc_str.split("..") except ValueError: assert ".." not in loc_str if "^" in loc_str: # A between location like "67^68" (one based counting) is a # special case (note it has zero length). In python slice # notation this is 67:67, a zero length slice. See Bug 2622 # Further more, on a circular genome of length N you can have # a location N^1 meaning the junction at the origin. See Bug 3098. # NOTE - We can imagine between locations like "2^4", but this # is just "3". Similarly, "2^5" is just "3..4" s, e = loc_str.split("^") if int(s) + 1 == int(e): pos = _pos(s) elif int(s) == expected_seq_length and e == "1": pos = _pos(s) else: raise ValueError("Invalid between location %r" % loc_str) from None return SeqFeature.FeatureLocation(pos, pos, strand, ref=ref) else: # e.g. "123" s = loc_str e = loc_str # Attempt to fix features that span the origin s_pos = _pos(s, -1) e_pos = _pos(e) if int(s_pos) > int(e_pos): if seq_type is None or "circular" not in seq_type.lower(): warnings.warn( "It appears that %r is a feature that spans " "the origin, but the sequence topology is " "undefined. Skipping feature." % loc_str, BiopythonParserWarning, ) return None warnings.warn( "Attempting to fix invalid location %r as " "it looks like incorrect origin wrapping. " "Please fix input file, this could have " "unintended behavior." % loc_str, BiopythonParserWarning, ) f1 = SeqFeature.FeatureLocation(s_pos, expected_seq_length, strand) f2 = SeqFeature.FeatureLocation(0, int(e_pos), strand) if strand == -1: # For complementary features spanning the origin return f2 + f1 else: return f1 + f2 return SeqFeature.FeatureLocation(_pos(s, -1), _pos(e), strand, ref=ref) def _split_compound_loc(compound_loc): """Split a tricky compound location string (PRIVATE). >>> list(_split_compound_loc("123..145")) ['123..145'] >>> list(_split_compound_loc("123..145,200..209")) ['123..145', '200..209'] >>> list(_split_compound_loc("one-of(200,203)..300")) ['one-of(200,203)..300'] >>> list(_split_compound_loc("complement(123..145),200..209")) ['complement(123..145)', '200..209'] >>> list(_split_compound_loc("123..145,one-of(200,203)..209")) ['123..145', 'one-of(200,203)..209'] >>> list(_split_compound_loc("123..145,one-of(200,203)..one-of(209,211),300")) ['123..145', 'one-of(200,203)..one-of(209,211)', '300'] >>> list(_split_compound_loc("123..145,complement(one-of(200,203)..one-of(209,211)),300")) ['123..145', 'complement(one-of(200,203)..one-of(209,211))', '300'] >>> list(_split_compound_loc("123..145,200..one-of(209,211),300")) ['123..145', '200..one-of(209,211)', '300'] >>> list(_split_compound_loc("123..145,200..one-of(209,211)")) ['123..145', '200..one-of(209,211)'] >>> list(_split_compound_loc("complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905")) ['complement(149815..150200)', 'complement(293787..295573)', 'NC_016402.1:6618..6676', '181647..181905'] """ if "one-of(" in compound_loc: # Hard case while "," in compound_loc: assert compound_loc[0] != "," assert compound_loc[0:2] != ".." i = compound_loc.find(",") part = compound_loc[:i] compound_loc = compound_loc[i:] # includes the comma while part.count("(") > part.count(")"): assert "one-of(" in part, (part, compound_loc) i = compound_loc.find(")") part += compound_loc[: i + 1] compound_loc = compound_loc[i + 1 :] if compound_loc.startswith(".."): i = compound_loc.find(",") if i == -1: part += compound_loc compound_loc = "" else: part += compound_loc[:i] compound_loc = compound_loc[i:] # includes the comma while part.count("(") > part.count(")"): assert part.count("one-of(") == 2 i = compound_loc.find(")") part += compound_loc[: i + 1] compound_loc = compound_loc[i + 1 :] if compound_loc.startswith(","): compound_loc = compound_loc[1:] assert part yield part if compound_loc: yield compound_loc else: # Easy case yield from compound_loc.split(",") class Iterator: """Iterator interface to move over a file of GenBank entries one at a time (OBSOLETE). This class is likely to be deprecated in a future release of Biopython. Please use Bio.SeqIO.parse(..., format="gb") or Bio.GenBank.parse(...) for SeqRecord and GenBank specific Record objects respectively instead. """ def __init__(self, handle, parser=None): """Initialize the iterator. Arguments: - handle - A handle with GenBank entries to iterate through. - parser - An optional parser to pass the entries through before returning them. If None, then the raw entry will be returned. """ self.handle = handle self._parser = parser def __next__(self): """Return the next GenBank record from the handle. Will return None if we ran out of records. """ if self._parser is None: lines = [] while True: line = self.handle.readline() if not line: return None # Premature end of file? lines.append(line) if line.rstrip() == "//": break return "".join(lines) try: return self._parser.parse(self.handle) except StopIteration: return None def __iter__(self): """Iterate over the records.""" return iter(self.__next__, None) class ParserFailureError(Exception): """Failure caused by some kind of problem in the parser.""" pass class LocationParserError(Exception): """Could not Properly parse out a location from a GenBank file.""" pass _cleaner = FeatureValueCleaner() class FeatureParser: """Parse GenBank files into Seq + Feature objects (OBSOLETE). Direct use of this class is discouraged, and may be deprecated in a future release of Biopython. Please use Bio.SeqIO.parse(...) or Bio.SeqIO.read(...) instead. """ def __init__(self, debug_level=0, use_fuzziness=1, feature_cleaner=None): """Initialize a GenBank parser and Feature consumer. Arguments: - debug_level - An optional argument that species the amount of debugging information the parser should spit out. By default we have no debugging info (the fastest way to do things), but if you want you can set this as high as two and see exactly where a parse fails. - use_fuzziness - Specify whether or not to use fuzzy representations. The default is 1 (use fuzziness). - feature_cleaner - A class which will be used to clean out the values of features. This class must implement the function clean_value. GenBank.utils has a "standard" cleaner class, which is used by default. """ self._scanner = GenBankScanner(debug_level) self.use_fuzziness = use_fuzziness if feature_cleaner: self._cleaner = feature_cleaner else: self._cleaner = _cleaner # default def parse(self, handle): """Parse the specified handle.""" _consumer = _FeatureConsumer(self.use_fuzziness, self._cleaner) self._scanner.feed(handle, _consumer) return _consumer.data class RecordParser: """Parse GenBank files into Record objects (OBSOLETE). Direct use of this class is discouraged, and may be deprecated in a future release of Biopython. Please use the Bio.GenBank.parse(...) or Bio.GenBank.read(...) functions instead. """ def __init__(self, debug_level=0): """Initialize the parser. Arguments: - debug_level - An optional argument that species the amount of debugging information the parser should spit out. By default we have no debugging info (the fastest way to do things), but if you want you can set this as high as two and see exactly where a parse fails. """ self._scanner = GenBankScanner(debug_level) def parse(self, handle): """Parse the specified handle into a GenBank record.""" _consumer = _RecordConsumer() self._scanner.feed(handle, _consumer) return _consumer.data class _BaseGenBankConsumer: """Abstract GenBank consumer providing useful general functions (PRIVATE). This just helps to eliminate some duplication in things that most GenBank consumers want to do. """ # Special keys in GenBank records that we should remove spaces from # For instance, \translation keys have values which are proteins and # should have spaces and newlines removed from them. This class # attribute gives us more control over specific formatting problems. remove_space_keys = ["translation"] def __init__(self): pass @staticmethod def _split_keywords(keyword_string): """Split a string of keywords into a nice clean list (PRIVATE).""" # process the keywords into a python list if keyword_string == "" or keyword_string == ".": keywords = "" elif keyword_string[-1] == ".": keywords = keyword_string[:-1] else: keywords = keyword_string keyword_list = keywords.split(";") return [x.strip() for x in keyword_list] @staticmethod def _split_accessions(accession_string): """Split a string of accession numbers into a list (PRIVATE).""" # first replace all line feeds with spaces # Also, EMBL style accessions are split with ';' accession = accession_string.replace("\n", " ").replace(";", " ") return [x.strip() for x in accession.split() if x.strip()] @staticmethod def _split_taxonomy(taxonomy_string): """Split a string with taxonomy info into a list (PRIVATE).""" if not taxonomy_string or taxonomy_string == ".": # Missing data, no taxonomy return [] if taxonomy_string[-1] == ".": tax_info = taxonomy_string[:-1] else: tax_info = taxonomy_string tax_list = tax_info.split(";") new_tax_list = [] for tax_item in tax_list: new_items = tax_item.split("\n") new_tax_list.extend(new_items) while "" in new_tax_list: new_tax_list.remove("") return [x.strip() for x in new_tax_list] @staticmethod def _clean_location(location_string): """Clean whitespace out of a location string (PRIVATE). The location parser isn't a fan of whitespace, so we clean it out before feeding it into the parser. """ # Originally this imported string.whitespace and did a replace # via a loop. It's simpler to just split on whitespace and rejoin # the string - and this avoids importing string too. See Bug 2684. return "".join(location_string.split()) @staticmethod def _remove_newlines(text): """Remove any newlines in the passed text, returning the new string (PRIVATE).""" # get rid of newlines in the qualifier value newlines = ["\n", "\r"] for ws in newlines: text = text.replace(ws, "") return text @staticmethod def _normalize_spaces(text): """Replace multiple spaces in the passed text with single spaces (PRIVATE).""" # get rid of excessive spaces return " ".join(x for x in text.split(" ") if x) @staticmethod def _remove_spaces(text): """Remove all spaces from the passed text (PRIVATE).""" return text.replace(" ", "") @staticmethod def _convert_to_python_numbers(start, end): """Convert a start and end range to python notation (PRIVATE). In GenBank, starts and ends are defined in "biological" coordinates, where 1 is the first base and [i, j] means to include both i and j. In python, 0 is the first base and [i, j] means to include i, but not j. So, to convert "biological" to python coordinates, we need to subtract 1 from the start, and leave the end and things should be converted happily. """ new_start = start - 1 new_end = end return new_start, new_end class _FeatureConsumer(_BaseGenBankConsumer): """Create a SeqRecord object with Features to return (PRIVATE). Attributes: - use_fuzziness - specify whether or not to parse with fuzziness in feature locations. - feature_cleaner - a class that will be used to provide specialized cleaning-up of feature values. """ def __init__(self, use_fuzziness, feature_cleaner=None): from Bio.SeqRecord import SeqRecord _BaseGenBankConsumer.__init__(self) self.data = SeqRecord(None, id=None) self.data.id = None self.data.description = "" self._use_fuzziness = use_fuzziness self._feature_cleaner = feature_cleaner self._seq_type = "" self._seq_data = [] self._cur_reference = None self._cur_feature = None self._expected_size = None def locus(self, locus_name): """Set the locus name is set as the name of the Sequence.""" self.data.name = locus_name def size(self, content): """Record the sequence length.""" self._expected_size = int(content) def residue_type(self, type): """Record the sequence type (SEMI-OBSOLETE). This reflects the fact that the topology (linear/circular) and molecule type (e.g. DNA vs RNA) were a single field in early files. Current GenBank/EMBL files have two fields. """ self._seq_type = type.strip() def topology(self, topology): # noqa: D402 """Validate and record sequence topology (linear or circular as strings).""" if topology: if topology not in ["linear", "circular"]: raise ParserFailureError( "Unexpected topology %r should be linear or circular" % topology ) self.data.annotations["topology"] = topology def molecule_type(self, mol_type): """Validate and record the molecule type (for round-trip etc).""" if mol_type: if "circular" in mol_type or "linear" in mol_type: raise ParserFailureError( "Molecule type %r should not include topology" % mol_type ) # Writing out records will fail if we have a lower case DNA # or RNA string in here, so upper case it. # This is a bit ugly, but we don't want to upper case e.g. # the m in mRNA, but thanks to the strip we lost the spaces # so we need to index from the back if mol_type[-3:].upper() in ("DNA", "RNA") and not mol_type[-3:].isupper(): warnings.warn( "Non-upper case molecule type in LOCUS line: %s" % mol_type, BiopythonParserWarning, ) self.data.annotations["molecule_type"] = mol_type def data_file_division(self, division): self.data.annotations["data_file_division"] = division def date(self, submit_date): self.data.annotations["date"] = submit_date def definition(self, definition): """Set the definition as the description of the sequence.""" if self.data.description: # Append to any existing description # e.g. EMBL files with two DE lines. self.data.description += " " + definition else: self.data.description = definition def accession(self, acc_num): """Set the accession number as the id of the sequence. If we have multiple accession numbers, the first one passed is used. """ new_acc_nums = self._split_accessions(acc_num) # Also record them ALL in the annotations try: # On the off chance there was more than one accession line: for acc in new_acc_nums: # Prevent repeat entries if acc not in self.data.annotations["accessions"]: self.data.annotations["accessions"].append(acc) except KeyError: self.data.annotations["accessions"] = new_acc_nums # if we haven't set the id information yet, add the first acc num if not self.data.id: if len(new_acc_nums) > 0: # self.data.id = new_acc_nums[0] # Use the FIRST accession as the ID, not the first on this line! self.data.id = self.data.annotations["accessions"][0] def tls(self, content): self.data.annotations["tls"] = content.split("-") def tsa(self, content): self.data.annotations["tsa"] = content.split("-") def wgs(self, content): self.data.annotations["wgs"] = content.split("-") def add_wgs_scafld(self, content): self.data.annotations.setdefault("wgs_scafld", []).append(content.split("-")) def nid(self, content): self.data.annotations["nid"] = content def pid(self, content): self.data.annotations["pid"] = content def version(self, version_id): # Want to use the versioned accession as the record.id # This comes from the VERSION line in GenBank files, or the # obsolete SV line in EMBL. For the new EMBL files we need # both the version suffix from the ID line and the accession # from the AC line. if version_id.count(".") == 1 and version_id.split(".")[1].isdigit(): self.accession(version_id.split(".")[0]) self.version_suffix(version_id.split(".")[1]) elif version_id: # For backwards compatibility... self.data.id = version_id def project(self, content): """Handle the information from the PROJECT line as a list of projects. e.g.:: PROJECT GenomeProject:28471 or:: PROJECT GenomeProject:13543 GenomeProject:99999 This is stored as dbxrefs in the SeqRecord to be consistent with the projected switch of this line to DBLINK in future GenBank versions. Note the NCBI plan to replace "GenomeProject:28471" with the shorter "Project:28471" as part of this transition. """ content = content.replace("GenomeProject:", "Project:") self.data.dbxrefs.extend(p for p in content.split() if p) def dblink(self, content): """Store DBLINK cross references as dbxrefs in our record object. This line type is expected to replace the PROJECT line in 2009. e.g. During transition:: PROJECT GenomeProject:28471 DBLINK Project:28471 Trace Assembly Archive:123456 Once the project line is dropped:: DBLINK Project:28471 Trace Assembly Archive:123456 Note GenomeProject -> Project. We'll have to see some real examples to be sure, but based on the above example we can expect one reference per line. Note that at some point the NCBI have included an extra space, e.g.:: DBLINK Project: 28471 """ # During the transition period with both PROJECT and DBLINK lines, # we don't want to add the same cross reference twice. while ": " in content: content = content.replace(": ", ":") if content.strip() not in self.data.dbxrefs: self.data.dbxrefs.append(content.strip()) def version_suffix(self, version): """Set the version to overwrite the id. Since the version provides the same information as the accession number, plus some extra info, we set this as the id if we have a version. """ # e.g. GenBank line: # VERSION U49845.1 GI:1293613 # or the obsolete EMBL line: # SV U49845.1 # Scanner calls consumer.version("U49845.1") # which then calls consumer.version_suffix(1) # # e.g. EMBL new line: # ID X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP. # Scanner calls consumer.version_suffix(1) assert version.isdigit() self.data.annotations["sequence_version"] = int(version) def db_source(self, content): self.data.annotations["db_source"] = content.rstrip() def gi(self, content): self.data.annotations["gi"] = content def keywords(self, content): if "keywords" in self.data.annotations: # Multi-line keywords, append to list # Note EMBL states "A keyword is never split between lines." self.data.annotations["keywords"].extend(self._split_keywords(content)) else: self.data.annotations["keywords"] = self._split_keywords(content) def segment(self, content): self.data.annotations["segment"] = content def source(self, content): # Note that some software (e.g. VectorNTI) may produce an empty # source (rather than using a dot/period as might be expected). if content == "": source_info = "" elif content[-1] == ".": source_info = content[:-1] else: source_info = content self.data.annotations["source"] = source_info def organism(self, content): self.data.annotations["organism"] = content def taxonomy(self, content): """Record (another line of) the taxonomy lineage.""" lineage = self._split_taxonomy(content) try: self.data.annotations["taxonomy"].extend(lineage) except KeyError: self.data.annotations["taxonomy"] = lineage def reference_num(self, content): """Signal the beginning of a new reference object.""" # if we have a current reference that hasn't been added to # the list of references, add it. if self._cur_reference is not None: self.data.annotations["references"].append(self._cur_reference) else: self.data.annotations["references"] = [] self._cur_reference = SeqFeature.Reference() def reference_bases(self, content): """Attempt to determine the sequence region the reference entails. Possible types of information we may have to deal with: (bases 1 to 86436) (sites) (bases 1 to 105654; 110423 to 111122) 1 (residues 1 to 182) """ # first remove the parentheses assert content.endswith(")"), content ref_base_info = content[1:-1] all_locations = [] # parse if we've got 'bases' and 'to' if "bases" in ref_base_info and "to" in ref_base_info: # get rid of the beginning 'bases' ref_base_info = ref_base_info[5:] locations = self._split_reference_locations(ref_base_info) all_locations.extend(locations) elif "residues" in ref_base_info and "to" in ref_base_info: residues_start = ref_base_info.find("residues") # get only the information after "residues" ref_base_info = ref_base_info[(residues_start + len("residues ")) :] locations = self._split_reference_locations(ref_base_info) all_locations.extend(locations) # make sure if we are not finding information then we have # the string 'sites' or the string 'bases' elif ref_base_info == "sites" or ref_base_info.strip() == "bases": pass # otherwise raise an error else: raise ValueError( "Could not parse base info %s in record %s" % (ref_base_info, self.data.id) ) self._cur_reference.location = all_locations def _split_reference_locations(self, location_string): """Get reference locations out of a string of reference information (PRIVATE). The passed string should be of the form:: 1 to 20; 20 to 100 This splits the information out and returns a list of location objects based on the reference locations. """ # split possibly multiple locations using the ';' all_base_info = location_string.split(";") new_locations = [] for base_info in all_base_info: start, end = base_info.split("to") new_start, new_end = self._convert_to_python_numbers( int(start.strip()), int(end.strip()) ) this_location = SeqFeature.FeatureLocation(new_start, new_end) new_locations.append(this_location) return new_locations def authors(self, content): if self._cur_reference.authors: self._cur_reference.authors += " " + content else: self._cur_reference.authors = content def consrtm(self, content): if self._cur_reference.consrtm: self._cur_reference.consrtm += " " + content else: self._cur_reference.consrtm = content def title(self, content): if self._cur_reference is None: warnings.warn( "GenBank TITLE line without REFERENCE line.", BiopythonParserWarning ) elif self._cur_reference.title: self._cur_reference.title += " " + content else: self._cur_reference.title = content def journal(self, content): if self._cur_reference.journal: self._cur_reference.journal += " " + content else: self._cur_reference.journal = content def medline_id(self, content): self._cur_reference.medline_id = content def pubmed_id(self, content): self._cur_reference.pubmed_id = content def remark(self, content): """Deal with a reference comment.""" if self._cur_reference.comment: self._cur_reference.comment += " " + content else: self._cur_reference.comment = content def comment(self, content): try: self.data.annotations["comment"] += "\n" + "\n".join(content) except KeyError: self.data.annotations["comment"] = "\n".join(content) def structured_comment(self, content): self.data.annotations["structured_comment"] = content def features_line(self, content): """Get ready for the feature table when we reach the FEATURE line.""" self.start_feature_table() def start_feature_table(self): """Indicate we've got to the start of the feature table.""" # make sure we've added on our last reference object if self._cur_reference is not None: self.data.annotations["references"].append(self._cur_reference) self._cur_reference = None def feature_key(self, content): # start a new feature self._cur_feature = SeqFeature.SeqFeature() self._cur_feature.type = content self.data.features.append(self._cur_feature) def location(self, content): """Parse out location information from the location string. This uses simple Python code with some regular expressions to do the parsing, and then translates the results into appropriate objects. """ # clean up newlines and other whitespace inside the location before # parsing - locations should have no whitespace whatsoever location_line = self._clean_location(content) # Older records have junk like replace(266,"c") in the # location line. Newer records just replace this with # the number 266 and have the information in a more reasonable # place. So we'll just grab out the number and feed this to the # parser. We shouldn't really be losing any info this way. if "replace" in location_line: comma_pos = location_line.find(",") location_line = location_line[8:comma_pos] cur_feature = self._cur_feature # Handle top level complement here for speed if location_line.startswith("complement("): assert location_line.endswith(")") location_line = location_line[11:-1] strand = -1 elif "PROTEIN" in self._seq_type.upper(): strand = None else: # Assume nucleotide otherwise feature strand for # GenBank files with bad LOCUS lines set to None strand = 1 # Special case handling of the most common cases for speed if _re_simple_location.match(location_line): # e.g. "123..456" s, e = location_line.split("..") try: cur_feature.location = SeqFeature.FeatureLocation( int(s) - 1, int(e), strand ) except ValueError: # Could be non-integers, more likely bad origin wrapping cur_feature.location = _loc( location_line, self._expected_size, strand, seq_type=self._seq_type.lower(), ) return if ",)" in location_line: warnings.warn( "Dropping trailing comma in malformed feature location", BiopythonParserWarning, ) location_line = location_line.replace(",)", ")") if _solo_bond.search(location_line): # e.g. bond(196) # e.g. join(bond(284),bond(305),bond(309),bond(305)) warnings.warn( "Dropping bond qualifier in feature location", BiopythonParserWarning ) # There ought to be a better way to do this... for x in _solo_bond.finditer(location_line): x = x.group() location_line = location_line.replace(x, x[5:-1]) if _re_simple_compound.match(location_line): # e.g. join(<123..456,480..>500) i = location_line.find("(") # cur_feature.location_operator = location_line[:i] # we can split on the comma because these are simple locations locs = [] for part in location_line[i + 1 : -1].split(","): s, e = part.split("..") try: locs.append(SeqFeature.FeatureLocation(int(s) - 1, int(e), strand)) except ValueError: # Could be non-integers, more likely bad origin wrapping # In the case of bad origin wrapping, _loc will return # a CompoundLocation. CompoundLocation.parts returns a # list of the FeatureLocation objects inside the # CompoundLocation. locs.extend( _loc( part, self._expected_size, strand, self._seq_type.lower() ).parts ) if len(locs) < 2: # The CompoundLocation will raise a ValueError here! warnings.warn( "Should have at least 2 parts for compound location", BiopythonParserWarning, ) cur_feature.location = None return if strand == -1: cur_feature.location = SeqFeature.CompoundLocation( locs[::-1], operator=location_line[:i] ) else: cur_feature.location = SeqFeature.CompoundLocation( locs, operator=location_line[:i] ) return # Handle the general case with more complex regular expressions if _re_complex_location.match(location_line): # e.g. "AL121804.2:41..610" cur_feature.location = _loc( location_line, self._expected_size, strand, seq_type=self._seq_type.lower(), ) return if _re_complex_compound.match(location_line): i = location_line.find("(") # cur_feature.location_operator = location_line[:i] # Can't split on the comma because of positions like one-of(1,2,3) locs = [] for part in _split_compound_loc(location_line[i + 1 : -1]): if part.startswith("complement("): assert part[-1] == ")" part = part[11:-1] assert strand != -1, "Double complement?" part_strand = -1 else: part_strand = strand try: # There is likely a problem with origin wrapping. # Using _loc to return a CompoundLocation of the # wrapped feature and returning the two FeatureLocation # objects to extend to the list of feature locations. loc = _loc( part, self._expected_size, part_strand, seq_type=self._seq_type.lower(), ).parts except ValueError: print(location_line) print(part) raise # loc will be a list of one or two FeatureLocation items. locs.extend(loc) # Historically a join on the reverse strand has been represented # in Biopython with both the parent SeqFeature and its children # (the exons for a CDS) all given a strand of -1. Likewise, for # a join feature on the forward strand they all have strand +1. # However, we must also consider evil mixed strand examples like # this, join(complement(69611..69724),139856..140087,140625..140650) if strand == -1: # Whole thing was wrapped in complement(...) for l in locs: assert l.strand == -1 # Reverse the backwards order used in GenBank files # with complement(join(...)) cur_feature.location = SeqFeature.CompoundLocation( locs[::-1], operator=location_line[:i] ) else: cur_feature.location = SeqFeature.CompoundLocation( locs, operator=location_line[:i] ) return # Not recognised if "order" in location_line and "join" in location_line: # See Bug 3197 msg = ( 'Combinations of "join" and "order" within the same ' "location (nested operators) are illegal:\n" + location_line ) raise LocationParserError(msg) # This used to be an error.... cur_feature.location = None warnings.warn( BiopythonParserWarning( "Couldn't parse feature location: %r" % location_line ) ) def feature_qualifier(self, key, value): """When we get a qualifier key and its value. Can receive None, since you can have valueless keys such as /pseudo """ # Hack to try to preserve historical behaviour of /pseudo etc if value is None: # if the key doesn't exist yet, add an empty string if key not in self._cur_feature.qualifiers: self._cur_feature.qualifiers[key] = [""] return # otherwise just skip this key return # Remove enclosing quotation marks value = re.sub('^"|"$', "", value) # Handle NCBI escaping # Warn if escaping is not according to standard if re.search(r'[^"]"[^"]|^"[^"]|[^"]"$', value): warnings.warn( 'The NCBI states double-quote characters like " should be escaped as "" ' "(two double - quotes), but here it was not: %r" % value, BiopythonParserWarning, ) # Undo escaping, repeated double quotes -> one double quote value = value.replace('""', '"') if self._feature_cleaner is not None: value = self._feature_cleaner.clean_value(key, value) # if the qualifier name exists, append the value if key in self._cur_feature.qualifiers: self._cur_feature.qualifiers[key].append(value) # otherwise start a new list of the key with its values else: self._cur_feature.qualifiers[key] = [value] def feature_qualifier_name(self, content_list): """Use feature_qualifier instead (OBSOLETE).""" raise NotImplementedError("Use the feature_qualifier method instead.") def feature_qualifier_description(self, content): """Use feature_qualifier instead (OBSOLETE).""" raise NotImplementedError("Use the feature_qualifier method instead.") def contig_location(self, content): """Deal with CONTIG information.""" # Historically this was stored as a SeqFeature object, but it was # stored under record.annotations["contig"] and not under # record.features with the other SeqFeature objects. # # The CONTIG location line can include additional tokens like # Gap(), Gap(100) or Gap(unk100) which are not used in the feature # location lines, so storing it using SeqFeature based location # objects is difficult. # # We now store this a string, which means for BioSQL we are now in # much better agreement with how BioPerl records the CONTIG line # in the database. # # NOTE - This code assumes the scanner will return all the CONTIG # lines already combined into one long string! self.data.annotations["contig"] = content def origin_name(self, content): pass def base_count(self, content): pass def base_number(self, content): pass def sequence(self, content): """Add up sequence information as we get it. To try and make things speedier, this puts all of the strings into a list of strings, and then uses string.join later to put them together. Supposedly, this is a big time savings """ assert " " not in content self._seq_data.append(content.upper()) def record_end(self, content): """Clean up when we've finished the record.""" # Try and append the version number to the accession for the full id if not self.data.id: if "accessions" in self.data.annotations: raise ValueError( "Problem adding version number to accession: " + str(self.data.annotations["accessions"]) ) self.data.id = self.data.name # Good fall back? elif self.data.id.count(".") == 0: try: self.data.id += ".%i" % self.data.annotations["sequence_version"] except KeyError: pass # add the sequence information sequence = "".join(self._seq_data) if ( self._expected_size is not None and len(sequence) != 0 and self._expected_size != len(sequence) ): warnings.warn( "Expected sequence length %i, found %i (%s)." % (self._expected_size, len(sequence), self.data.id), BiopythonParserWarning, ) molecule_type = None if self._seq_type: # mRNA is really also DNA, since it is actually cDNA if "DNA" in self._seq_type.upper() or "MRNA" in self._seq_type.upper(): molecule_type = "DNA" # are there ever really RNA sequences in GenBank? elif "RNA" in self._seq_type.upper(): # Even for data which was from RNA, the sequence string # is usually given as DNA (T not U). Bug 3010 molecule_type = "RNA" elif ( "PROTEIN" in self._seq_type.upper() or self._seq_type == "PRT" ): # PRT is used in EMBL-bank for patents molecule_type = "protein" # work around ugly GenBank records which have circular or # linear but no indication of sequence type elif self._seq_type in ["circular", "linear", "unspecified"]: pass # we have a bug if we get here else: raise ValueError( "Could not determine molecule_type for seq_type %s" % self._seq_type ) # Don't overwrite molecule_type if molecule_type is not None: self.data.annotations["molecule_type"] = self.data.annotations.get( "molecule_type", molecule_type ) if not sequence and self._expected_size: self.data.seq = UnknownSeq( self._expected_size, character="X" if molecule_type == "protein" else "N", ) else: self.data.seq = Seq(sequence) class _RecordConsumer(_BaseGenBankConsumer): """Create a GenBank Record object from scanner generated information (PRIVATE).""" def __init__(self): _BaseGenBankConsumer.__init__(self) from . import Record self.data = Record.Record() self._seq_data = [] self._cur_reference = None self._cur_feature = None self._cur_qualifier = None def tls(self, content): self.data.tls = content.split("-") def tsa(self, content): self.data.tsa = content.split("-") def wgs(self, content): self.data.wgs = content.split("-") def add_wgs_scafld(self, content): self.data.wgs_scafld.append(content.split("-")) def locus(self, content): self.data.locus = content def size(self, content): self.data.size = content def residue_type(self, content): # Be lenient about parsing, but technically lowercase residue types are malformed. if "dna" in content or "rna" in content: warnings.warn( "Invalid seq_type (%s): DNA/RNA should be uppercase." % content, BiopythonParserWarning, ) self.data.residue_type = content def data_file_division(self, content): self.data.data_file_division = content def date(self, content): self.data.date = content def definition(self, content): self.data.definition = content def accession(self, content): for acc in self._split_accessions(content): if acc not in self.data.accession: self.data.accession.append(acc) def molecule_type(self, mol_type): """Validate and record the molecule type (for round-trip etc).""" if mol_type: if "circular" in mol_type or "linear" in mol_type: raise ParserFailureError( "Molecule type %r should not include topology" % mol_type ) # Writing out records will fail if we have a lower case DNA # or RNA string in here, so upper case it. # This is a bit ugly, but we don't want to upper case e.g. # the m in mRNA, but thanks to the strip we lost the spaces # so we need to index from the back if mol_type[-3:].upper() in ("DNA", "RNA") and not mol_type[-3:].isupper(): warnings.warn( "Non-upper case molecule type in LOCUS line: %s" % mol_type, BiopythonParserWarning, ) self.data.molecule_type = mol_type def topology( self, topology ): # noqa: D402 # flake8 thinks this line is a function signature. It ain't """Validate and record sequence topology (linear or circular as strings).""" if topology: if topology not in ["linear", "circular"]: raise ParserFailureError( "Unexpected topology %r should be linear or circular" % topology ) self.data.topology = topology def nid(self, content): self.data.nid = content def pid(self, content): self.data.pid = content def version(self, content): self.data.version = content def db_source(self, content): self.data.db_source = content.rstrip() def gi(self, content): self.data.gi = content def keywords(self, content): self.data.keywords = self._split_keywords(content) def project(self, content): self.data.projects.extend(p for p in content.split() if p) def dblink(self, content): self.data.dblinks.append(content) def segment(self, content): self.data.segment = content def source(self, content): self.data.source = content def organism(self, content): self.data.organism = content def taxonomy(self, content): self.data.taxonomy = self._split_taxonomy(content) def reference_num(self, content): """Grab the reference number and signal the start of a new reference.""" # check if we have a reference to add if self._cur_reference is not None: self.data.references.append(self._cur_reference) from . import Record self._cur_reference = Record.Reference() self._cur_reference.number = content def reference_bases(self, content): self._cur_reference.bases = content def authors(self, content): self._cur_reference.authors = content def consrtm(self, content): self._cur_reference.consrtm = content def title(self, content): if self._cur_reference is None: warnings.warn( "GenBank TITLE line without REFERENCE line.", BiopythonParserWarning ) return self._cur_reference.title = content def journal(self, content): self._cur_reference.journal = content def medline_id(self, content): self._cur_reference.medline_id = content def pubmed_id(self, content): self._cur_reference.pubmed_id = content def remark(self, content): self._cur_reference.remark = content def comment(self, content): self.data.comment += "\n".join(content) def structured_comment(self, content): self.data.structured_comment = content def primary_ref_line(self, content): """Save reference data for the PRIMARY line.""" self.data.primary.append(content) def primary(self, content): pass def features_line(self, content): """Get ready for the feature table when we reach the FEATURE line.""" self.start_feature_table() def start_feature_table(self): """Signal the start of the feature table.""" # we need to add on the last reference if self._cur_reference is not None: self.data.references.append(self._cur_reference) def feature_key(self, content): """Grab the key of the feature and signal the start of a new feature.""" # first add on feature information if we've got any self._add_feature() from . import Record self._cur_feature = Record.Feature() self._cur_feature.key = content def _add_feature(self): """Add a feature to the record, with relevant checks (PRIVATE). This does all of the appropriate checking to make sure we haven't left any info behind, and that we are only adding info if it exists. """ if self._cur_feature is not None: # if we have a left over qualifier, add it to the qualifiers # on the current feature if self._cur_qualifier is not None: self._cur_feature.qualifiers.append(self._cur_qualifier) self._cur_qualifier = None self.data.features.append(self._cur_feature) def location(self, content): self._cur_feature.location = self._clean_location(content) def feature_qualifier(self, key, value): self.feature_qualifier_name([key]) if value is not None: self.feature_qualifier_description(value) def feature_qualifier_name(self, content_list): """Deal with qualifier names. We receive a list of keys, since you can have valueless keys such as /pseudo which would be passed in with the next key (since no other tags separate them in the file) """ from . import Record for content in content_list: # the record parser keeps the /s -- add them if we don't have 'em if not content.startswith("/"): content = "/%s" % content # add on a qualifier if we've got one if self._cur_qualifier is not None: self._cur_feature.qualifiers.append(self._cur_qualifier) self._cur_qualifier = Record.Qualifier() self._cur_qualifier.key = content def feature_qualifier_description(self, content): # if we have info then the qualifier key should have a ='s if "=" not in self._cur_qualifier.key: self._cur_qualifier.key = "%s=" % self._cur_qualifier.key cur_content = self._remove_newlines(content) # remove all spaces from the value if it is a type where spaces # are not important for remove_space_key in self.__class__.remove_space_keys: if remove_space_key in self._cur_qualifier.key: cur_content = self._remove_spaces(cur_content) self._cur_qualifier.value = self._normalize_spaces(cur_content) def base_count(self, content): self.data.base_counts = content def origin_name(self, content): self.data.origin = content def contig_location(self, content): """Signal that we have contig information to add to the record.""" self.data.contig = self._clean_location(content) def sequence(self, content): """Add sequence information to a list of sequence strings. This removes spaces in the data and uppercases the sequence, and then adds it to a list of sequences. Later on we'll join this list together to make the final sequence. This is faster than adding on the new string every time. """ assert " " not in content self._seq_data.append(content.upper()) def record_end(self, content): """Signal the end of the record and do any necessary clean-up.""" # add together all of the sequence parts to create the # final sequence string self.data.sequence = "".join(self._seq_data) # add on the last feature self._add_feature() def parse(handle): """Iterate over GenBank formatted entries as Record objects. >>> from Bio import GenBank >>> with open("GenBank/NC_000932.gb") as handle: ... for record in GenBank.parse(handle): ... print(record.accession) ['NC_000932'] To get SeqRecord objects use Bio.SeqIO.parse(..., format="gb") instead. """ return iter(Iterator(handle, RecordParser())) def read(handle): """Read a handle containing a single GenBank entry as a Record object. >>> from Bio import GenBank >>> with open("GenBank/NC_000932.gb") as handle: ... record = GenBank.read(handle) ... print(record.accession) ['NC_000932'] To get a SeqRecord object use Bio.SeqIO.read(..., format="gb") instead. """ iterator = parse(handle) try: record = next(iterator) except StopIteration: raise ValueError("No records found in handle") from None try: next(iterator) raise ValueError("More than one record found in handle") except StopIteration: pass return record if __name__ == "__main__": from Bio._utils import run_doctest run_doctest()