cpt_genome_editor: gff3.py comparison

comparison gff3.py @ 3:134bb2d7cdfd draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

author	cpt
date	Mon, 05 Jun 2023 02:43:21 +0000
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comparison

equal deleted inserted replaced

-:787ce84e8d16
+:134bb2d7cdfd
+import copy
+import logging
+log = logging.getLogger()
+log.setLevel(logging.WARN)
+def feature_lambda(
+feature_list,
+test,
+test_kwargs,
+subfeatures=True,
+parent=None,
+invert=False,
+recurse=True,
+):
+"""Recursively search through features, testing each with a test function, yielding matches.
+GFF3 is a hierachical data structure, so we need to be able to recursively
+search through features. E.g. if you're looking for a feature with
+ID='bob.42', you can't just do a simple list comprehension with a test
+case. You don't know how deeply burried bob.42 will be in the feature tree. This is where feature_lambda steps in.
+:type feature_list: list
+:param feature_list: an iterable of features
+:type test: function reference
+:param test: a closure with the method signature (feature, **kwargs) where
+the kwargs are those passed in the next argument. This
+function should return True or False, True if the feature is
+to be yielded as part of the main feature_lambda function, or
+False if it is to be ignored. This function CAN mutate the
+features passed to it (think "apply").
+:type test_kwargs: dictionary
+:param test_kwargs: kwargs to pass to your closure when it is called.
+:type subfeatures: boolean
+:param subfeatures: when a feature is matched, should just that feature be
+yielded to the caller, or should the entire sub_feature
+tree for that feature be included? subfeatures=True is
+useful in cases such as searching for a gene feature,
+and wanting to know what RBS/Shine_Dalgarno_sequences
+are in the sub_feature tree (which can be accomplished
+with two feature_lambda calls). subfeatures=False is
+useful in cases when you want to process (and possibly
+return) the entire feature tree, such as applying a
+qualifier to every single feature.
+:type invert: boolean
+:param invert: Negate/invert the result of the filter.
+:rtype: yielded list
+:return: Yields a list of matching features.
+"""
+# Either the top level set of [features] or the subfeature attribute
+for feature in feature_list:
+feature._parent = parent
+if not parent:
+# Set to self so we cannot go above root.
+feature._parent = feature
+test_result = test(feature, **test_kwargs)
+# if (not invert and test_result) or (invert and not test_result):
+if invert ^ test_result:
+if not subfeatures:
+feature_copy = copy.deepcopy(feature)
+feature_copy.sub_features = list()
+yield feature_copy
+else:
+yield feature
+if recurse and hasattr(feature, "sub_features"):
+for x in feature_lambda(
+feature.sub_features,
+test,
+test_kwargs,
+subfeatures=subfeatures,
+parent=feature,
+invert=invert,
+recurse=recurse,
+):
+yield x
+def fetchParent(feature):
+if not hasattr(feature, "_parent") or feature._parent is None:
+return feature
+else:
+return fetchParent(feature._parent)
+def feature_test_true(feature, **kwargs):
+return True
+def feature_test_type(feature, **kwargs):
+if "type" in kwargs:
+return str(feature.type).upper() == str(kwargs["type"]).upper()
+elif "types" in kwargs:
+for x in kwargs["types"]:
+if str(feature.type).upper() == str(x).upper():
+return True
+return False
+raise Exception("Incorrect feature_test_type call, need type or types")
+def feature_test_qual_value(feature, **kwargs):
+"""Test qualifier values.
+For every feature, check that at least one value in
+feature.quailfiers(kwargs['qualifier']) is in kwargs['attribute_list']
+"""
+if isinstance(kwargs["qualifier"], list):
+for qualifier in kwargs["qualifier"]:
+for attribute_value in feature.qualifiers.get(qualifier, []):
+if attribute_value in kwargs["attribute_list"]:
+return True
+else:
+for attribute_value in feature.qualifiers.get(kwargs["qualifier"], []):
+if attribute_value in kwargs["attribute_list"]:
+return True
+return False
+def feature_test_location(feature, **kwargs):
+if "strand" in kwargs:
+if feature.location.strand != kwargs["strand"]:
+return False
+return feature.location.start <= kwargs["loc"] <= feature.location.end
+def feature_test_quals(feature, **kwargs):
+"""
+Example::
+a = Feature(qualifiers={'Note': ['Some notes', 'Aasdf']})
+# Check if a contains a Note
+feature_test_quals(a, {'Note': None})  # Returns True
+feature_test_quals(a, {'Product': None})  # Returns False
+# Check if a contains a note with specific value
+feature_test_quals(a, {'Note': ['ome']})  # Returns True
+# Check if a contains a note with specific value
+feature_test_quals(a, {'Note': ['other']})  # Returns False
+"""
+for key in kwargs:
+if key not in feature.qualifiers:
+return False
+# Key is present, no value specified
+if kwargs[key] is None:
+return True
+# Otherwise there is a key value we're looking for.
+# so we make a list of matches
+matches = []
+# And check all of the feature qualifier valuse
+for value in feature.qualifiers[key]:
+# For that kwargs[key] value
+for x in kwargs[key]:
+matches.append(x in value)
+# If none matched, then we return false.
+if not any(matches):
+return False
+return True
+def feature_test_contains(feature, **kwargs):
+if "index" in kwargs:
+return feature.location.start < kwargs["index"] < feature.location.end
+elif "range" in kwargs:
+return (
+feature.location.start < kwargs["range"]["start"] < feature.location.end
+and feature.location.start < kwargs["range"]["end"] < feature.location.end
+)
+else:
+raise RuntimeError("Must use index or range keyword")
+def get_id(feature=None, parent_prefix=None):
+result = ""
+if parent_prefix is not None:
+result += parent_prefix + "|"
+if "locus_tag" in feature.qualifiers:
+result += feature.qualifiers["locus_tag"][0]
+elif "gene" in feature.qualifiers:
+result += feature.qualifiers["gene"][0]
+elif "Gene" in feature.qualifiers:
+result += feature.qualifiers["Gene"][0]
+elif "product" in feature.qualifiers:
+result += feature.qualifiers["product"][0]
+elif "Product" in feature.qualifiers:
+result += feature.qualifiers["Product"][0]
+elif "Name" in feature.qualifiers:
+result += feature.qualifiers["Name"][0]
+else:
+return feature.id
+# Leaving in case bad things happen.
+# result += '%s_%s_%s_%s' % (
+# feature.id,
+# feature.location.start,
+# feature.location.end,
+# feature.location.strand
+# )
+return result
+def get_gff3_id(gene):
+return gene.qualifiers.get("Name", [gene.id])[0]
+def ensure_location_in_bounds(start=0, end=0, parent_length=0):
+# This prevents frameshift errors
+while start < 0:
+start += 3
+while end < 0:
+end += 3
+while start > parent_length:
+start -= 3
+while end > parent_length:
+end -= 3
+return (start, end)
+def coding_genes(feature_list):
+for x in genes(feature_list):
+if (
+len(
+list(
+feature_lambda(
+x.sub_features,
+feature_test_type,
+{"type": "CDS"},
+subfeatures=False,
+)
+)
+)
+> 0
+):
+yield x
+def genes(feature_list, feature_type="gene", sort=False):
+"""
+Simple filter to extract gene features from the feature set.
+"""
+if not sort:
+for x in feature_lambda(
+feature_list, feature_test_type, {"type": feature_type}, subfeatures=True
+):
+yield x
+else:
+data = list(genes(feature_list, feature_type=feature_type, sort=False))
+data = sorted(data, key=lambda feature: feature.location.start)
+for x in data:
+yield x
+def wa_unified_product_name(feature):
+"""
+Try and figure out a name. We gave conflicting instructions, so
+this isn't as trivial as it should be. Sometimes it will be in
+'product' or 'Product', othertimes in 'Name'
+"""
+# Manually applied tags.
+protein_product = feature.qualifiers.get(
+"product", feature.qualifiers.get("Product", [None])
+)[0]
+# If neither of those are available ...
+if protein_product is None:
+# And there's a name...
+if "Name" in feature.qualifiers:
+if not is_uuid(feature.qualifiers["Name"][0]):
+protein_product = feature.qualifiers["Name"][0]
+return protein_product
+def is_uuid(name):
+return name.count("-") == 4 and len(name) == 36
+def get_rbs_from(gene):
+# Normal RBS annotation types
+rbs_rbs = list(
+feature_lambda(
+gene.sub_features, feature_test_type, {"type": "RBS"}, subfeatures=False
+)
+)
+rbs_sds = list(
+feature_lambda(
+gene.sub_features,
+feature_test_type,
+{"type": "Shine_Dalgarno_sequence"},
+subfeatures=False,
+)
+)
+# Fraking apollo
+apollo_exons = list(
+feature_lambda(
+gene.sub_features, feature_test_type, {"type": "exon"}, subfeatures=False
+)
+)
+apollo_exons = [x for x in apollo_exons if len(x) < 10]
+# These are more NCBI's style
+regulatory_elements = list(
+feature_lambda(
+gene.sub_features,
+feature_test_type,
+{"type": "regulatory"},
+subfeatures=False,
+)
+)
+rbs_regulatory = list(
+feature_lambda(
+regulatory_elements,
+feature_test_quals,
+{"regulatory_class": ["ribosome_binding_site"]},
+subfeatures=False,
+)
+)
+# Here's hoping you find just one ;)
+return rbs_rbs + rbs_sds + rbs_regulatory + apollo_exons
+def nice_name(record):
+"""
+get the real name rather than NCBI IDs and so on. If fails, will return record.id
+"""
+name = record.id
+likely_parental_contig = list(genes(record.features, feature_type="contig"))
+if len(likely_parental_contig) == 1:
+name = likely_parental_contig[0].qualifiers.get("organism", [name])[0]
+return name
+def fsort(it):
+for i in sorted(it, key=lambda x: int(x.location.start)):
+yield i

Mercurial > repos > cpt > cpt_genome_editor

comparison gff3.py @ 3:134bb2d7cdfd draft