diff gff3_rebase.py @ 0:d78175596286 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff3_rebase.py	Mon Jan 08 09:20:33 2024 +0000
@@ -0,0 +1,209 @@
+#!/usr/bin/env python
+import argparse
+import copy
+import logging
+import sys
+
+from BCBio import GFF
+from Bio.SeqFeature import FeatureLocation
+
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger(__name__)
+
+__author__ = "Eric Rasche"
+__version__ = "0.4.0"
+__maintainer__ = "Eric Rasche"
+__email__ = "[e-mail]"
+
+
+def feature_lambda(feature_list, test, test_kwargs, subfeatures=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.
+
+    :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:
+        if test(feature, **test_kwargs):
+            if not subfeatures:
+                feature_copy = copy.deepcopy(feature)
+                feature_copy.sub_features = []
+                yield feature_copy
+            else:
+                yield feature
+
+        if hasattr(feature, "sub_features"):
+            for x in feature_lambda(
+                feature.sub_features, test, test_kwargs, subfeatures=subfeatures
+            ):
+                yield x
+
+
+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']
+    """
+    for attribute_value in feature.qualifiers.get(kwargs["qualifier"], []):
+        if attribute_value in kwargs["attribute_list"]:
+            return True
+    return False
+
+
+def __get_features(child, interpro=False):
+    child_features = {}
+    for rec in GFF.parse(child):
+        # Only top level
+        for feature in rec.features:
+            # Get the record id as parent_feature_id (since this is how it will be during remapping)
+            parent_feature_id = rec.id
+            # If it's an interpro specific gff3 file
+            if interpro:
+                # Then we ignore polypeptide features as they're useless
+                if feature.type == "polypeptide":
+                    continue
+                # If there's an underscore, we strip up to that underscore?
+                # I do not know the rationale for this, removing.
+                # if '_' in parent_feature_id:
+                # parent_feature_id = parent_feature_id[parent_feature_id.index('_') + 1:]
+
+            try:
+                child_features[parent_feature_id].append(feature)
+            except KeyError:
+                child_features[parent_feature_id] = [feature]
+            # Keep a list of feature objects keyed by parent record id
+    return child_features
+
+
+def __update_feature_location(feature, parent, protein2dna):
+    start = feature.location.start
+    end = feature.location.end
+    if protein2dna:
+        start *= 3
+        end *= 3
+
+    if parent.location.strand >= 0:
+        ns = parent.location.start + start
+        ne = parent.location.start + end
+        st = +1
+    else:
+        ns = parent.location.end - end
+        ne = parent.location.end - start
+        st = -1
+
+    # Don't let start/stops be less than zero. It's technically valid for them
+    # to be (at least in the model I'm working with) but it causes numerous
+    # issues.
+    #
+    # Instead, we'll replace with %3 to try and keep it in the same reading
+    # frame that it should be in.
+    if ns < 0:
+        ns %= 3
+    if ne < 0:
+        ne %= 3
+
+    feature.location = FeatureLocation(ns, ne, strand=st)
+
+    if hasattr(feature, "sub_features"):
+        for subfeature in feature.sub_features:
+            __update_feature_location(subfeature, parent, protein2dna)
+
+
+def rebase(parent, child, interpro=False, protein2dna=False, map_by="ID"):
+    # get all of the features we will be re-mapping in a dictionary, keyed by parent feature ID
+    child_features = __get_features(child, interpro=interpro)
+
+    for rec in GFF.parse(parent):
+        replacement_features = []
+        for feature in feature_lambda(
+            rec.features,
+            # Filter features in the parent genome by those that are
+            # "interesting", i.e. have results in child_features array.
+            # Probably an unnecessary optimisation.
+            feature_test_qual_value,
+            {
+                "qualifier": map_by,
+                "attribute_list": child_features.keys(),
+            },
+            subfeatures=False,
+        ):
+
+            # Features which will be re-mapped
+            to_remap = child_features[feature.id]
+            # TODO: update starts
+            fixed_features = []
+            for x in to_remap:
+                # Then update the location of the actual feature
+                __update_feature_location(x, feature, protein2dna)
+
+                if interpro:
+                    for y in ("status", "Target"):
+                        try:
+                            del x.qualifiers[y]
+                        except Exception:
+                            pass
+
+                fixed_features.append(x)
+            replacement_features.extend(fixed_features)
+        # We do this so we don't include the original set of features that we
+        # were rebasing against in our result.
+        rec.features = replacement_features
+        rec.annotations = {}
+        GFF.write([rec], sys.stdout)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="rebase gff3 features against parent locations", epilog=""
+    )
+    parser.add_argument(
+        "parent", type=argparse.FileType("r"), help="Parent GFF3 annotations"
+    )
+    parser.add_argument(
+        "child",
+        type=argparse.FileType("r"),
+        help="Child GFF3 annotations to rebase against parent",
+    )
+    parser.add_argument(
+        "--interpro", action="store_true", help="Interpro specific modifications"
+    )
+    parser.add_argument(
+        "--protein2dna",
+        action="store_true",
+        help="Map protein translated results to original DNA data",
+    )
+    parser.add_argument("--map_by", help="Map by key", default="ID")
+    args = parser.parse_args()
+    rebase(**vars(args))