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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc

#!/usr/bin/env python
"""Convert a GFF and associated FASTA file into GenBank format.

Usage:
gff_to_genbank.py <GFF annotation file> <FASTA sequence file>
"""
import argparse
import sys
import re
import copy
import itertools
import logging
from Bio import SeqIO

# from Bio.Alphabet import generic_dna
from Bio.SeqFeature import CompoundLocation, FeatureLocation
from CPT_GFFParser import gffParse, gffWrite
from gff3 import (
    feature_lambda,
    wa_unified_product_name,
    is_uuid,
    feature_test_type,
    fsort,
    feature_test_true,
    feature_test_quals,
)

default_name = re.compile(r"^gene_(\d+)$")
logging.basicConfig(level=logging.INFO)


def rename_key(ds, k_f, k_t):
    """Rename a key in a dictionary and return it, FP style"""
    # If they key is not in the dictionary, just return immediately
    if k_f not in ds:
        return ds

    # Otherwise, we check if the target key is in there
    if k_t in ds:
        # If it is, we need to append
        ds[k_t] += ds[k_f]
    else:
        # if not, we can just set.
        ds[k_t] = ds[k_f]

    # Remove source
    del ds[k_f]
    return ds


def gff3_to_genbank(gff_file, fasta_file, transltbl):
    fasta_input = SeqIO.to_dict(SeqIO.parse(fasta_file, "fasta"))  # , generic_dna))
    gff_iter = gffParse(gff_file, fasta_input)

    for record in gff_iter:
        yield handle_record(record, transltbl)


def handle_non_gene_features(features):
    # These are NON-GENE features (maybe terminators? etc?)
    for feature in feature_lambda(
        features,
        feature_test_type,
        {"type": "gene"},
        subfeatures=False,
        invert=True,
        recurse=True,  #  used to catch RBS from new apollo runs (used to be False)
    ):
        if feature.type in (
            "terminator",
            "tRNA",
            "Shine_Dalgarno_sequence",
            "sequence_feature",
            "recombination_feature",
            "sequence_alteration",
            "binding_site",
        ):
            yield feature
        elif feature.type in ("CDS",):
            pass
        else:
            yield feature


def fminmax(feature):
    fmin = None
    fmax = None
    for sf in feature_lambda([feature], feature_test_true, {}, subfeatures=True):
        if fmin is None:
            fmin = sf.location.start
            fmax = sf.location.end
        if sf.location.start < fmin:
            fmin = sf.location.start
        if sf.location.end > fmax:
            fmax = sf.location.end
    return fmin, fmax


def fix_gene_boundaries(feature):
    # There is a frustrating bug in apollo whereby we have created gene
    # features which are LARGER than expected, but we cannot see this.
    # We only see a perfect sized gene + great SD together.
    #
    # So, we have this awful hack to clamp the location of the gene
    # feature to the contained mRNAs. This is good enough for now.
    fmin, fmax = fminmax(feature)
    if feature.location.strand > 0:
        feature.location = FeatureLocation(fmin, fmax, strand=1)
    else:
        feature.location = FeatureLocation(fmin, fmax, strand=-1)
    return feature


def fix_gene_qualifiers(name, feature, fid):
    for mRNA in feature.sub_features:
        mRNA.qualifiers["locus_tag"] = "CPT_%s_%03d" % (name, fid)
        # And some exons below that
        sf_replacement = []
        for sf in mRNA.sub_features:
            # We set a locus_tag on ALL sub features
            sf.qualifiers["locus_tag"] = "CPT_%s_%03d" % (name, fid)
            # Remove Names which are UUIDs
            # NOT GOOD PRACTICE
            try:
                if is_uuid(sf.qualifiers["Name"][0]):
                    del sf.qualifiers["Name"]
            except KeyError:
                continue  # might should go back to pass, I have not put thought into this still

            # If it is the RBS exon (mis-labelled by apollo as 'exon')
            if sf.type == "exon" and len(sf) < 10:
                sf.type = "Shine_Dalgarno_sequence"
                sf_replacement.append(sf)
            # and if it is the CDS
            elif sf.type == "CDS":
                # Update CDS qualifiers with all info that was on parent
                sf.qualifiers.update(feature.qualifiers)
                sf_replacement.append(sf)
            else:
                sf_replacement.append(sf)
        if mRNA.type == "tRNA":
            mRNA.qualifiers["product"] = mRNA.qualifiers["Name"]
        # Handle multiple child CDS features by merging them.
        # Replace the subfeatures on the mRNA
        mRNA.sub_features = merge_multi_cds(sf_replacement)
    return feature


def fix_frameshifted(features):
    logging.info("Fixing Frameshifted group: [%s]", str(features))
    genes = features
    # Find all mRNAs (plus reduce nested list into flattened one)
    mRNAs = sum([f.sub_features for f in genes], [])
    # Find all CDSs (plus reduce nested list into flattened one)
    cdss = sum([m.sub_features for m in mRNAs], [])
    # List to store the RBSs which we'll break apart + re-attach later.
    rbss = []
    # List to store all of the CDSs (i.e. cdss - rbss)
    cdss2 = []
    # Copy genes + clean out subfeatures. We'll re-use these constructs.
    fixed_features = copy.deepcopy(genes)
    for f in fixed_features:
        f.sub_features = []
    # Copy / empty out mRNAs
    fixed_mrnas = copy.deepcopy(mRNAs)
    for f in fixed_mrnas:
        f.sub_features = []
        f.qualifiers = {}
    # Fill rbss + cdss2
    for cds in cdss:
        if "frameshift" in cds.qualifiers:
            del cds.qualifiers["frameshift"]
        # Ignore short features, as those are RBSs
        if len(cds) < 15:
            rbss.append(cds)
            continue
        # Otherwise cdss.
        else:
            cdss2.append(cds)
    # Ok, now have cdss2 to deal with.
    other = []
    # Find the two with least value for distance between end / start (strand aware).
    # For every possible pair, we'll check their distance
    match_data = {}
    for (a, b) in itertools.permutations(cdss2, 2):
        if a.location.start < b.location.start:
            # A is downstream of B
            match_data[(a, b)] = b.location.start - a.location.end
        else:
            match_data[(a, b)] = a.location.start - b.location.end

    # Now we'll find the features which are closest in terms of start/end
    ((merge_a, merge_b), value) = max(match_data.items(), key=lambda kv: kv[1])
    # And get the non-matching features into other
    for f in cdss2:
        if f != merge_a and f != merge_b:
            other.append(f)
    # Back to the merge_a/b
    # With those, we'll merge them into one feature, and discard the other.
    merge_a.location = CompoundLocation([merge_a.location, merge_b.location])
    # The gene + RBSs should be identical and two/two.
    assert len(fixed_features) == 2
    # If not, we can just duplicate the RBS, doesn't matter.
    noRBS = len(rbss) == 0
    if len(rbss) != 2 and not noRBS:
        rbss = [rbss[0], copy.deepcopy(rbss[0])]
    # Now re-construct.
    gene_0 = fixed_features[0]
    gene_1 = fixed_features[1]
    mRNA_0 = fixed_mrnas[0]
    mRNA_1 = fixed_mrnas[1]

    if not noRBS:
        mRNA_0.sub_features = [rbss[0], merge_a]
        mRNA_1.sub_features = other + [rbss[1]]
    else:
        mRNA_0.sub_features = [merge_a]
        mRNA_1.sub_features = other
    mRNA_0 = fix_gene_boundaries(mRNA_0)
    mRNA_1 = fix_gene_boundaries(mRNA_1)

    gene_0.sub_features = [mRNA_0]
    gene_1.sub_features = [mRNA_1]
    gene_0 = fix_gene_boundaries(gene_0)
    gene_1 = fix_gene_boundaries(gene_1)

    return fixed_features


def fix_frameshifts(features):
    # Collect all gene features where at least one subfeature has a
    # frameshift=??? annotation.
    def has_frameshift_qual(f):
        return (
            len(
                list(
                    feature_lambda(
                        f.sub_features, feature_test_quals, {"frameshift": None}
                    )
                )
            )
            > 0
        )

    def has_frameshift_qual_val(f, val):
        return (
            len(
                list(
                    feature_lambda(
                        f.sub_features, feature_test_quals, {"frameshift": val}
                    )
                )
            )
            > 0
        )

    def get_frameshift_qual(f):
        for f in feature_lambda(
            f.sub_features, feature_test_quals, {"frameshift": None}
        ):
            return f.qualifiers["frameshift"]

    to_frameshift = [x for x in features if x.type == "gene" and has_frameshift_qual(x)]
    fixed = [x for x in features if x not in to_frameshift]

    frameshift_keys = set(sum(map(get_frameshift_qual, to_frameshift), []))
    for key in frameshift_keys:
        # Get features matching that key
        current = [x for x in to_frameshift if has_frameshift_qual_val(x, key)]
        # Fix them and append them
        fixed += fix_frameshifted(current)

    return fixed


def remove_useless_features(features):
    # Drop mRNAs, apollo crap, useless CDSs
    for f in features:
        if f.type in (
            "non_canonical_three_prime_splice_site",
            "non_canonical_five_prime_splice_site",
            "stop_codon_read_through",
            "mRNA",
            "exon",
        ):
            continue
        else:
            if f.type == "CDS" and len(f) < 10:
                # Another RBS mistake
                continue
            # We use the full GO term, but it should be less than that.
            if f.type == "Shine_Dalgarno_sequence":
                f.type = "RBS"

            if f.type == "sequence_feature":
                f.type = "misc_feature"

            if f.type == "recombination_feature":
                f.type = "misc_recomb"

            if f.type == "sequence_alteration":
                f.type = "variation"

            if f.type == "binding_site":
                f.type = "misc_binding"

            yield f


def merge_multi_cds(mRNA_sf):
    cdss = [x for x in mRNA_sf if x.type == "CDS"]
    non_cdss = [x for x in mRNA_sf if x.type != "CDS"]
    if len(cdss) <= 1:
        return non_cdss + cdss
    else:
        # Grab all locations, and sort them so we can work with them rationally.
        locations = sorted([x.location for x in cdss], key=lambda y: y.start)
        # Pick randomly a main CDS
        main_cds = cdss[0]
        # We'll merge the other CDSs into this one.
        main_cds.location = CompoundLocation(locations)
        return non_cdss + [main_cds]


def handle_record(record, transltbl):
    full_feats = []
    for feature in fsort(record.features):
        if (
            feature.type == "region"
            and "source" in feature.qualifiers
            and "GenBank" in feature.qualifiers["source"]
        ):
            feature.type = "source"

            if "comment1" in feature.qualifiers:
                del feature.qualifiers["comment1"]

            if "Note" in feature.qualifiers:
                record.annotations = feature.qualifiers
                if len(feature.qualifiers["Note"]) > 1:
                    record.annotations["comment"] = feature.qualifiers["Note"][1]
                del feature.qualifiers["Note"]

            if "comment" in feature.qualifiers:
                del feature.qualifiers["comment"]

    # We'll work on a separate copy of features to avoid modifying a list
    # we're iterating over
    replacement_feats = []
    replacement_feats += list(handle_non_gene_features(record.features))

    # Renumbering requires sorting
    fid = 0
    for feature in fsort(
        feature_lambda(
            record.features, feature_test_type, {"type": "gene"}, subfeatures=True
        )
    ):
        # Our modifications only involve genes
        fid += 1

        feature = fix_gene_boundaries(feature)
        # Which have mRNAs we'll drop later
        feature = fix_gene_qualifiers(record.id, feature, fid)

        # Wipe out the parent gene's data, leaving only a locus_tag
        feature.qualifiers = {"locus_tag": "CPT_%s_%03d" % (record.id, fid)}

        # Patch our features back in (even if they're non-gene features)
        replacement_feats.append(feature)

    replacement_feats = fix_frameshifts(replacement_feats)
    # exit(0)
    flat_features = feature_lambda(
        replacement_feats, lambda x: True, {}, subfeatures=True
    )

    flat_features = remove_useless_features(flat_features)

    # Meat of our modifications
    for flat_feat in flat_features:
        # Try and figure out a name. We gave conflicting instructions, so
        # this isn't as trivial as it should be.
        protein_product = wa_unified_product_name(flat_feat)

        for x in (
            "source",
            "phase",
            "Parent",
            "ID",
            "owner",
            "date_creation",
            "date_last_modified",
            "datasetSource",
        ):
            if x in flat_feat.qualifiers:
                if x == "ID":
                    flat_feat._ID = flat_feat.qualifiers["ID"]
                del flat_feat.qualifiers[x]

        # Add product tag
        if flat_feat.type == "CDS":
            flat_feat.qualifiers["product"] = [protein_product]
            flat_feat.qualifiers["transl_table"] = [transltbl]
            if "Product" in flat_feat.qualifiers:
                del flat_feat.qualifiers["Product"]
        elif flat_feat.type == "RBS":
            if "locus_tag" not in flat_feat.qualifiers.keys():
                continue

        elif flat_feat.type == "terminator":
            flat_feat.type = "regulatory"
            flat_feat.qualifiers = {"regulatory_class": "terminator"}

        # In genbank format, note is lower case.
        flat_feat.qualifiers = rename_key(flat_feat.qualifiers, "Note", "note")
        flat_feat.qualifiers = rename_key(flat_feat.qualifiers, "description", "note")
        flat_feat.qualifiers = rename_key(flat_feat.qualifiers, "protein", "note")
        flat_feat.qualifiers = rename_key(flat_feat.qualifiers, "Dbxref", "db_xref")
        if "Name" in flat_feat.qualifiers:
            del flat_feat.qualifiers["Name"]

        # more apollo nonsense
        if "Manually set translation start" in flat_feat.qualifiers.get("note", []):
            flat_feat.qualifiers["note"].remove("Manually set translation start")

        # Append the feature
        full_feats.append(flat_feat)

    # Update our features
    record.features = fsort(full_feats)
    # Strip off record names that would cause crashes.
    record.name = record.name[0:16]
    return record


if __name__ == "__main__":
    # Grab all of the filters from our plugin loader
    parser = argparse.ArgumentParser(description="Convert gff3 to gbk")
    parser.add_argument("gff_file", type=argparse.FileType("r"), help="GFF3 file")
    parser.add_argument("fasta_file", type=argparse.FileType("r"), help="Fasta Input")
    parser.add_argument(
        "--transltbl",
        type=int,
        default=11,
        help="Translation Table choice for CDS tag, default 11",
    )
    args = parser.parse_args()

    for record in gff3_to_genbank(**vars(args)):
        record.annotations["molecule_type"] = "DNA"
        # record.seq.alphabet = generic_dna
        SeqIO.write([record], sys.stdout, "genbank")