annotate gbk_compare.py @ 1:1909729a1fd3 draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

#!/usr/bin/env python3
"""
Copyright 2019 Ryan Wick ([e-mail])
https://github.com/rrwick/Compare-annotations/
This program is free software: you can redistribute it and/or modify it under the terms of the GNU
General Public License as published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License along with this program.  If not,
see <https://www.gnu.org/licenses/>.
"""

import argparse
from Bio import SeqIO
from Bio import pairwise2
from Bio.pairwise2 import format_alignment
import itertools
import sys


def addArr(arrA, arrB):
    res = []
    for x in range(0, min(len(arrA), len(arrB))):
        res.append(arrA[x] + arrB[x])
    return res


def get_arguments():
    parser = argparse.ArgumentParser(
        description="Compare GenBank annotations",
        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
    )

    parser.add_argument(
        "annotation_1", type=str, help="First annotated genome in Genbank format"
    )
    parser.add_argument(
        "annotation_2", type=str, help="Second annotated genome in Genbank format"
    )

    parser.add_argument(
        "--match_identity_threshold",
        type=float,
        default=0.7,
        help="Two genes must have at least this identity to be considerd the same (0.0 to 1.0)",
    )
    parser.add_argument(
        "--allowed_skipped_genes",
        type=int,
        default=10,
        help="This many missing genes are allowed when aligning the annotations",
    )
    parser.add_argument("--addNotes", action="store_true", help="Add Note fields")

    parser.add_argument("-sumOut", type=argparse.FileType("w"), help="Summary out file")
    args = parser.parse_args()
    return args


def main():
    args = get_arguments()

    # Load in the CDS features from the two assemblies.
    old = SeqIO.parse(args.annotation_1, "genbank")
    new = SeqIO.parse(args.annotation_2, "genbank")
    old_record = next(old)
    new_record = next(new)
    old_features, new_features = [], []
    for f in old_record.features:
        if f.type == "CDS":
            old_features.append(f)
    for f in new_record.features:
        if f.type == "CDS":
            new_features.append(f)

    args.sumOut.write(
        "Features in First Genbank's assembly:\t" + str(len(old_features)) + "\n"
    )
    args.sumOut.write(
        "Features in Second Genbank's assembly:\t" + str(len(new_features)) + "\n\n"
    )

    # Align the features to each other.
    offsets = sorted(
        list(
            itertools.product(
                range(args.allowed_skipped_genes + 1),
                range(args.allowed_skipped_genes + 1),
            )
        ),
        key=lambda x: x[0] + x[1],
    )
    old_i, new_i = 0, 0
    exactRec = 0
    inexactRec = [0, 0, 0]
    hypoRec = [0, 0, 0]
    newCount = 0
    oldCount = 0
    if args.addNotes:
        print(
            "First Record CDS Product\tSimilarity\tSecond Record CDS Product\tPercent Identity\tLength Difference\tFirst Gbk's CDS Location\tSecond Gbk's CDS Location\tHypothetical Status\tFirst Record's Notes\tSecond Record's Notes\n"
        )
    else:
        print(
            "First Record CDS Product\tSimilarity\tSecond Record CDS Product\tPercent Identity\tLength Difference\tFirst Gbk's CDS Location\tSecond Gbk's CDS Location\tHypothetical Status\n"
        )
    while True:
        if old_i >= len(old_features) and new_i >= len(new_features):
            break

        for old_offset, new_offset in offsets:
            try:
                old_feature = old_features[old_i + old_offset]
            except IndexError:
                old_feature = None
            try:
                new_feature = new_features[new_i + new_offset]
            except IndexError:
                new_feature = None
            try:
                match, identity, length_diff = compare_features(
                    old_feature,
                    new_feature,
                    old_record,
                    new_record,
                    args.match_identity_threshold,
                )
            except TypeError:
                break
            if match:
                for j in range(old_offset):
                    print_in_old_not_new(old_features[old_i + j])
                    oldCount += 1
                for j in range(new_offset):
                    print_in_new_not_old(new_features[new_i + j])
                    newCount += 1
                if identity == 1.0:
                    exactRec += 1
                res1, res2 = print_match(
                    old_features[old_i + old_offset],
                    new_features[new_i + new_offset],
                    identity,
                    length_diff,
                    args.addNotes,
                )
                inexactRec = addArr(inexactRec, res1)
                hypoRec = addArr(hypoRec, res2)
                old_i += old_offset
                new_i += new_offset
                break
        else:
            sys.stderr.write(
                "Exceeded allowed number of skipped genes ("
                + str(args.allowed_skipped_genes)
                + "), unable to maintain alignment and continue comparison.\n"
            )
            exit(2)

        if old_feature is None and new_feature is None:
            break

        old_i += 1
        new_i += 1

    args.sumOut.write("Exact Match:\t" + str(exactRec) + "\n\n")

    args.sumOut.write(
        "Inexact Match:\t" + str(inexactRec[0] + inexactRec[1] + inexactRec[2]) + "\n"
    )
    args.sumOut.write("  Same length:\t" + str(inexactRec[0]) + "\n")
    args.sumOut.write("  Second Gbk Seq longer:\t" + str(inexactRec[2]) + "\n")
    args.sumOut.write("  First Gbk Seq longer:\t" + str(inexactRec[1]) + "\n\n")

    args.sumOut.write("In Second Gbk but not in first:\t" + str(newCount) + "\n")
    args.sumOut.write("In First Gbk but not in second:\t" + str(oldCount) + "\n\n")

    args.sumOut.write(
        "Hypothetical Annotation Change:\t" + str(hypoRec[1] + hypoRec[2]) + "\n"
    )
    args.sumOut.write("Hypothetical:\t" + str(hypoRec[0] + hypoRec[2]) + "\n")


def print_match(f1, f2, identity, length_diff, outNotes):
    # print('', flush=True)
    line = f1.qualifiers["product"][0] + "\t"
    matchArr = [0, 0, 0]
    hypoArr = [0, 0, 0]
    if identity == 1.0:
        #        print('Exact match')
        line += "Exact match\t" + f2.qualifiers["product"][0] + "\t100.0\tSame Length\t"
    else:
        #        print('Inexact match (' + '%.2f' % (identity * 100.0) + '% ID, ', end='')
        line += (
            "Inexact match\t"
            + f2.qualifiers["product"][0]
            + "\t%.2f\t" % (identity * 100.0)
        )
        if length_diff == 0:
            #            print('same length)')
            line += "Same Length\t"
            matchArr[0] += 1
        elif length_diff > 0:
            #            print('old seq longer)')
            line += "First Gbk Seq Longer\t"
            matchArr[1] += 1
        elif length_diff < 0:
            #            print('new seq longer)')
            line += "Second Gbk Seq Longer\t"
            matchArr[2] += 1
    #    print('  old: ', end='')
    #    print_feature_one_line(f1)
    line += print_feature_one_line(f1) + "\t"
    #    print('  new: ', end='')
    #    print_feature_one_line(f2)
    line += print_feature_one_line(f2) + "\t"
    p1 = f1.qualifiers["product"][0].lower()
    p2 = f2.qualifiers["product"][0].lower()
    if "hypothetical" in p1 and "hypothetical" in p2:
        #        print('  still hypothetical')
        line += "Hypothetical\t"
        hypoArr[0] += 1
    elif "hypothetical" in p1 and "hypothetical" not in p2:
        #        print('  no longer hypothetical')
        line += "No Longer Hypothetical\t"
        hypoArr[1] += 1
    elif "hypothetical" not in p1 and "hypothetical" in p2:
        #        print('  became hypothetical')
        line += "Became Hypothetical\t"
        hypoArr[2] += 1
    else:
        line += "'Hypothetical' not in second nor first Gbk's product tag"

    if outNotes:
        line += "\t"
        if "note" in f1.qualifiers.keys():
            for x in f1.qualifiers["note"]:
                line += x
            line += "\t"
        else:
            line += "N/A\t"
        if "note" in f2.qualifiers.keys():
            for x in f2.qualifiers["note"]:
                line += x
        else:
            line += "N/A"

    print(line)
    return matchArr, hypoArr


def print_in_old_not_new(f):  # rename file outputs
    line = (
        f.qualifiers["product"][0]
        + "\tIn First Gbk but not Second\tN/A\t0.00\t"
        + str(f.location.end - f.location.start)
        + "\t"
        + print_feature_one_line(f)
        + "\tN/A\tN/A"
    )
    #    print('')
    #    print('In old but not in new:')
    #    print('  ', end='')
    #    print_feature_one_line(f)
    print(line)


def print_in_new_not_old(f):  # rename file outputs
    line = (
        "N/A\tIn Second Gbk but not First\t"
        + f.qualifiers["product"][0]
        + "\t0.00\t"
        + str(f.location.end - f.location.start)
        + "\tN/A\t"
        + print_feature_one_line(f)
        + "\tN/A"
    )
    # print('')
    # print('In new but not in old:')
    # print('  ', end='')
    # print_feature_one_line(f)
    print(line)


def print_feature_one_line(f):
    # f_str = f.qualifiers['product'][0]
    f_str = ""
    strand = "+" if f.location.strand == 1 else "-"
    f_str += (
        "(" + str(f.location.start) + "-" + str(f.location.end) + " " + strand + ", "
    )
    f_str += str(f.location.end - f.location.start) + " bp)"
    return f_str


def compare_features(f1, f2, r1, r2, match_identity_threshold):
    if f1 is None or f2 is None:
        return False

    s1 = f1.extract(r1).seq
    s2 = f2.extract(r2).seq
    score = pairwise2.align.globalms(s1, s2, 1, 0, 0, 0, score_only=True)
    identity = score / max(len(s1), len(s2))
    match = identity >= match_identity_threshold
    length_diff = len(s1) - len(s2)
    return match, identity, length_diff


if __name__ == "__main__":
    main()