Skip to main content
  • Home
  • Development
  • Documentation
  • Donate
  • Operational login
  • Browse the archive

swh logo
SoftwareHeritage
Software
Heritage
Archive
Features
  • Search

  • Downloads

  • Save code now

  • Add forge now

  • Help

https://github.com/fenderglass/Ragout
05 April 2024, 18:02:13 UTC
  • Code
  • Branches (21)
  • Releases (0)
  • Visits
    • Branches
    • Releases
    • HEAD
    • refs/heads/chr_map
    • refs/heads/devel
    • refs/heads/gh-pages
    • refs/heads/ismb_2014
    • refs/heads/master
    • refs/heads/path_cover
    • refs/heads/py3
    • refs/heads/rr_devel
    • refs/heads/tree_infer
    • refs/remotes/origin/devel
    • refs/tags/1.0
    • refs/tags/1.1
    • refs/tags/2.0
    • refs/tags/2.1
    • refs/tags/2.1.1
    • refs/tags/2.2
    • refs/tags/2.3
    • refs/tags/v0.1b
    • refs/tags/v0.2b
    • refs/tags/v0.3b
    • refs/tags/v1.2
    No releases to show
  • e0f14d1
  • /
  • scripts
  • /
  • verify-order.py
Raw File Download
Take a new snapshot of a software origin

If the archived software origin currently browsed is not synchronized with its upstream version (for instance when new commits have been issued), you can explicitly request Software Heritage to take a new snapshot of it.

Use the form below to proceed. Once a request has been submitted and accepted, it will be processed as soon as possible. You can then check its processing state by visiting this dedicated page.
swh spinner

Processing "take a new snapshot" request ...

Permalinks

To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

  • content
  • directory
  • revision
  • snapshot
origin badgecontent badge Iframe embedding
swh:1:cnt:d15da99c8498e1a0dfb1b45daa95e3846db49393
origin badgedirectory badge Iframe embedding
swh:1:dir:25ec9b1d502bf3196a06047af7c7b8d27e893e09
origin badgerevision badge
swh:1:rev:bd35cb59f602ed33794dc1697a1503375eabef80
origin badgesnapshot badge
swh:1:snp:12412e9d5850529b00b9f75cc3a4b47d1a47cc92
Citations

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

  • content
  • directory
  • revision
  • snapshot
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Tip revision: bd35cb59f602ed33794dc1697a1503375eabef80 authored by Mikhail Kolmogorov on 05 March 2015, 20:35:08 UTC
added extra condition in split_by_instance
Tip revision: bd35cb5
verify-order.py
#!/usr/bin/env python2.7

#(c) 2013-2014 by Authors
#This file is a part of Ragout program.
#Released under the BSD license (see LICENSE file)

"""
This script checks correctness of Ragout results
if a 'true' reference is available
"""

from __future__ import print_function
import sys
import os
import argparse
from collections import namedtuple, defaultdict
from itertools import product

from utils.nucmer_parser import parse_nucmer_coords
from utils.common import (filter_by_coverage, join_collinear,
                          group_by_chr, get_order)

Scaffold = namedtuple("Scaffold", ["name", "contigs"])
Contig = namedtuple("Contig", ["name", "sign"])


def parse_links_file(filename):
    scaffolds = []

    def add_contig(string):
        name = string.replace("=", "_")      #fix for nucmer
        without_sign = name[1:].strip()
        sign = 1 if name[0] == "+" else -1
        scaffolds[-1].contigs.append(Contig(without_sign, sign))

    with open(filename, "r") as f:
        for line in f:
            line = line.strip()
            if not line or line.startswith("--") or line.startswith("contig_1"):
                continue

            if line[0] not in ["+", "-"]:
                scaffolds.append(Scaffold(line, []))
            else:
                left_cont, right_cont = line.split()[0:2]
                add_contig(left_cont)
        add_contig(right_cont)

    return scaffolds


def parse_ord_file(filename):
    scaffolds = []

    with open(filename, "r") as f:
        for line in f:
            line = line.strip()
            if not line:
                continue

            if line.startswith(">"):
                scaffolds.append(Scaffold(line[1:], []))
            else:
                sign = 1 if line[0] == "+" else -1
                scaffolds[-1].contigs.append(Contig(line[1:], sign))

    return scaffolds


def parse_contigs_order(filename):
    _filename, ext = os.path.splitext(filename)
    if ext[1:] == "ord":
        return parse_ord_file(filename)
    else:
        return parse_links_file(filename)


def gap_count(lst_1, lst_2):
    if not lst_1 or not lst_2:
        return 0

    gaps = sys.maxsize
    for i, j in product(lst_1, lst_2):
        gaps = min(gaps, abs(i.index - j.index) - 1)
    return gaps


def agreement_ord(increasing, lst_1, lst_2, chr_len_dict):
    if not lst_1 or not lst_2:
        return True

    for i, j in product(lst_1, lst_2):
        same_chr = i.chr == j.chr
        if not same_chr:
            continue

        chr_len = chr_len_dict[i.chr]
        lower = chr_len * 0.2
        higher = chr_len * 0.8
        over_zero = ((increasing and i.coord > higher and j.coord < lower) or
                    (not increasing and i.coord < lower and j.coord > higher))

        if ((j.index > i.index) == increasing and
            abs(i.coord - j.coord) < chr_len / 3) or over_zero:
            return True
    return False


def agreement_strands(lst_1, lst_2):
    for i, j in product(lst_1, lst_2):
        if i == j:
            return True
    return False


def do_job(nucmer_coords, scaffolds_ord):
    alignment = parse_nucmer_coords(nucmer_coords)
    alignment = join_collinear(alignment)
    alignment = filter_by_coverage(alignment, 0.45)
    entry_ord, chr_len, contig_len = get_order(alignment)
    scaffolds = parse_contigs_order(scaffolds_ord)

    total_breaks = 0
    total_gaps = 0
    total_contigs = 0
    for s in scaffolds:
        print("\n>" + s.name)

        prev_aln = None
        prev_strand = None
        increasing = None
        breaks = []
        for contig in s.contigs:
            miss_ord = False
            miss_strand = False

            #checking order
            if prev_aln:
                if increasing is not None:
                    if not agreement_ord(increasing, prev_aln,
                                         entry_ord[contig.name], chr_len):
                        increasing = None
                        breaks.append(contig.name)
                        total_breaks += 1
                        miss_ord = True
                elif len(entry_ord[contig.name]) == 1 and len(prev_aln) == 1:
                    increasing = (entry_ord[contig.name][0].index >
                                  prev_aln[0].index)

            #checking strand
            cur_strand = list(map(lambda h: h.sign * contig.sign,
                                  entry_ord[contig.name]))
            if not miss_ord and prev_strand and cur_strand:
                if not agreement_strands(prev_strand, cur_strand):
                    breaks.append(contig.name)
                    total_breaks += 1
                    miss_strand = True
                    prev_strand = None
                    increasing = None

            if gap_count(prev_aln, entry_ord[contig.name]) > 0:
                total_gaps += 1

            #only if this contig has alignments
            if entry_ord[contig.name]:
                prev_aln = entry_ord[contig.name]
                if not miss_strand:
                    prev_strand = cur_strand

            #output
            sign = "+" if contig.sign > 0 else "-"
            pos_list = list(map(str, entry_ord[contig.name]))
            pos_list_str = str(pos_list) if len(pos_list) < 6 else "[..a lot of alignments..]"
            print("{0}{1}\t{2}\t{3}".format(sign, contig.name,
                                            contig_len[contig.name], pos_list_str),
                                            end="")
            print("\t<<<order" if miss_ord else "", end="")
            print("\t<<<strand" if miss_strand else "", end="")
            print("")
            total_contigs += 1
            ###
        print("\tmiss-ordered: ", len(breaks))

    print("\nTotal miss-ordered:", total_breaks)
    print("Total gaps:", total_gaps)
    print("Total contigs:", total_contigs)
    print("Total scaffolds:", len(scaffolds))


def main():
    descr = ("A verification script for Ragout. It requires a contigs "
            "alignment on \"true\" reference in nucmer coords format. "
            "Given an alignment and a \"links\" file output by Ragout "
            "the script finds missassembled contigs and calculates some "
            "statistics.")
    parser = argparse.ArgumentParser(description=descr)
    parser.add_argument("nucmer_coords", metavar="nucmer_coords",
                        help="path to contigs alignment on 'true' reference")
    parser.add_argument("links_file", metavar="links_file",
                        help="path to 'links' file output by Ragout")
    args = parser.parse_args()

    do_job(args.nucmer_coords, args.links_file)


if __name__ == "__main__":
    main()

Software Heritage — Copyright (C) 2015–2025, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Contact— JavaScript license information— Web API

back to top