Added fasta_synteny sub workflow

assets/schema_xref_assemblies.json

@@ -0,0 +1,32 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/master/assets/schema_input.json",
+    "title": "plant-food-research-open/assemblyqc pipeline - params.synteny_xref_assemblies schema",
+    "description": "Schema for the file provided with params.synteny_xref_assemblies",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "tag": {
+                "type": "string",
+                "pattern": "^\\w+$",
+                "errorMessage": "Assembly tags must be provided and can only contain alphanumeric characters including '_'"
+            },
+            "fasta": {
+                "type": "string",
+                "pattern": "^\\S+\\.f(ast|as|sa|na)?\\.gz$",
+                "errorMessage": "FASTA file path cannot contain spaces and must have extension '.f(ast|as|sa|na)' or '.f(ast|as|sa|na).gz'"
+            },
+            "synteny_labels": {
+                "errorMessage": "Synteny labels tsv path cannot contain spaces and must have extension '.tsv'",
+                "anyOf": [
+                    {
+                        "type": "string",
+                        "pattern": "^\\S+\\.tsv$"
+                    }
+                ]
+            }
+        },
+        "required": ["tag", "fasta", "synteny_labels"]
+    }
+}

bin/colorbundlesbycontig.py

@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+
+import sys
+import re
+
+bundled_links_file_name = sys.argv[1]
+
+
+def natural_key(string):
+    """Return a list of keys that sort naturally."""
+    return [int(s) if s.isdigit() else s for s in re.split(r"(\d+)", string)]
+
+
+def hsv2rgb(h, s, v):
+    """Convert HSV color to RGB color."""
+    h = float(h)
+    s = float(s)
+    v = float(v)
+    h60 = h / 60.0
+    h60f = int(h60)
+    hi = int(h60f) % 6
+    f = h60 - h60f
+    p = v * (1 - s)
+    q = v * (1 - f * s)
+    t = v * (1 - (1 - f) * s)
+    r, g, b = 0, 0, 0
+    if hi == 0:
+        r, g, b = v, t, p
+    elif hi == 1:
+        r, g, b = q, v, p
+    elif hi == 2:
+        r, g, b = p, v, t
+    elif hi == 3:
+        r, g, b = p, q, v
+    elif hi == 4:
+        r, g, b = t, p, v
+    elif hi == 5:
+        r, g, b = v, p, q
+    return int(r * 255), int(g * 255), int(b * 255)
+
+
+def generate_colors(num_colors):
+    """Generate a list of colors"""
+    hue_step = int(360 / num_colors)
+    hue = 0
+    colors = []
+    for i in range(num_colors):
+        red, green, blue = hsv2rgb(hue, 0.8, 0.8)
+        colors.append(f"{red},{green},{blue},0.5")
+        hue += hue_step
+    return colors
+
+
+def read_file_lines(file_path):
+    with open(file_path, "r") as f:
+        return f.readlines()
+
+
+def generate_colors_by_ids(bundle_file_lines):
+    """Create a dictionary to map unique target ids to colors"""
+    unique_ids = set(
+        line.split()[3] for line in bundle_file_lines
+    )  # index 3: Target ids
+    num_unique_ids = len(unique_ids)
+    colors = generate_colors(num_unique_ids)
+    return dict(zip(sorted(unique_ids, key=natural_key), colors))
+
+
+if __name__ == "__main__":
+    bundle_file_lines = read_file_lines(bundled_links_file_name)
+    id_to_color = generate_colors_by_ids(bundle_file_lines)
+
+    for line in bundle_file_lines:
+        parts = line.strip().split()
+        unique_id = parts[3]  # index 3: Target ids
+        color = id_to_color[unique_id]
+        print(" ".join(parts[0:6] + [f"color=({color})", parts[6]]))

bin/colorbundlesbysize.pl

@@ -0,0 +1,181 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+
+=head1 DESCRIPTION
+
+Adds colours to a CIRCOS bundle file.
+
+=head1 AUTHOR
+
+Original: Ross Crowhurst L<mailto:ross.crowhurst@plantandfood.co.nz>
+Modified: Usman Rashid L<mailto:usman.rashid@plantandfood.co.nz>
+
+=cut
+
+my $low = 0;
+
+my %bundleColorsRGB = (
+        3000 => "128,0,0,0.5",
+        2000 => "229,0,10,0.5",
+        1500 => "229,19,9,0.5",
+        1000 => "216,38,8,0.5",
+        500  => "210,57,7,0.5",
+        250  => "204,76,6,0.5",
+        100  => "198,95,5,0.5",
+        50   => "192,114,4,0.5",
+        25   => "186,113,3,0.5",
+        10   => "180,152,2,0.5",
+        5    => "174,171,1,0.5",
+        0    => "168,191,0,0.5"
+);
+
+my %bundleColorsRGBLow = (
+        55 => "128,0,0,0.5",
+        50 => "229,0,10,0.5",
+        45 => "229,19,9,0.5",
+        40 => "216,38,8,0.5",
+        35  => "210,57,7,0.5",
+        30  => "204,76,6,0.5",
+        25  => "198,95,5,0.5",
+        20   => "192,114,4,0.5",
+        15 => "186,113,3,0.5",
+        10 => "180,152,2,0.5",
+        5    => "174,171,1,0.5",
+        0    => "168,191,0,0.5"
+);
+
+sub usage {
+	print "USAGE: $0 -i=bundle_file_in -o=colored_bundle_file_out [-low]\n";
+	print "To get colors:\n\n";
+	print "       $0 -colorsRGB [or -colorsRGBAsHTMLTable] [-low]\n";
+	print "or\n";
+	print "       $0 -colorsHex [-low]\n";
+	print "or\n";
+	print "       $0 -colorsHexAsHTMLKeyTable [-low]\n";
+	exit(0);
+}
+
+sub exportRGB {
+	if ($low)
+	{
+		foreach my $threshold (sort {$a <=> $b} keys %bundleColorsRGBLow)
+		{
+			print "$threshold\t$bundleColorsRGBLow{$threshold}\n";
+		}
+	}
+	else
+	{
+		foreach my $threshold (sort {$a <=> $b} keys %bundleColorsRGB)
+		{
+			print "$threshold\t$bundleColorsRGB{$threshold}\n";
+		}
+	}
+	exit(0);
+}
+
+sub exportRGBHTMLTable {
+	print "<table border=1>\n";
+	print "<tr><th>Bundled Links</th><th>RGB</th></tr>\n";
+	if ($low)
+	{
+		foreach my $threshold (sort {$a <=> $b} keys %bundleColorsRGBLow)
+		{
+			my $cellBgColor = rgbToHex($bundleColorsRGBLow{$threshold});
+			print qq{<tr><td>$threshold</td><td bgcolor="$cellBgColor">$bundleColorsRGBLow{$threshold}</td></tr>\n};
+		}
+	}
+	else
+	{
+		foreach my $threshold (sort {$a <=> $b} keys %bundleColorsRGB)
+        	{
+			my $cellBgColor = rgbToHex($bundleColorsRGB{$threshold});
+                	print qq{<tr><td>$threshold</td><td bgcolor="$cellBgColor">$bundleColorsRGB{$threshold}</td></tr>\n};
+        	}
+	}
+	print "</table>\n";
+	exit(0);
+}
+
+sub exportAsHTMLKeyTable {
+        print "<table border=1>\n";
+        print "<tr><th>Bundled Links</th></tr>\n";
+        if ($low)
+	{
+		foreach my $threshold (sort {$a <=> $b} keys %bundleColorsRGBLow)
+		{
+			my $cellBgColor = rgbToHex($bundleColorsRGBLow{$threshold});
+			print qq{<tr><td bgcolor="$cellBgColor">&nbsp;<span style="color:white">$threshold</span></td></tr>\n};
+		}
+	}
+	else
+	{
+		foreach my $threshold (sort {$a <=> $b} keys %bundleColorsRGB)
+        	{
+                	my $cellBgColor = rgbToHex($bundleColorsRGB{$threshold});
+                	print qq{<tr><td bgcolor="$cellBgColor">&nbsp;<span style="color:white">$threshold</span></td></tr>\n};
+        	}
+	}
+        print "</table>\n";
+	exit(0);
+}
+sub rgbToHex {
+	my ($r, $g, $b) = split/,/, $_[0];
+	return sprintf ("#%2.2X%2.2X%2.2X", $r, $g, $b);
+}
+
+my $bundleFileIn = "";
+my $bundleFileOut = "";
+
+(@ARGV) or usage();
+foreach my $arg (@ARGV)
+{
+	($arg =~ m/^-(h|help)$/) and usage();
+	($arg =~ m/^-low$/) and $low = 1;
+	($arg =~ m/^-colorsRGB$/) and exportRGB();
+	($arg =~ m/^-colorsRGBAsHTMLTable$/) and exportRGBHTMLTable();
+	($arg =~ m/^-colorsHexAsHTMLKeyTable$/) and exportAsHTMLKeyTable();
+	($arg =~ m/^-i=(.+)$/) and $bundleFileIn = $1;
+	($arg =~ m/^-o=(.+)$/) and $bundleFileOut = $1;
+}
+
+open(OUT, ">$bundleFileOut") or die "ERROR: can not open bundle out file $bundleFileOut $!\n";
+open(IN, "<$bundleFileIn") or die "ERROR: can not open bundle in file $bundleFileIn $!\n";
+while (my $line = <IN>)
+{
+#ASB_LG19 13470754 14218750 Ss262 2177839 2976275 nlinks=672,bsize1=150447,bsize2=150419,bidentity1=0.201133,bidentity2=0.188392,depth1=0,depth2=0,
+#ASB_LG19 14250080 15061508 Ss262 1303606 2191377 nlinks=1076,bsize1=279892,bsize2=278553,bidentity1=0.344937,bidentity2=0.313766,depth1=0,depth2=0,
+#ASB_LG19 14314359 14314420 Ss262 7198136 7198167 nlinks=9,bsize1=62,bsize2=32,bidentity1=1.000000,bidentity2=1.000000,depth1=1,depth2=1,
+#ASB_LG19 15064224 15625360 Ss262 672993 1254783 nlinks=881,bsize1=305520,bsize2=304727,bidentity1=0.544466,bidentity2=0.523774,depth1=0,depth2=0,
+#ASB_LG19 15650721 16282135 Ss262 8995 672359 nlinks=786,bsize1=199405,bsize2=198505,bidentity1=0.315807,bidentity2=0.299239,depth1=0,depth2=0,
+#ASB_LG19 17026943 17042421 Ss262 965 7848 nlinks=35,bsize1=7610,bsize2=4363,bidentity1=0.491634,bidentity2=0.633788,depth1=0,depth2=0,
+	chomp $line;
+	my @data = split/\s+/, $line;
+	my @bundleFields = split/,/, $data[6];
+	my ($label, $count) = split/=/, $bundleFields[0];
+	my $colorText = "color=(168,191,0)";
+	if ($low)
+	{
+		foreach my $threshold (sort {$a <=> $b} keys %bundleColorsRGBLow)
+		{
+			if ($count > $threshold)
+			{
+				$colorText = "color=($bundleColorsRGBLow{$threshold})";
+			}
+		}
+	}
+	else
+	{
+		foreach my $threshold (sort {$a <=> $b} keys %bundleColorsRGB)
+		{
+			if ($count > $threshold)
+			{
+				$colorText = "color=($bundleColorsRGB{$threshold})";
+			}
+		}
+	}
+	my $newline = join(" ", $data[0], $data[1], $data[2], $data[3], $data[4], $data[5], $colorText, $data[6]);
+	select OUT; print OUT "$newline\n";
+}
+close(OUT);
+exit(0);

bin/validateseqlists.sh

@@ -0,0 +1,39 @@
+#!/usr/bin/env bash
+
+seqFileA=$1
+seqFileB=$2
+
+linesFileA=()
+linesFileB=()
+
+while IFS= read -r line; do
+    linesFileA+=("$line")
+    columns=($line)
+    if [[ ${#columns[@]} -ne 2 ]]; then
+        echo "Error: Sequence file $(basename "$seqFileA") does not have exactly two columns." >&2
+        exit 1
+    fi
+done < "$seqFileA"
+
+while IFS= read -r line; do
+    linesFileB+=("$line")
+    columns=($line)
+    if [[ ${#columns[@]} -ne 2 ]]; then
+        echo "Error: Sequence file $(basename "$seqFileB") does not have exactly two columns." >&2
+        exit 1
+    fi
+done < "$seqFileB"
+
+outputLines=("${linesFileA[@]}" "${linesFileB[@]}")
+
+secondColumn=()
+for line in "${outputLines[@]}"; do
+    columns=($line)
+    secondColumn+=("${columns[1]}")
+done
+
+uniqueSecondColumn=($(echo "${secondColumn[@]}" | tr ' ' '\n' | sort -u))
+if [[ ${#secondColumn[@]} -ne ${#uniqueSecondColumn[@]} ]]; then
+    echo "Error: Duplicate sequence labels detected in second column for pair: $(basename "$seqFileA"), $(basename "$seqFileB")" >&2
+    exit 1
+fi

conf/base.config

@@ -71,6 +71,9 @@ process {
     withName:SAMBLASTER {
         time   = { check_max( 20.h  * task.attempt, 'time'    ) }
     }
+    withName:DNADIFF {
+        time   = { check_max( 7.day  * task.attempt, 'time'    ) }
+    }
     withName:CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false
     }