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plinktomap.pl
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plinktomap.pl
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#!/usr/bin/perl
# $Revision: 0.21 $
# $Date: 2021/02/16 $
# $Id: plinktomap.pl $
# $Author: Michael Bekaert $
#
# RAD-tags to Genetic Map (radmap)
# Copyright (C) 2016-2021 Bekaert M <michael.bekaert@stir.ac.uk>
#
# 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 <http://www.gnu.org/licenses/>.
#
# POD documentation - main docs before the code
=head1 NAME
RAD-tags to Genetic Map (radmap)
=head1 SYNOPSIS
# Command line help
..:: RAD-tags to Genetic Map ::..
Usage: ./genetic_mapper.pl [options]
# LepMap pre-processing
--lepmap MANDATORY
or
--lepmap3 MANDATORY
--ped MANDATORY
--meta MANDATORY
STDOUT > LepMap (linkage) input file
# Pre-processing
--snpassoc MANDATORY
or
--arff MANDATORY
or
--ade MANDATORY
--plink MANDATORY
--ped MANDATORY
--meta MANDATORY
--fst OPTIONAL
--threshold OPTIONAL
--map OPTIONAL
--gmap OPTIONAL
--female OPTIONAL
STDOUT > SNPassoc input file
STDERR 2> Genetic Map
# Post GWAS processing
--genetic MANDATORY
--extra MANDATORY (at least once)
--markers OPTIONAL
--fasta OPTIONAL
--pos OPTIONAL
--lod OPTIONAL
STDOUT > Genetic Map
# Export marker and genotype for publication (Table S)
--plink MANDATORY
--ped MANDATORY
--markers OPTIONAL
--fasta OPTIONAL
--pos OPTIONAL
--table MANDATORY
# Manual editing
--ped MANDATORY
--genetic MANDATORY
--edit MANDATORY
STDOUT > Mappable markers list
Options
--meta <pedigree file>
The pedigree file consists of on columns 1-4+. The columns are separated by
tabs. The columns 1-4 are individual name, father, mother and sex; the next
columns are for extra phenotypes: phenotype_1 to phenotype_n. The phenotypes
are not required, but will be helpful for the GWAS analysis.
sample father mother sex phenotype_1
F1_C2_070 P0_sir P0_dam M 30
F1_C2_120 P0_sir P0_dam F 1
P0_dam 0 0 F -
P0_sir 0 0 M -
--plink <plink map file>
PLINK MAP file path with full haplotypes.
--ped <plink ped file>
PLINK PED file path with full haplotypes.
--map <mappable markers list>
Mappable markers list as generated by LepMap "SeparateChromosomes" and
"JoinSingles" functions.
--gmap <ordered markers file>
Ordered genetic map generated by LepMap.
--genetic <genetic map file>
Genetic Map as generated by R/SNPAssoc pre-processing step.
--markers <batch_<n>.catalog.tags.tsv file>
Path to STACKS catalog.tag file, including marker sequences and positions.
(incompatible with --fasta)
--fasta <uniq.full.fasta file>
Path to dDocent uniq.full.fasta file, including marker sequences. (incompatible
with --markers)
--fst <xxx.phistats.tsv>
Fst values for each marker (requires --threshold)
--hwe <xxx..hapstats.tsv>
HWE values for each marker (requires --fst)
--threshold
Fst threshold for selection (requires --fst)
--extra
GWAS results generated by R/SNPassoc (csv format) to be added to the genetic map.
--lod
Convert the P-value of the GWAS results to LOD (LOD=-log(P-value)/log(10)).
--pos
Provide the marker chromosome/contig and location. (requires --markers)
--female
Select the female only map rather than male or average mapping. (requires --gmap)
--snpassoc
Enable R/SNPAssoc pre-processing.
--arff
Enable Weka ARFF format.
--ade
Enable R/ade pre-processing.
--lepmap
Enable LepMap pre-processing.
--table
Enable export for publication for markers and genotypes.
--edit
Enable Manual editing mode.
--select
Provide the list of id to select
=head1 DESCRIPTION
Perl script for the analyse RAD-tags and generate the Genetic Map with GWAS. The script
handles the multiple file conversions. PLINK _classic_ file L<PED|http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped>
and L<MAP|http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#map> are required as well as a pedigree file.
=head1 FEEDBACK
User feedback is an integral part of the evolution of this modules. Send your comments
and suggestions preferably to author.
=head1 AUTHOR
B<Michael Bekaert> (michael.bekaert@stir.ac.uk)
The latest version of genetic_mapper.pl is available at
https://github.com/pseudogene/radmap
=head1 LICENSE
Copyright 2016-2021 - Michael Bekaert
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 L<http://www.gnu.org/licenses/>.
=cut
use strict;
use warnings;
use Getopt::Long;
#----------------------------------------------------------
our ($VERSION) = 0.21;
#----------------------------------------------------------
my ($threads, $threshold, $female, $tableS, $arff, $remap, $lepmap, $lepmap3, $ade, $snpassoc, $edit, $loc, $lod, $plink, $ped, $parentage, $map, $genmap, $genetic, $markers, $fasta, $hwe_file, $fst_file, $selectlist) = (10, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0);
my @extra;
GetOptions(
'plink:s' => \$plink,
'ped:s' => \$ped,
'meta:s' => \$parentage,
'map:s' => \$map,
'gmap:s' => \$genmap,
'genetic:s' => \$genetic,
'extra:s' => \@extra,
'female!' => \$female,
'lepmap!' => \$lepmap,
'lepmap3!' => \$lepmap3,
'pos!' => \$loc,
'lod!' => \$lod,
'edit!' => \$edit,
'ade!' => \$ade,
'snpassoc!' => \$snpassoc,
'table!' => \$tableS,
'markers:s' => \$markers,
'fasta:s' => \$fasta,
'threshold:f' => \$threshold,
'fst:s' => \$fst_file,
'hwe:s' => \$hwe_file,
'select:s' => \$selectlist,
'arff!' => \$arff,
'remap!' => \$remap
);
my %parents_table;
my $count_meta = 0;
if (defined $parentage && -r $parentage && open(my $in, q{<}, $parentage))
{
#
#sample father mother Sex [..]
#
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data >= 4 && defined $data[0] && defined $data[1] && defined $data[2] && defined $data[3])
{
$count_meta = scalar @data - 4 if ($count_meta < scalar @data - 4);
@{$parents_table{$data[0]}} = @data;
}
}
close $in;
}
my %selected;
if (defined $selectlist && -r $selectlist && open(my $in, q{<}, $selectlist))
{
while (<$in>)
{
next if (m/^#/);
chomp;
my @tmp = split m/\t/x;
$selected{$tmp[0]} = $tmp[0] if (exists $tmp[0]);
}
close $in;
}
if (defined $fst_file && -r $fst_file && (open my $IN, q{<}, $fst_file))
{
my %fst;
while (<$IN>)
{
next if (m/^#/);
chomp;
my @tmp = split m/\t/x;
if (scalar @tmp >= 10) {
if (defined $selectlist && exists($selected{$tmp[0]}) && $tmp[6] < $threshold) { delete $selected{$tmp[0]}; }
elsif (!defined $selectlist && $tmp[6] >= $threshold) { $fst{$tmp[0]} = $tmp[6]; }
}
}
close $IN;
if (%fst) {
$selectlist = $fst_file;
%selected = %fst
}
}
if (defined $hwe_file && -r $hwe_file && (open my $IN, q{<}, $hwe_file))
{
my %hwe;
while (<$IN>)
{
next if (m/^#/);
chomp;
my @tmp = split m/\t/x;
if (scalar @tmp >= 14) {
if (defined $selectlist && exists($selected{$tmp[0]}) && $tmp[12] > 0.05) { delete $selected{$tmp[0]}; }
elsif (!defined $selectlist && exists($hwe{$tmp[0]}) && $tmp[12] > 0.05) { delete $hwe{$tmp[0]}; }
elsif (!defined $selectlist && $tmp[12] <= 0.05) { $hwe{$tmp[0]} = $tmp[12]; }
}
}
close $IN;
if (%hwe) {
$selectlist = $hwe_file;
%selected = %hwe
}
}
#To LepMap
if (scalar keys %parents_table > 0 && ($lepmap || $lepmap3) && defined $ped && -r $ped && open(my $in, q{<}, $ped))
{
my %table = (A => 1, C => 2, G => 3, T => 4, N => 0, 0 => 0);
my $last = 0;
# PEB
# # Stacks v1.42; PLINK v1.07; October 06, 2016
# C7 F1_dam_C7 0 0 0 0 G T A A G T A G G ...
# LINKAGE
# #java Filtering data=C07_LSalAtl2sD140.linkage.txt dataTolerance=0.001
# C7 P0_sir_C7 0 0 1 0 1 1 0 0 1 2 1 2 1 2 1 2 ...
# C7 F1_dam_C7 P0_sir_C7 P0_dam_C7 2 0 1 2 0 0 2 2 1 2 1 1 1 ...
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data > 8 && defined $data[0] && defined $data[1] && exists $parents_table{$data[1]})
{
if ($lepmap3)
{
if (!exists $table{$data[1]}) { $table{$data[1]} = ++$last; }
if (!exists $table{$parents_table{$data[1]}[1]}) { $table{$parents_table{$data[1]}[1]} = ++$last; }
if (!exists $table{$parents_table{$data[1]}[2]}) { $table{$parents_table{$data[1]}[2]} = ++$last; }
print $data[0], "\t", $table{$data[1]}, "\t", $table{$parents_table{$data[1]}[1]}, "\t", $table{$parents_table{$data[1]}[2]}, "\t", ($parents_table{$data[1]}[3] =~ /^F/i ? q{2} : ($parents_table{$data[1]}[3] =~ /^M/i ? q{1} : q{0})),
"\t0";
for (my $i = 6 ; $i < scalar @data ; $i = $i + 2)
{
print "\t", (defined $data[$i] && exists $table{$data[$i]} ? $table{$data[$i]} : q{0});
print q{ }, (defined $data[$i + 1] && exists $table{$data[$i + 1]} ? $table{$data[$i + 1]} : q{0});
}
}
else
{
print $data[0], "\t", $data[1], "\t", $parents_table{$data[1]}[1], "\t", $parents_table{$data[1]}[2], "\t", ($parents_table{$data[1]}[3] =~ /^F/i ? q{2} : ($parents_table{$data[1]}[3] =~ /^M/i ? q{1} : q{0})), "\t0";
for my $i (6 .. (scalar @data) - 1) { print "\t", (defined $data[$i] && exists $table{$data[$i]} ? $table{$data[$i]} : q{0}); }
}
print "\n";
}
}
close $in;
}
#To SNPAssoc
elsif (scalar keys %parents_table > 0 && ($snpassoc || $ade || $arff) && defined $ped && -r $ped && defined $plink && -r $plink && open($in, q{<}, $plink))
{
my (@list_marker, @mask_marker);
# PEB
# # Stacks v1.42; PLINK v1.07; October 06, 2016
# C7 F1_dam_C7 0 0 0 0 G T A A G T A G G ...
# plink MAP
# # Stacks v1.42; PLINK v1.07; October 06, 2016
# LSalAtl2s1 19757_13 0 4466
# LSalAtl2s1 19756_74 0 4550
# LSalAtl2s1 19491_4 0 106094
# LSalAtl2s1 19492_81 0 106518
# LSalAtl2s1 19498_31 0 118987
# LSalAtl2s1 19749_27 0 381049
# LEPMAP MAP
# #java SeparateChromosomes data=C07_LSalAtl2sD140_f.linkage.txt lodLimit=6.5 sizeLimit=2
# 0
# 6
# 6
# 6
# 0
# 0
# SNPAssoc
# id Sex Surviving 33 40 60 120 136 157 180
# F2_C7_073 Female 2 A/A - A/B A/B A/B A/B
# F2_C7_074 Female 2 A/A - B/B A/B A/B A/A
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data >= 2 && defined $data[0] && defined $data[1]) { push @list_marker, $data[1]; push @mask_marker, 1 if (defined $genmap || defined $map || defined $selectlist); }
}
close $in;
if (scalar @list_marker > 0 && defined $genmap && -r $genmap && open($in, q{<}, $genmap))
{
my $lg;
# genmap
# #java OrderMarkers map=mapLOD5_js.txt data=C07_LSalAtl2sD140_f.linkage.txt sexAveraged=1 useKosambi=1
# #*** LG = 1 likelihood = -5811.6314 with alpha penalty = -5811.6314
# #marker_number male_position female_position ( error_estimate )[ duplicate* OR phases] C7
# 1886 0.000 0.000 ( 0 ) 11
# 2789 0.270 0.270 ( 0 ) 11
# 2749 2.568 2.568 ( 0.2398 ) 10
# 4119 3.455 3.455 ( 0 ) -1
print {*STDERR} "Marker\tLG\tPosition\n";
while (<$in>)
{
if (m/^(#|\*)/)
{
if (m/LG = (\d+(\.\d+)?)/) { $lg = $1; }
}
else
{
chomp;
my @data = split m/\t/;
if (scalar @data > 3 && defined $data[0] && defined $data[1] && defined $data[2] && exists $list_marker[$data[0] - 1] && defined $lg)
{
undef $mask_marker[$data[0] - 1];
print {*STDERR} $list_marker[$data[0] - 1], "\t", $lg, "\t", $data[($female ? 2 : 1)], "\n";
}
}
}
close $in;
}
elsif (scalar @list_marker > 0 && defined $map && -r $map && open($in, q{<}, $map))
{
my $i = 0;
while (<$in>)
{
next if (m/^#/);
chomp;
if ($_ ne '0') { undef $mask_marker[$i]; }
$i++;
}
close $in;
}
if (defined $selectlist) {
for my $j (0 .. (scalar @list_marker) - 1) {
my $tmp = $list_marker[$j];
if ($tmp =~ m/^(\d+)_\d+/) { $tmp = $1; }
elsif ($tmp =~ m/^(dDocent.*):\d+/) { $tmp = $1; }
if (exists $selected{$tmp}) {
undef $mask_marker[$j];
}
}
}
#else { undef @mask_marker; }
if (scalar @list_marker > 0 && open($in, q{<}, $ped))
{
if ($ade)
{
my @group;
my %atcg = (A => 1, C => 2, G => 3, T => 4, N => 0, 0 => 0);
print "Samples";
for my $j (0 .. (scalar @list_marker) - 1) { print "\t", $list_marker[$j] if (!defined $mask_marker[$j]); }
print "\n";
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data > 8 && defined $data[0] && defined $data[1] && exists $parents_table{$data[1]} && exists $parents_table{$data[1]}[4])
{
print $data[1];
push @group, $parents_table{$data[1]}[4];
my $i = 6;
for my $j (0 .. (scalar @list_marker) - 1) {
print "\t", (defined $data[$i + $j * 2] && $data[$i + $j * 2] ne q{0} && defined $data[$i + $j * 2 + 1] && $data[$i + $j * 2 + 1] ne q{0} ? $atcg{$data[$i + $j * 2]} . $atcg{$data[$i + $j * 2 + 1]} : " ")
if (!defined $mask_marker[$j]);
}
print "\n";
}
}
print {*STDERR} 'pop <- c(\'', join("','",@group),"');\n";
} elsif ($arff) {
print {*STDOUT} "\@RELATION default\n\n\@ATTRIBUTE id STRING\n\@ATTRIBUTE sex {F,M}\n";
for my $j (1 .. $count_meta) { print {*STDOUT} "\@ATTRIBUTE phenotype_$j {}\n"; }
for my $j (0 .. (scalar @list_marker) - 1) { print {*STDOUT} '@ATTRIBUTE ', $list_marker[$j], " {AA,AC,AG,AT,CC,CG,CT,GG,GT,TT}\n", if (!defined $mask_marker[$j]); }
print {*STDOUT} "\n\@DATA\n";
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data > 8 && defined $data[0] && defined $data[1] && exists $parents_table{$data[1]} && $parents_table{$data[1]}[3] =~ /^(M|F)/i)
{
print {*STDOUT} $data[1], q{,}, ($parents_table{$data[1]}[3] =~ /^F/i ? q{F} : ($parents_table{$data[1]}[3] =~ /^M/i ? q{M} : q{?}));
for my $j (1 .. $count_meta) { print {*STDOUT} q{,} , (exists $parents_table{$data[1]}[3 + $j] ? $parents_table{$data[1]}[3 + $j] : q{?}) }
my $i = 6;
for my $j (0 .. (scalar @list_marker) - 1) {
print {*STDOUT} q{,}, (defined $data[$i + $j * 2] && $data[$i + $j * 2] ne q{0} && defined $data[$i + $j * 2 + 1] && $data[$i + $j * 2 + 1] ne q{0} ? $data[$i + $j * 2] . $data[$i + $j * 2 + 1] : q{?})
if (!defined $mask_marker[$j]);
}
print "\n";
}
}
} else {
print "id\tsex";
for my $j (1 .. $count_meta) { print "\tphenotype_$j", }
for my $j (0 .. (scalar @list_marker) - 1) { print "\t", $list_marker[$j] if (!defined $mask_marker[$j]); }
print "\n";
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data > 8 && defined $data[0] && defined $data[1] && exists $parents_table{$data[1]} && $parents_table{$data[1]}[3] =~ /^(M|F)/i)
{
print $data[1], "\t", ($parents_table{$data[1]}[3] =~ /^F/i ? 'Female' : 'Male');
for my $j (1 .. $count_meta) { print "\t", (exists $parents_table{$data[1]}[3 + $j] ? $parents_table{$data[1]}[3 + $j] : q{}) }
my $i = 6;
for my $j (0 .. (scalar @list_marker) - 1) {
print "\t", (defined $data[$i + $j * 2] && $data[$i + $j * 2] ne q{0} && defined $data[$i + $j * 2 + 1] && $data[$i + $j * 2 + 1] ne q{0} ? $data[$i + $j * 2] . q{/} . $data[$i + $j * 2 + 1] : q{-})
if (!defined $mask_marker[$j]);
}
print "\n";
}
}
}
close $in;
}
}
elsif ($remap && scalar @extra > 0 && defined $genetic && -r $genetic && open($in, q{<}, $genetic))
{
my (%list_markers, %list2_markers, %list_sequences);
open(my $seqfile, q{>}, '/tmp/blast_' . $genetic . '.fasta');
while (<$in>)
{
next if (m/^(#|Marker)/);
chomp;
my @data = split m/\t/;
if (scalar @data >= 4 && defined $data[0] && defined $data[1] && defined $data[2] && defined $data[-1])
{
@{$list_markers{$data[0]}} = @data;
print {$seqfile} '>', $data[0], "\n", $data[-1], "\n";
}
}
close $seqfile;
close $in;
foreach my $infile (@extra)
{
if (defined $infile && -r $infile && open(my $in2, q{<}, $infile))
{
#Extra
# "","comments","codominant"
# "X67793_33",NA,0.02511912
while (<$in2>)
{
chomp;
my @data = split m/,/;
if (scalar @data >= 3 && defined $data[0] && defined $data[2] && $data[2] ne 'NA')
{
if ($data[0] =~ m/X([\d\w\_\.]+)/) { $list2_markers{$1} = 1; }
elsif ($data[0] =~ m/(dDocent.*)\.(\d+)/) { $list2_markers{$1 . q{:} . $2} = 1; }
}
}
close $in2;
}
}
my %tmp2_list;
for my $item (keys %list2_markers)
{
if ($item =~ m/^(\d+)_\d+/) { $tmp2_list{$1} = $item; $tmp2_list{$item} = $1; }
elsif ($item =~ m/^(dDocent.*):\d+/) { $tmp2_list{$1} = $item; $tmp2_list{$item} = $1; }
else { $tmp2_list{$item} = $item; }
}
open(my $queryfile, q{>}, '/tmp/query_' . $genetic . '.fasta');
if (defined $markers && -r $markers)
{
my %unique;
if (defined $ped && -r $ped && defined $plink && -r $plink && open($in, q{<}, $plink))
{
my @list_full;
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data >= 2 && defined $data[0] && defined $data[1]) { push @list_full, $data[1]; }
}
close $in;
}
if (open($in, q{<}, $markers))
{
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data > 9 && defined $data[1] && defined $data[5] && exists $tmp2_list{$data[1]}) { print {$queryfile} '>', $tmp2_list{$data[1]}, "\n", $data[5], "\n"; }
# if (scalar @data > 9 && defined $data[2] && defined $data[9] && exists $tmp2_list{$data[2]}) { print {$queryfile} '>', $tmp2_list{$data[2]}, "\n", $data[9], "\n"; }
}
close $in;
}
}
elsif (defined $fasta && -r $fasta)
{
if (open($in, q{<}, $fasta))
{
my ($seq, $header) = (q{});
while (<$in>)
{
next if /^\s*$/;
chomp;
if (/^>/)
{ # fasta header line
my $h = $_;
$h =~ s/^>//;
if (defined $header && length $seq > 10)
{
print {$queryfile} '>', $tmp2_list{$header}, "\n", $seq, "\n" if (exists $tmp2_list{$header});
$header = $h;
$seq = q{};
}
else { $header = $h }
}
else
{
s/\W+//;
$seq .= $_;
}
}
if (defined $header && length $seq > 10) { print {$queryfile} '>', $tmp2_list{$header}, "\n", $seq, "\n" if (exists $tmp2_list{$header}); }
close $in;
}
}
close $queryfile;
if (system('makeblastdb -dbtype nucl -in "' . '/tmp/blast_' . $genetic . '.fasta' . '" -parse_seqids -hash_index -out "' . '/tmp/blast_' . $genetic . '_db" >/dev/null') != 0)
{
print {*STDERR} "ERROR: makeblastdb failed to execute: $!\n";
system('rm -f /tmp/query_' . $genetic . '.* /tmp/blast_' . $genetic . '*');
exit 10;
}
if (
system(
'blastn'
. ' -query '
. '/tmp/query_'
. $genetic
. '.fasta'
. ' -db "'
. '/tmp/blast_'
. $genetic
. '_db" -task blastn -dust yes -outfmt "6 std qlen slen" -max_target_seqs 1'
. (int($threads) > 1 ? ' -num_threads ' . int($threads) : q{})
. ' -out /tmp/query_'
. $genetic
. '.blast'
) != 0
)
{
print {*STDERR} "ERROR: blastn failed to execute: $!\n";
system('rm -f /tmp/query_' . $genetic . '.* /tmp/blast_' . $genetic . '*');
exit 10;
}
my %remap;
if (open($in, q{<}, '/tmp/query_' . $genetic . '.blast'))
{
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data >= 14 && defined $data[0] && defined $data[1] && defined $data[2] && defined $data[3] && defined $data[12] && defined $data[13])
{
# NEED CLEAN UP
if (int($data[2]) >= 90 && (int($data[3]) == int($data[12]) || int($data[3]) == int($data[13]) || int($data[3]) >= 99))
{
$remap{$data[0]} = $list_markers{$data[1]};
print {*STDERR} $data[0], "\t", $list_markers{$data[1]}[0], "\n";
}
}
}
close $in;
}
system('rm -f /tmp/query_' . $genetic . '.* /tmp/blast_' . $genetic . '*');
print {*STDOUT} "Marker\tLG\tPosition\n";
for my $item (keys %list2_markers) { print {*STDOUT} $item, "\t", (exists $remap{$item} ? $remap{$item}[1] . "\t" . $remap{$item}[2] : "Unk\t0"), "\n"; }
}
elsif ($tableS && defined $ped && -r $ped && defined $plink && -r $plink && open($in, q{<}, $plink))
{
my (@list_marker, @samples, %unique, %list_markers, %list_sequences );
# PEB
# # Stacks v1.42; PLINK v1.07; October 06, 2016
# C7 F1_dam_C7 0 0 0 0 G T A A G T A G G ...
# plink MAP
# # Stacks v1.42; PLINK v1.07; October 06, 2016
# LSalAtl2s1 19757_13 0 4466
# LSalAtl2s1 19756_74 0 4550
# LSalAtl2s1 19491_4 0 106094
# LSalAtl2s1 19492_81 0 106518
# LSalAtl2s1 19498_31 0 118987
# LSalAtl2s1 19749_27 0 381049
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data >= 2 && defined $data[0] && defined $data[1]) { @{$list_markers{$data[1]}} = @data; push @list_marker,$data[1]; }
}
close $in;
my %tmp_list;
for my $item (keys %list_markers)
{
if ($item =~ m/^(\d+)_\d+/) { $tmp_list{$1} = $item; $tmp_list{$item} = $1; }
elsif ($item =~ m/^(dDocent.*):\d+/) { $tmp_list{$1} = $item; $tmp_list{$item} = $1; }
else { $tmp_list{$item} = $item; }
}
if (scalar keys %list_markers > 0 && open($in, q{<}, $ped))
{
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data > 8)
{
push @samples, $data[1];
for my $j (0 .. (scalar @list_marker) - 1)
{
if (defined $list_marker[$j] && exists $list_markers{$list_marker[$j]})
{
if (!exists $unique{$list_marker[$j]}) { $unique{$list_marker[$j]} = q{} }
$unique{$list_marker[$j]} .= (defined $data[6 + $j * 2] && $data[6 + $j * 2] ne q{0} && defined $data[6 + $j * 2 + 1] && $data[6 + $j * 2 + 1] ne q{0} ? $data[6 + $j * 2] . $data[6 + $j * 2 + 1] : q{}) . "\t";
}
}
}
}
close $in;
}
if (defined $markers && -r $markers)
{
if (open($in, q{<}, $markers))
{
# ## cstacks version 1.42; catalog generated on 2016-09-22 22:24:20
# 0 2 1 LSalAtl2s1000 1022 - consensus 0 263_8... CATGTTTATGTATCATTTGTACTATTATAAAACTGAAATATATATTTTTATGTTTTTGTAAAAATGTTTAATTTATTATCTATAACCATTCCTATTCGCC 0 0 0 0
# 0 2 2 LSalAtl2s1000 132767 + consensus 0 263_13... CATGGTAAATTCGTGGTTTACACTATCATTGTCAGACAAAATTGTTGTGAGTACTATCATCTTGAAGCAATGTCGATGCAAGCAATAAGATTGTAAGTAA 0 0 0 0
# # cstacks version 2.3e; catalog generated on 2019-05-20 16:12:34
# 0 1 consensus 0 148_1... CATGCATGTTACTTAAGGGTAGTTTCAGAGGAGCAAGTGGCACATCCCTCCCTCTGCATTTTCAAATGACTGTTGTTGATTTTATTAAAACAAATTCTCCAAATTAAAGTGTAAAATCTTGGTAACCTTTGGAAGTAAAGT 0 0 0
my $seqpos = 5;
my $seqid = 1;
my $line = <$in>;
if ($line =~ m/version 1/) {
$seqpos = 9;
$seqid = 2;
}
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data > $seqpos && defined $data[$seqid] && defined $data[$seqpos] && exists $tmp_list{$data[$seqid]})
{
my $snploc;
if ($tmp_list{$data[$seqid]} =~ m/\_(\d+)/) { $snploc = $1; }
elsif ($tmp_list{$data[$seqid]} =~ m/dDocent.*\.(\d+)/) { $snploc = $1; }
my $tmp = $unique{$tmp_list{$data[$seqid]}};
$tmp =~ s/(.)(?=.*?\1)//g;
$tmp =~ s/\W//g;
my $seq = (defined $tmp && defined $snploc ? substr($data[$seqpos], 0, $snploc) . q{[} . $tmp . q{]} . substr($data[$seqpos], $snploc + 1) : $data[$seqpos]);
# to be check for v2+
$list_sequences{$tmp_list{$data[$seqid]}} = (int($loc) > 0 && defined $data[3] && defined $data[4] ? $data[3] . "\t" . $data[4] . "\t" . $seq : $seq);
}
}
close $in;
}
}
elsif (defined $fasta && -r $fasta)
{
if (open($in, q{<}, $fasta))
{
# >dDocent_Contig_12
# TGCAGAAAACACTCTCTCCCCAGACGGGTTTTGATAGAGTAGAACTCCGTCTCGATAGAAAGCAAAGTTGTTATATATATAGTAATAACTAGAGGGATTANNNNNNNNNNCATGTTTAATTTTAAAACATTTTCACACAACCTTAGATGGCTTTTATATTTAATATTCTATTCGAAATTTAAAAGATTTTGTAGCGGTGGATATTTTTGT
my ($seq, $header) = (q{});
while (<$in>)
{
next if /^\s*$/;
chomp;
if (/^>/)
{ # fasta header line
my $h = $_;
$h =~ s/^>//;
if (defined $header && length $seq > 10)
{
if ($header =~ /^(\d+) pos=([^:]+):(\d+):(.) NS=/) {
my ($a, $b, $c, $d) = ($1, $2, $3, $4);
if (exists $tmp_list{$a}) {
my $snploc;
if ($tmp_list{$a} =~ m/\_(\d+)/) { $snploc = $1; }
elsif ($tmp_list{$a} =~ m/dDocent.*\.(\d+)/) { $snploc = $1; }
my $tmp = $unique{$tmp_list{$a}};
$tmp =~ s/(.)(?=.*?\1)//g;
$tmp =~ s/\W//g;
my $seq = (defined $snploc ? substr($seq, 0, $snploc) . q{[} . $tmp . q{]} . substr($seq, $snploc + 1) : $seq);
$list_sequences{$tmp_list{$a}} = $b . "\t" . $c . "\t" . $d . "\t" . $seq;
}
} else {
$list_sequences{$header} = $seq if (exists $tmp_list{$header});
}
$header = $h;
$seq = q{};
}
else { $header = $h }
}
else
{
s/\W+//;
$seq .= $_;
}
}
if (defined $header && length $seq > 10) { if ($header =~ /^(\d+) pos=([^:]+):(\d+):(.) NS=/) {
my ($a, $b, $c, $d) = ($1, $2, $3, $4);
if (exists $tmp_list{$a}) {
my $snploc;
if ($tmp_list{$a} =~ m/\_(\d+)/) { $snploc = $1; }
elsif ($tmp_list{$a} =~ m/dDocent.*\.(\d+)/) { $snploc = $1; }
my $tmp = $unique{$tmp_list{$a}};
$tmp =~ s/(.)(?=.*?\1)//g;
$tmp =~ s/\W//g;
my $seq = (defined $snploc ? substr($seq, 0, $snploc) . q{[} . $tmp . q{]} . substr($seq, $snploc + 1) : $seq);
$list_sequences{$tmp_list{$a}} = $b . "\t" . $c . "\t" . $d . "\t" . $seq;
}
} else {
$list_sequences{$header} = $seq if (exists $tmp_list{$header});
} }
close $in;
}
}
print {*STDOUT} "Marker\t", join("\t", @samples), (defined $markers && -r $markers ? "\t" . 'Details' : (defined $fasta && -r $fasta ? "\t" . 'Marker' : q{})), "\n";
for my $item (keys %list_markers) {
if(!%selected || exists $selected{$item}){
print {*STDOUT} $item, "\t", substr($unique{$item},0,length($unique{$item}) -1), (exists $list_sequences{$item} ? "\t" . $list_sequences{$item} : (exists $tmp_list{$item} && exists $list_sequences{$tmp_list{$item}} ? "\t" . $list_sequences{$tmp_list{$item}} : q{})), "\n";
}
}
}
elsif (scalar @extra > 0 && defined $genetic && -r $genetic && open($in, q{<}, $genetic))
{
my (%list_markers, %list_sequences);
# genetic
# Marker LG Position
# 67793_33 1 0.000
# 65135_20 1 1.561
# 47811_36 1 4.114
# 47815_44 1 4.114
# 11332_62 1 6.270
# 47683_83 1 6.537
while (<$in>)
{
next if (m/^(#|Marker)/);
chomp;
my @data = split m/\t/;
if (scalar @data >= 2 && defined $data[0] && defined $data[1] && defined $data[2]) { @{$list_markers{$data[0]}} = @data; }
}
close $in;
foreach my $infile (@extra)
{
if (defined $infile && -r $infile && open(my $in2, q{<}, $infile))
{
my %tmp_list;
#Extra
# "","comments","codominant"
# "X67793_33",NA,0.02511912
while (<$in2>)
{
chomp;
my @data = split m/,/;
if (scalar @data >= 3 && defined $data[0] && defined $data[2] && $data[2] ne 'NA')
{
if ($data[0] =~ m/X([\d\w\_\.]+)/) { $tmp_list{$1} = $data[2]; }
elsif ($data[0] =~ m/(dDocent.*)\.(\d+)/) { $tmp_list{$1 . q{:} . $2} = $data[2]; }
}
}
close $in2;
if (scalar keys %tmp_list > 0)
{
for my $item (keys %list_markers) { push @{$list_markers{$item}}, (exists $tmp_list{$item} ? ($lod ? -log($tmp_list{$item}) / log(10) : $tmp_list{$item}) : q{-}); }
}
}
}
my %tmp_list;
for my $item (keys %list_markers)
{
if ($item =~ m/^(\d+)_\d+/) { $tmp_list{$1} = $item; $tmp_list{$item} = $1; }
elsif ($item =~ m/^(dDocent.*):\d+/) { $tmp_list{$1} = $item; $tmp_list{$item} = $1; }
else { $tmp_list{$item} = $item; }
}
my %unique;
if (defined $ped && -r $ped && defined $plink && -r $plink && open($in, q{<}, $plink))
{
my @list_full;
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data >= 2 && defined $data[0] && defined $data[1]) { push @list_full, $data[1]; }
}
close $in;
if (scalar @list_full > 0 && open($in, q{<}, $ped))
{
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data > 8)
{
for my $j (0 .. (scalar @list_full) - 1)
{
if (defined $list_full[$j] && exists $list_markers{$list_full[$j]})
{
if (!exists $unique{$list_full[$j]}) { $unique{$list_full[$j]} = q{} }
$unique{$list_full[$j]} .= (defined $data[6 + $j * 2] && $data[6 + $j * 2] ne q{0} && defined $data[6 + $j * 2 + 1] && $data[6 + $j * 2 + 1] ne q{0} ? $data[6 + $j * 2] . $data[6 + $j * 2 + 1] : q{});
}
}
}
}
close $in;
}
}
if (defined $markers && -r $markers)
{
if (open($in, q{<}, $markers))
{
# ## cstacks version 1.48; catalog generated on 2018-09-22 22:24:20
# 0 2 1 LSalAtl2s1000 1022 - consensus 0 263_8... CATGTTTATGTATCATTTGTACTATTATAAAACTGAAATATATATTTTTATGTTTTTGTAAAAATGTTTAATTTATTATCTATAACCATTCCTATTCGCC 0 0 0 0
# 0 2 2 LSalAtl2s1000 132767 + consensus 0 263_13... CATGGTAAATTCGTGGTTTACACTATCATTGTCAGACAAAATTGTTGTGAGTACTATCATCTTGAAGCAATGTCGATGCAAGCAATAAGATTGTAAGTAA 0 0 0 0
# # cstacks version 2.3e; catalog generated on 2019-05-20 16:12:34
# 0 1 consensus 0 148_1... CATGCATGTTACTTAAGGGTAGTTTCAGAGGAGCAAGTGGCACATCCCTCCCTCTGCATTTTCAAATGACTGTTGTTGATTTTATTAAAACAAATTCTCCAAATTAAAGTGTAAAATCTTGGTAACCTTTGGAAGTAAAGT 0 0 0
my $seqpos = 5;
my $seqid = 1;
my $line = <$in>;
if ($line =~ m/version 1/) {
$seqpos = 9;
$seqid = 2;
}
while (<$in>)
{
next if (m/^#/);
chomp;
my @data = split m/\t/;
if (scalar @data > $seqpos && defined $data[$seqid] && defined $data[$seqpos] && exists $tmp_list{$data[$seqid]})
{
my $snploc;
if ($tmp_list{$data[$seqid]} =~ m/\_(\d+)/) { $snploc = $1; }
elsif ($tmp_list{$data[$seqid]} =~ m/dDocent.*\.(\d+)/) { $snploc = $1; }
$unique{$tmp_list{$data[$seqid]}} =~ s/(.)(?=.*?\1)//g;
my $seq = (exists $unique{$tmp_list{$data[$seqid]}} && defined $snploc ? substr($data[$seqpos], 0, $snploc) . q{[} . $unique{$tmp_list{$data[$seqid]}} . q{]} . substr($data[$seqpos], $snploc + 1) : $data[$seqpos]);
# to be check for v2+
$list_sequences{$tmp_list{$data[$seqid]}} = (int($loc) > 0 && defined $data[3] && defined $data[4] ? $data[3] . "\t" . $data[4] . "\t" . $seq : $seq);
}
}
close $in;
}
}
elsif (defined $fasta && -r $fasta)
{
if (open($in, q{<}, $fasta))
{
# >dDocent_Contig_12
# TGCAGAAAACACTCTCTCCCCAGACGGGTTTTGATAGAGTAGAACTCCGTCTCGATAGAAAGCAAAGTTGTTATATATATAGTAATAACTAGAGGGATTANNNNNNNNNNCATGTTTAATTTTAAAACATTTTCACACAACCTTAGATGGCTTTTATATTTAATATTCTATTCGAAATTTAAAAGATTTTGTAGCGGTGGATATTTTTGT
my ($seq, $header) = (q{});
while (<$in>)
{
next if /^\s*$/;
chomp;
if (/^>/)
{ # fasta header line
my $h = $_;
$h =~ s/^>//;
if (defined $header && length $seq > 10)
{
if ($header =~ /^(\d+) pos=([^:]+):(\d+):(.) NS=/) {
my ($a, $b, $c, $d) = ($1, $2, $3, $4);
if (exists $tmp_list{$a}) {
my $snploc;
if ($tmp_list{$a} =~ m/\_(\d+)/) { $snploc = $1; }
elsif ($tmp_list{$a} =~ m/dDocent.*\.(\d+)/) { $snploc = $1; }
my $tmp = $unique{$tmp_list{$a}};
$tmp =~ s/(.)(?=.*?\1)//g;
$tmp =~ s/\W//g;
my $seq = (defined $snploc ? substr($seq, 0, $snploc) . q{[} . $tmp . q{]} . substr($seq, $snploc + 1) : $seq);
$list_sequences{$tmp_list{$a}} = $b . "\t" . $c . "\t" . $d . "\t" . $seq;
}
} else {
$list_sequences{$header} = $seq if (exists $tmp_list{$header});
}
$header = $h;
$seq = q{};
}
else { $header = $h }
}