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#!/usr/bin/env perl
#
# Copyright 2010-2021, Julian Catchen <jcatchen@illinois.edu>
#
# This file is part of Stacks.
#
# Stacks 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.
#
# Stacks 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 Stacks. If not, see <http://www.gnu.org/licenses/>.
#
use strict;
use POSIX;
use File::Temp qw/ mktemp /;
use File::Spec;
use constant stacks_version => "_VERSION_";
use constant true => 1;
use constant false => 0;
my $dry_run = false;
my $exe_path = "_BINDIR_";
my $out_path = "";
my $popmap_path = "";
my $sample_path = "";
my $db = "";
my $sample_id = 1;
my $gzip = false;
my $time = "";
my @parents;
my @progeny;
my @samples;
my (@_gstacks, @_populations);
my $cmd_str = $0 . " " . join(" ", @ARGV);
parse_command_line();
#
# Check for the existence of the necessary pipeline programs
#
foreach my $prog ("gstacks", "populations") {
die "Unable to find '" . $exe_path . $prog . "'.\n" if (!-e $exe_path . $prog);
}
my ($log, $log_fh, $sample);
my (@sample_list, %pop_ids, %pops, %grp_ids, %grps, %sample_ids);
parse_population_map(\@sample_list, \%pop_ids, \%pops, \%grp_ids, \%grps);
initialize_samples(\@parents, \@progeny, \@samples, \@sample_list, \%pop_ids, \%grp_ids);
#
# Open the log file
#
$log = "$out_path/ref_map.log";
open($log_fh, ">$log") or die("Unable to open log file '$log'; $!\n");
print $log_fh
"ref_map.pl version ", stacks_version, " started at ", strftime("%Y-%m-%d %H:%M:%S", (localtime(time))), "\n",
$cmd_str, "\n";
execute_stacks($log_fh, $sample_id, \@parents, \@progeny, \@samples, \%sample_ids);
print $log_fh "\nref_map.pl completed at ", strftime("%Y-%m-%d %H:%M:%S", (localtime(time))), "\n";
close($log_fh);
sub check_return_value {
# $? is a 16 bit int. Exit code is given by `$? & 255` if the process was
# terminated by a signal, and by `$? >> 8` if it exited normally.
my ($rv, $log_fh, $last_cmd) = @_;
if ($rv != 0) {
my $code = ($rv >> 8) & 127;
if ($rv & 255 || ($rv >> 8) > 127) {
$code += 128;
}
my $msg = "\nref_map.pl: Aborted because the last command failed ($code";
if ($code == 129 || $code == 130 || $code == 131) {
$msg .= "/interrupted";
} elsif ($code == 137 || $code == 143) {
$msg .= "/killed";
} elsif ($code == 134) {
$msg .= "/SIGABRT";
} elsif ($code == 139) {
$msg .= "/segmentation fault";
}
$msg .= ")";
print $log_fh ($msg . ".\n");
print $log_fh "Last command executed by ref_map.pl was:\n $last_cmd\n";
print STDERR ($msg . "; see ref_map.log file.\n");
print STDERR "Last command executed by ref_map.pl was:\n $last_cmd\n";
exit 1;
}
}
sub execute_stacks {
my ($log_fh, $sample_id, $parents, $progeny, $samples, $sample_ids) = @_;
my (@results, @depths_of_cov);
my ($pop_cnt, $sample, $num_files, $i, $cmd, $pipe_fh, $path, $cat_file);
#
# Call genotypes.
#
print STDERR "Calling variants, genotypes and haplotypes...\n";
print $log_fh "\ngstacks\n==========\n";
$cmd = $exe_path . "gstacks -I $sample_path -M $popmap_path -O $out_path";
foreach (@_gstacks) {
$cmd .= " " . $_;
}
print STDERR " $cmd\n\n";
print $log_fh "$cmd\n\n";
if (!$dry_run) {
open($pipe_fh, "$time $cmd 2>&1 |");
while (<$pipe_fh>) {
print $log_fh $_;
}
close($pipe_fh);
check_return_value($?, $log_fh, $cmd);
}
printf(STDERR "Calculating population-level summary statistics\n");
print $log_fh "\npopulations\n==========\n";
$cmd = $exe_path . "populations" . " -P $out_path " . join(" ", @_populations);
print STDERR " $cmd\n\n";
print $log_fh "$cmd\n\n";
if (!$dry_run) {
open($pipe_fh, "$time $cmd 2>&1 |");
while (<$pipe_fh>) {
print $log_fh $_;
}
close($pipe_fh);
check_return_value($?, $log_fh, $cmd);
}
print STDERR "ref_map.pl is done.\n";
print $log_fh "ref_map.pl is done.\n";
}
sub parse_population_map {
my ($sample_list, $pop_ids, $pops, $grp_ids, $grps) = @_;
my ($fh, @parts, $line, $sample);
return if (length($popmap_path) == 0);
open($fh, "<$popmap_path") or die("Unable to open population map, '$popmap_path', $!\n");
while ($line = <$fh>) {
chomp $line;
next if ($line =~ /^\s*#/);
@parts = split(/\t/, $line);
if (scalar(@parts) != 2 and scalar(@parts) != 3) {
die("Unable to parse population map, '$popmap_path' (expected 2 or 3 columns, found " . scalar(@parts) . "); at line:\n$line\n");
}
foreach my $part (@parts) {
$part =~ s/^\s*|\s*$//g;
}
push(@{$sample_list}, $parts[0]);
$pop_ids->{$parts[0]} = $parts[1];
$pops->{$parts[1]}++;
if (scalar(@parts) > 2) {
$grp_ids->{$parts[0]} = $parts[2];
$grps->{$parts[2]}++;
}
}
if (scalar(keys %{$grps}) == 0) {
$grps->{"1"}++;
foreach $sample (@{$sample_list}) {
$grp_ids->{$sample} = "1";
}
}
print STDERR "Parsed population map: ", scalar(@{$sample_list}), " files in ", scalar(keys %{$pops});
scalar(keys %{$pops}) == 1 ? print STDERR " population" : print STDERR " populations";
print STDERR " and ", scalar(keys %{$grps});
scalar(keys %{$grps}) == 1 ? print STDERR " group.\n" : print STDERR " groups.\n";
close($fh);
}
sub initialize_samples {
my ($parents, $progeny, $samples, $sample_list, $pop_ids, $grp_ids) = @_;
my ($local_gzip, $file, $prefix, $suffix, $path, $found, $i);
if (scalar(@{$sample_list}) > 0 && scalar(@{$samples}) == 0) {
my @suffixes = ("bam");
my @fmts = ("bam");
#
# If a population map was specified and no samples were provided on the command line.
#
foreach $sample (@{$sample_list}) {
$found = false;
for ($i = 0; $i < scalar(@suffixes); $i++) {
$path = $sample_path . $sample . "." . $suffixes[$i];
if (-e $path) {
$gzip = true if ($i == 1);
push(@{$samples}, {'path' => $sample_path,
'file' => $sample,
'suffix' => $suffixes[$i],
'type' => "sample",
'fmt' => $fmts[$i]});
$found = true;
last;
}
}
if ($found == false) {
die("Error: Failed to open '$sample_path$sample.bam'.\n");
}
}
}
#
# If a population map was specified, make sure all samples in the list were found (and vice versa) and assign popualtion IDs.
#
if (scalar(@{$sample_list}) > 0) {
my %sample_hash;
foreach $sample (@{$samples}) {
$sample_hash{$sample->{'file'}}++;
if (!defined($pop_ids->{$sample->{'file'}})) {
die("Unable to find an entry for '" . $sample->{'file'} . "' in the population map, '$popmap_path'.\n");
} else {
$sample->{'pop_id'} = $pop_ids->{$sample->{'file'}};
}
if (!defined($grp_ids->{$sample->{'file'}})) {
die("Unable to find an entry for '" . $sample->{'file'} . "' in the population map, '$popmap_path'.\n");
} else {
$sample->{'grp_id'} = $grp_ids->{$sample->{'file'}};
}
}
foreach $sample (@{$sample_list}) {
if (!defined($sample_hash{$sample})) {
die("Unable to find a file corresponding to the population map entry '" . $sample . "' in the population map, '$popmap_path'.\n");
}
}
} else {
foreach $sample (@{$parents}, @{$progeny}, @{$samples}) {
$sample->{'pop_id'} = "1";
$sample->{'grp_id'} = "1";
$pop_ids->{$sample->{'file'}} = $sample->{'pop_id'};
$grp_ids->{$sample->{'file'}} = $sample->{'grp_id'};
}
}
#
# Check that no duplicate files were specified.
#
my (%files, $file);
foreach $file (@{$parents}, @{$progeny}, @{$samples}) {
$files{$file}++;
}
foreach $file (keys %files) {
if ($files{$file} > 1) {
die("A duplicate file was specified which may create undefined results, '$file'\n");
}
}
print STDERR "Found ", scalar(@{$parents}), " parental file(s).\n\n" if (scalar(@{$parents}) > 0);
print STDERR "Found ", scalar(@{$progeny}), " progeny file(s).\n\n" if (scalar(@{$progeny}) > 0);
print STDERR "Found ", scalar(@{$samples}), " sample file(s).\n\n" if (scalar(@{$samples}) > 0);
if ( scalar(@{$samples}) > 0 && (scalar(@{$parents}) > 0 || scalar(@{$progeny}) > 0) ) {
die("Both samples and parents/progeny were specified either on the command line (-s/-r/-p) or within the population map. Only one of the other may be specified.\n");
}
}
sub write_results {
my ($results, $log_fh) = @_;
my $line;
foreach $line (@{$results}) {
if ($line =~ /\r/) {
$line =~ s/^.+\r(.*\n)$/\1/;
}
print $log_fh $line;
}
}
sub write_depths_of_cov {
my ($depths, $log_fh) = @_;
print STDERR "\nDepths of Coverage for Processed Samples:\n";
print $log_fh "\nDepths of Coverage for Processed Samples:\n";
foreach $a (@{$depths}) {
print STDERR $a->[0], ": ", $a->[1], "x\n";
print $log_fh $a->[0], ": ", $a->[1], "x\n";
}
}
sub parse_command_line {
my ($arg);
while (@ARGV) {
$_ = shift @ARGV;
if ($_ =~ /^-v$/ || $_ =~ /^--version$/) { version(); exit 1; }
elsif ($_ =~ /^-h$/) { usage(); }
elsif ($_ =~ /^-d$/ || $_ =~ /^--dry-run$/) { $dry_run = true; }
elsif ($_ =~ /^-o$/ || $_ =~ /^--out-path$/) { $out_path = shift @ARGV; }
elsif ($_ =~ /^-e$/) { $exe_path = shift @ARGV; }
elsif ($_ =~ /^--samples$/) {
$sample_path = shift @ARGV;
} elsif ($_ =~ /^-O$/ || $_ =~ /^--popmap$/) {
$popmap_path = shift @ARGV;
push(@_populations, "-M " . $popmap_path);
} elsif ($_ =~ /^--unpaired$/) {
push(@_gstacks, "--unpaired");
} elsif ($_ =~ /^--ignore-pe-reads$/) {
push(@_gstacks, "--ignore-pe-reads");
} elsif ($_ =~ /^-T$/) {
$arg = shift @ARGV;
push(@_gstacks, "-t " . $arg);
push(@_populations, "-t " . $arg);
} elsif ($_ =~ /^--rm-pcr-duplicates$/) {
push(@_gstacks, "--rm-pcr-duplicates");
} elsif ($_ =~ /^--var-alpha$/) {
$arg = shift @ARGV;
push(@_gstacks, "--var-alpha " . $arg);
} elsif ($_ =~ /^--gt-alpha$/) {
$arg = shift @ARGV;
push(@_gstacks, "--gt-alpha " . $arg);
} elsif ($_ =~ /^-r$/ || $_ =~ /^--min-samples-per-pop$/) {
push(@_populations, "--min-samples-per-pop " . shift @ARGV);
} elsif ($_ =~ /^-p$/ || $_ =~ /^--min-populations$/) {
push(@_populations, "--min-populations " . shift @ARGV);
} elsif ($_ =~ /^-X$/) {
#
# Pass an arbitrary command-line option to a pipeline program.
#
# Command line option must be of the form '-X "program:option"'
#
$arg = shift @ARGV;
my ($prog, $opt) = ($arg =~ /^(\w+):(.+)$/);
if ($prog eq "gstacks") {
push(@_gstacks, $opt);
} elsif ($prog eq "populations") {
push(@_populations, $opt);
} else {
print STDERR "Unknown pipeline program, '$arg'\n";
usage();
}
} elsif ($_ =~ /^--time-components$/) {
$time = '/usr/bin/time';
if (! -e $time) {
die "Error: '$time': No such file or directory.\n";
}
} else {
print STDERR "Unknown command line option: '$_'\n";
usage();
}
}
$exe_path = $exe_path . "/" if (substr($exe_path, -1) ne "/");
$out_path = substr($out_path, 0, -1) if (substr($out_path, -1) eq "/");
if (length($popmap_path) == 0) {
print STDERR "You must specify a population map that lists your sample names (--popmap).\n";
usage();
}
if (length($sample_path) == 0) {
print STDERR "You must specify the path to the directory containing the samples (--samples).\n";
usage();
}
if (length($sample_path) > 0) {
$sample_path .= "/" if (substr($sample_path, -1) ne "/");
}
}
sub version {
print STDERR "ref_map.pl ", stacks_version, "\n";
}
sub usage {
version();
print STDERR <<EOQ;
ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...]
Input/Output files:
--samples: path to the directory containing the samples BAM (or SAM) alignment files.
--popmap: path to a population map file (format is "<name> TAB <pop>", one sample per line).
-s: spacer for file names: by default this is empty and the program looks for files
named 'SAMPLE_NAME.bam'; if this option is given the program looks for files
named 'SAMPLE_NAME.SPACER.bam'.
-o,--out-path: path to an output directory.
General options:
-X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50"
-T: the number of threads/CPUs to use (default: 1).
-d: Dry run. Do not actually execute anything, just print the individual pipeline commands
that would be executed.
SNP model options:
--var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05).
--gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05).
Paired-end options:
--rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have
the same insert length.
--ignore-pe-reads: ignore paired-end reads even if present in the input
--unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's)
Population filtering options:
-r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0)
-p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1)
Miscellaneous:
--time-components (for benchmarking)
EOQ
exit 1;
}
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