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tseemanntseemann
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Add some helper scripts (only useful to MDU-PHL really)
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‎scripts/mdu-make_nullarbor_input.pl‎

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#!/usr/bin/env perl
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use strict;
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use warnings;
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use Getopt::Long;
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use File::Spec;
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use Cwd qw(abs_path);
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use Spreadsheet::Read;
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use Data::Dumper;
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use Cwd;
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my $id_re = '\b(\d{4}-\d{5})\b';
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my $read_re = '_R?([12])(?:_\d+)?.f';
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my $in = '';
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my $dir = '/mnt/seq/MDU/READS';
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my $out = 'samples.tab';
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my $longid = 0;
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my $verbose = 0;
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sub usage {
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print "$0 [--verbose] [--longid] [--fastqdir $dir] [--out $out] --in jobdetails.xlsx\n";
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exit;
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}
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@ARGV or usage();
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GetOptions(
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"help" => \&usage,
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"verbose!" => \&verbose,
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"in=s" => \$in,
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"fastqdir=s" => \$dir,
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"out=s" => \$out,
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"longid!" => \$longid,
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"id_regexp=s" => \$id_re,
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"read_regexp=s" => \$read_re,
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)
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or usage();
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if (!$in and @ARGV > 0) {
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$in = shift @ARGV;
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print STDERR "Guessing --in $in\n";
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}
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$in or die "need ID file with --in job.xls";
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-r $in or die "can't read ID file '$in'";
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$dir or die "need top-level folder containing FASTQ files with --dir";
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-d $dir or die "--dir '$dir' is not a directory";
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$out or die "need --out file to save results to";
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# compile regexps
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$id_re = qr"$id_re";
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$read_re = qr"$read_re";
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print STDERR "Scanning '$in' for MDU sample IDs...\n";
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my $book = ReadData( $in, cells=>0, strip=>3, attr=>1 );
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#print Dumper($book); exit;
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my @row = Spreadsheet::Read::rows($book->[1]);
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my %id;
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for my $row (@row) {
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my $line = join(' ', grep { defined $_ } @$row);
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if ($line =~ $id_re) {
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my $ID = $1;
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$line =~ s/\s+/--/g;
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$line =~ s/[_-]+$//;
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$line =~ s/^[_-]+//;
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$id{$ID} = $line;
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}
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}
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printf STDERR "Found %d sample IDs:\n", scalar(keys %id);
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if (0 == keys %id) {
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print STDERR "ERROR: no IDs found in '$in'\n";
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exit -1;
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}
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print STDERR map { "$_\n" } sort keys %id if $verbose;
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print STDERR "Scanning '$dir' for read files...\n";
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my %want_id = (map { ($_ => 1) } keys %id);
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my %sample;
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open DIR, "find $dir -type f -name '*.f*q.gz' |";
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while (my $file = <DIR>) {
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chomp $file;
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if ($file =~ $id_re and exists $want_id{$1}) {
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my $id = $1;
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my(undef, undef, $name) = File::Spec->splitpath($file);
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if ($name =~ $read_re) {
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my $read = $1;
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# print STDERR "$id $read\n";
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$sample{$id}{$read} = abs_path($file);
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print STDERR "Found $id $read : $file\n" if $verbose;
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}
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else {
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print STDERR "WARNING: found $id but not $read_re in $name\n";
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}
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}
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}
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print STDERR "Creating output file: $out\n";
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open OUT, '>', $out;
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#use Data::Dumper;
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#print STDERR Dumper(\%id);
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for my $id (sort keys %id) {
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if (exists $sample{$id}{1} and exists $sample{$id}{2}) {
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my $label = $longid ? $id{$id} : $id;
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print STDERR "$id - both reads found, labelling as '$label'\n";
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printf OUT join("\t", $label, $sample{$id}{1}, $sample{$id}{2})."\n";
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}
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elsif (!exists $sample{$id}{1} and !exists $sample{$id}{2}) {
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print STDERR "$id - NO READ FOUNDS !!!\n";
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}
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elsif (!exists $sample{$id}{1}) {
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print STDERR "$id - MISSING Read 1 FILE !!!\n";
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}
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elsif (!exists $sample{$id}{2}) {
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print STDERR "$id - MISSING Read 2 FILE !!!\n";
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}
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else {
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print STDERR "$id - THIS LINE SHOULD NEVER BE REACHED\n";
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}
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}
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print STDERR "Result in '$out'\n";
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print STDERR "Done.\n";
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my $name = qx(basename `pwd`);
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chomp $name;
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my $cmd = "nullarbor.pl --name $name --outdir nullarbor --input samples.tab --cpus 4 --mlst FIXME --ref FIXME";
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print STDERR "Your next command is probably this:\n$cmd\n";
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‎scripts/xlsx2tsv.pl‎

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#!/usr/bin/env perl
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use warnings;
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use strict;
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use Spreadsheet::Read;
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use Data::Dumper;
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my(@Options, $verbose, $sep, $informat);
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setOptions();
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my $book = ReadData( $ARGV[0], cells=>0, strip=>1 );
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my @row = Spreadsheet::Read::rows($book->[1]);
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for my $row (@row) {
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my @r = map { $_ || '' } @$row;
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print join($sep, @r),"\n";
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}
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#----------------------------------------------------------------------
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# Option setting routines
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sub setOptions {
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use Getopt::Long;
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@Options = (
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{OPT=>"help", VAR=>\&usage, DESC=>"This help"},
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{OPT=>"verbose!", VAR=>\$verbose, DEFAULT=>0, DESC=>"Verbose output"},
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# {OPT=>"informat=s", VAR=>\$informat, DEFAULT=>"xlsx", DESC=>"Input format: xls xlsx csv ods sxc"},
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{OPT=>"sep=s", VAR=>\$sep, DEFAULT=>"\t", DESC=>"Output separator"},
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);
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#(!@ARGV) && (usage());
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&GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) || usage();
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# Now setup default values.
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foreach (@Options) {
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if (defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) {
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${$_->{VAR}} = $_->{DEFAULT};
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}
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}
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}
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sub usage {
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print "Usage: $0 [options] [<] file.xlsx > file.csv\n";
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foreach (@Options) {
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printf " --%-13s %s%s.\n",$_->{OPT},$_->{DESC},
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defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
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}
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exit(1);
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}
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#----------------------------------------------------------------------

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