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SampleSheetTool.pl
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SampleSheetTool.pl
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use warnings;
use strict;
use Data::Dumper;
use Getopt::Std;
use POSIX;
#use JSON;
my $use =<<"END";
use: perl $0 [merge|addfile|reformat|reformatmin|stats|uniq|batch|help]
END
scalar
main();
sub main {
ToolRunner();
}
sub ToolRunner {
my $tool = shift @ARGV;
if(not($tool)){
warn $use;
exit(0);
}
if($tool eq 'merge'){
MergeSampleSheets($tool);
}elsif($tool eq 'addfile'){
AddFilesSampleSheet($tool);
}elsif($tool eq 'jsondump'){
JsonSampleSheet($tool);
}elsif($tool eq 'reformat'){
ReformatSampleSheet($tool);
}elsif($tool eq 'reformatillumina'){
ReformatSampleSheetIllumina($tool);
}elsif($tool eq 'reformatmin'){
ReformatSampleSheetMin($tool);
}elsif($tool eq 'stats'){
CollectStatsSampleSheet($tool);
}elsif($tool eq 'uniq'){
UniquefySamplesheets($tool);
}elsif($tool eq 'valid'){
ValidateSamplesheet($tool);
}elsif($tool eq 'batch'){
BatchSamplesheet($tool);
}elsif($tool eq 'split'){
SplitSamplesheetByProject($tool);
}elsif($tool eq 'arch'){
ArchiveDataSamplesheet($tool);
}elsif($tool eq 'help'){
Help($tool);
}else{
die "ERROR tool '$tool' is not correctly specified specified. $use";
}
}
##############################################################
###Tools
sub Help {
my $tool = shift @_;
my $use .=<<"END";
use: perl $0 [merge|addfile|reformat|stats|uniq|help] commands
toolkit to work with molgenis-compute sample configuration files
- merge Merge the tables based on header
use: perl $0 merge samplesheet_1.csv samplesheet_2.csv [samplesheet_n.csv] > samplesheet.merge.csv
- addfile Add fastq filenames to gcc spec based on lane/barcode/sample/read info
use: perl $0 addfile \
gccsamplesheet.csv \
fastqdir > samplesheet.filename.csv
- reformat Converts gcc spec to my own spec
use: perl $0 reformat \
samplesheet.filename.csv > samplesheet.reformat.csv
- reformatmin Converts minimal (tsv with fq1,fq2,fq3,sampleName) spec to my own spec
use: perl $0 reformatmin \
samplesheet.filename.csv > samplesheet.reformat.csv
- stats Collect statistics on samplesheet
use: perl $0 stats \
- uniq wip! get uniq record by specifying fields and merge prio by
specification order -f specifies the order of fields as csv
use: perl $0 uniq \
samplesheet1.csv samplesheet2.csv \
-f field1[,field2] >uniq.csv
- validate wip! Validate samplesheets using all modules default or only specified modules
use: perl $0 valid \
[-m module[,moduleN]]
samplesheet.csv
- batch wip! Batches projectnames based on PROJECTBASE and max INT samples in batches
also adds a controlsample in here.
use: perl $0 $tool -p PROJECTBASE -b INT -c CONTROLSAMPLENAME samplesheet.csv
- help This!
use: find it by `history| tail -n 2` and rtfm
END
warn $use
}
######################################################################
#main modules
#to be done FqUniq
#
######################################################################
sub MergeSampleSheets {
my $tool = shift @_;
my $use .=<<"END";
use: perl $0 $tool samplesheet_1.csv samplesheet_2.csv [samplesheet_n.csv] > samplesheet.merge.csv
END
if(not(scalar(@ARGV))){
warn $use;
exit(1);
}
my $mergedSamplesheet;
while(scalar(@ARGV)){
my $samplesheetfile = shift @ARGV;
warn "[INFO] Processing samplesheetfile='$samplesheetfile'";
my $samplesheet = ReadSamplesheet($samplesheetfile);
#add original file
for my $sample (@$samplesheet){
if(not($sample -> {'OrignalCsv'})){
if(substr(0,1) eq '/'){
$sample -> {'OrignalCsv'}=$samplesheetfile;
}else{
my $pwd=`pwd`;
chomp($pwd);
$sample -> {'OrignalCsv'}=$pwd."/".$samplesheetfile;#warn $pwd."/".$samplesheetfile. " ";
}
}
}
warn "[INFO] imported ".scalar(@$samplesheet)." from samplesheetfile='$samplesheetfile'";
#add to merged samplesheet
push(@$mergedSamplesheet,@$samplesheet);
}
print SamplesheetAsString($mergedSamplesheet);
warn "[INFO] Done";
}
######################################################################
sub AddFilesSampleSheet {
my $tool = shift @_;
my $use .=<<"END";
use: perl $0 $tool gccsamplesheet.csv fastqdir > samplesheet.filename.csv
END
my $samplesheetfile = shift @ARGV;
my $prefix = shift @ARGV;
warn "## ".localtime(time())." ## INFO ## $0 init with samplesheetfile='$samplesheetfile';prefix='$prefix'.\n";
my $targetprefix = shift @ARGV;
my $samplesheet = ReadSamplesheet($samplesheetfile);
$samplesheet = AddReadFileNames($samplesheet,$prefix);
#die Dumper($samplesheet);
print SamplesheetAsString($samplesheet);
}
##############################################################################
sub ReformatSampleSheet {
my $tool = shift @_;
my $use .=<<"END";
use: perl $0 $tool gccsamplesheetwithfilenames.csv > samplesheet.reformat.csv
END
my $samplesheetfile = shift @ARGV;
#my $prefix = shift @ARGV;
warn "## ".localtime(time())." ## INFO ## $0 init with samplesheetfile='$samplesheetfile'.\n";
my $samplesheet = ReadSamplesheet($samplesheetfile);
my $reformatTemplate=ReformatHashGccToRnaSeq();
$samplesheet=ConvertSampleSheet($samplesheet,$reformatTemplate);
#die Dumper($samplesheet);
print SamplesheetAsString($samplesheet);
}
##############################################################################
sub ReformatSampleSheetMin {
my $tool = shift @_;
my $use .=<<"END";
use: perl $0 $tool minsamplesheetwithfilenames.csv > samplesheet.reformat.csv
note the header should contain fq1/fq2/fq3/fq4 etc
example for creating from scratch:
ls *_R1.fastq.gz| perl -wne 'BEGIN{print "fq1,fq2,sampleName\n"};chomp;print \$_;s/_R1\./_R2./g; print ",\$_"; s/.*-(\\d\\d\\d)_.*/\$1/g; print ",\$_" ;print "\n"'
END
my $samplesheetfile = shift @ARGV;
#my $prefix = shift @ARGV;
warn "## ".localtime(time())." ## INFO ## $0 init with samplesheetfile='$samplesheetfile'.\n";
my $samplesheet = ReadSamplesheet($samplesheetfile);
#die Dumper($samplesheet)." ";
my $samplesheetann = AnnotateSamplesheet($samplesheet);
#die Dumper($samplesheetann)." ";
#my $reformatTemplate=ReformatHashGccToRnaSeq();
#$samplesheet=ConvertSampleSheet($samplesheet,$reformatTemplate);
#die Dumper($samplesheet);
print SamplesheetAsString($samplesheetann);
}
##############################################################################
sub ReformatSampleSheetIllumina {
my $tool = shift @_;
my $use .=<<"END";
use: perl $0 $tool gccsamplesheetwithfilenames.csv > samplesheet.reformat.csv
END
my $samplesheetfile = shift @ARGV;
#my $prefix = shift @ARGV;
warn "## ".localtime(time())." ## INFO ## $0 init with samplesheetfile='$samplesheetfile'.\n";
my $samplesheet = ReadSamplesheetIllumina($samplesheetfile);
my $reformatTemplate=ReformatHashIlluminaToSampleSheet();
$samplesheet=ConvertSampleSheet($samplesheet,$reformatTemplate);
#die Dumper($samplesheet);
print SamplesheetAsString($samplesheet);
}
#############################################################################
sub JsonSampleSheet {
my $tool = shift @_;
my $use .=<<"END";
Somewhat stupid json dump... wip...
use: perl $0 $tool gccsamplesheetwithfilenames.csv > samplesheet.json
END
my $samplesheetfile = shift @ARGV;
#my $prefix = shift @ARGV;
warn "## ".localtime(time())." ## INFO ## $0 init with samplesheetfile='$samplesheetfile'.\n";
my $samplesheet = ReadSamplesheet($samplesheetfile);
#my $samplesheetann = AnnotateSamplesheet($samplesheet);
#my $reformatTemplate=ReformatHashIlluminaToSampleSheet();
#$samplesheet=ConvertSampleSheet($samplesheet,$reformatTemplate);
#die Dumper($samplesheet);
print SamplesheetAsJSONString($samplesheet);
}
######################################################################
sub CollectStatsSampleSheet {
my $tool = shift @_;
my $use .=<<"END";
use: perl $0 $tool gccsamplesheetwithfilenames.csv > samplesheet.reformat.csv
END
my $samplesheetfile = shift @ARGV;
#my $prefix = shift @ARGV;
warn "## ".localtime(time())." ## INFO ## $0 init with samplesheetfile='$samplesheetfile'.\n";
my $samplesheet = ReadSamplesheet($samplesheetfile);
my $stats=StatsCollecterSampleSheet($samplesheet);
exit();
}
########################################################################
sub UniquefySamplesheets {
my $tool = shift @_;
my $use .=<<"END";
use: perl $0 $tool -f field, samplesheet.csv samplesheet2.csv > samplesheet.uniq.csv
END
my $opts;%{$opts}=();
getopts('f:', $opts);
my $mergedSamplesheet;
if(not(scalar(@ARGV))){
warn $use;
exit(1);
}
while(scalar(@ARGV)){
my $samplesheetfile = shift @ARGV;
warn "[INFO] Processing samplesheetfile='$samplesheetfile'";
my $samplesheet = ReadSamplesheet($samplesheetfile);
#add original file
for my $sample (@$samplesheet){
if(not($sample -> {'OrignalCsv'})){
if(substr(0,1) eq '/'){
$sample -> {'OrignalCsv'}=$samplesheetfile;
}else{
my $pwd=`pwd`;
chomp($pwd);
$sample -> {'OrignalCsv'}=$pwd."/".$samplesheetfile;#warn $pwd."/".$samplesheetfile. " ";
}
}
}
warn "[INFO] imported ".scalar(@$samplesheet)." from samplesheetfile='$samplesheetfile'";
#add to merged samplesheet
push(@$mergedSamplesheet,@$samplesheet);
}
#subroutines
my @fields;
my $fields;%{$fields} =();
my $samplesheetNew;
@$samplesheetNew=();
warn "[INFO] start uniquefy\n";
if($opts -> {'f'}){
my $h;%{$h}=();
#collect samples by fields
@fields = split(',',$opts -> {'f'});
for my $sample (@$mergedSamplesheet){
my $ref = $h;
for my $field (@fields){
my $val = $sample -> {$field};
if(not(defined($ref -> {$val}))){
%{$ref -> {$val}} = ();
}
#move the hash ref a step down the construct
$ref = $ref -> {$val};
}
push(@{$ref -> {'samples'}},$sample);
}
#Iterate $h leaves which are arrays of samples and prio samples
#https://stackoverflow.com/questions/2363142/how-to-iterate-through-hash-of-hashes-in-perl
my $samplelist;
@{$samplelist}=();
HashWalkBestSamples($h, [],$samplelist, \&CollectBestSamples);
warn "[INFO] end uniquefy\n";
print SamplesheetAsString($samplelist);
#for my $mod (@mods){
# die "Invalid mod $mod this should be 'controls', 'fastq', chars, cols and/or 'id'" if(not($mod eq 'controls' || $mod eq 'fastq' || $mod eq 'id' || $mod eq 'chars' || $mod eq 'cols'));
# $mods -> {$mod} ++ if($mod eq 'chars' || $mod eq 'cols');
#}
}else{
warn "Specify field(s) -f field1[,field2]\n";
warn $use;
exit(1);
#run all mods
#$mods -> {'cols'} ++;
#$mods -> {'chars'} ++;
}
my $samplesheetfile = shift @ARGV;
#my $prefix = shift @ARGV;
warn "## ".localtime(time())." ## INFO ## $0 end.\n";
exit();
}
##########################################################################
sub ValidateSamplesheet {
my $tool = shift @_;
my $opts;%{$opts}=();
getopts('m:', $opts);
my $mergedSamplesheet;
my $use .=<<"END";
WIP use: perl $0 $tool [-m MODULE,[MODULE]] samplesheet.csv
check for valid samplesheet files using different features with modules. defaults to all modules and possible vals:'controls', 'fastq', chars, cols and/or 'id.
END
#subroutines
my @subs = ("controls","fastq","id","cols");
my $mods;%{$mods} =();
my @mods;
if($opts -> {m}){
@mods = split(',',$opts -> {m});
for my $mod (@mods){
die "Invalid mod $mod this should be 'controls', 'fastq', chars, cols and/or 'id'" if(not($mod eq 'controls' || $mod eq 'fastq' || $mod eq 'id' || $mod eq 'chars' || $mod eq 'cols'));
$mods -> {$mod} ++ if($mod eq 'chars' || $mod eq 'cols');
}
}else{
#run all mods
$mods -> {'cols'} ++;
$mods -> {'chars'} ++;
}
while(scalar(@ARGV)){
my $samplesheetfile = shift @ARGV;
my $samplesheet = ReadSamplesheetWithValidation($samplesheetfile,$mods);
push(@$mergedSamplesheet,@$samplesheet);
}
if($opts -> {m}){
for my $mod (@mods){
#ValidateHeader# eq 'head' some of these are in teh old file incoded in the reader and should be separated to toggle
#ValidateColvalues#eq 'cols'
#ValidateSpecialChars#eq 'chars'
ValidateControlSampleNames($mergedSamplesheet) if($mod eq 'controls');
ValidateFqFiles($mergedSamplesheet) if($mod eq 'fastq');
ValidateInternalId($mergedSamplesheet) if($mod eq 'id');
ValidateSequence($mergedSamplesheet) if($mod eq 'seq');
}
}else{
ValidateControlSampleNames($mergedSamplesheet);
ValidateFqFiles($mergedSamplesheet);
ValidateInternalId($mergedSamplesheet);
ValidateSequence($mergedSamplesheet);#ILLUMINA,SLX,SOLEXA,SOLID,454,LS454,COMPLETE,PACBIO,IONTORRENT,CAPILLARY,HELICOS,UNKNOWN
}
print SamplesheetAsString($mergedSamplesheet);
}
##########################################################################
sub BatchSamplesheet {
my $tool = shift @_;
my $opts;%{$opts}=();
getopts('p:b:c:m:', $opts);
my $samplesheetfile = shift @ARGV;
my $use .=<<"END";
WIP use: perl $0 $tool -p PROJECTBASE -b INT -c CONTROLSAMPLENAME -m MOARCONTROLS samplesheet.csv
Batches projectnames based on PROJECTBASE and about INT samples in batches also adds a CONTROLSAMPLE in here. When MOARCONTROLS is a comma separated list of samplenames these get added as additional controlsamples.
END
die "ERROR: At least one of these missing -p PROJECTBASE -b INT -c CONTROLSAMPLENAME -m MOARCONTROLS. $use." if(not( $opts -> {'p'} && $opts -> {'b'} && $opts -> {'c'}&& $opts -> {'m'} ));
my $samplesheet = ReadSamplesheet($samplesheetfile);
my $batchedss = Batcher($samplesheet,$opts -> {'p'},$opts -> {'b'},$opts -> {'c'},$opts -> {'m'});
print SamplesheetAsString($batchedss);
}
################################
sub SplitSamplesheetByProject {
my $tool = shift @_;
my $opts;%{$opts}=();
getopts('p:b:c:m:', $opts);
my $samplesheetfile = shift @ARGV;
my $use .=<<"END";
WIP use: perl $0 $tool -p PREFIX samplesheet.csv
Splits samplesheets based on projects and will put them in prefix_projectname.csv
END
die "ERROR: At least one of these missing -p PREFIX . $use." if(not( $opts -> {'p'}));
my $samplesheet = ReadSamplesheet($samplesheetfile);
my @splitss = SplitByProject($samplesheet);
for my $ss (@splitss){
warn "INFO: Creating ".$opts -> {'p'}."_".$ss -> [0] -> {'project'}.".csv ...";
open(my $fh, ">", $opts -> {'p'}."_".$ss -> [0] -> {'project'}.".csv" );
print $fh SamplesheetAsString($ss);
close $fh;
}
}
################################
sub ArchiveDataSamplesheet {
my $tool = shift @_;
my $opts;%{$opts}=();
getopts('i:a:', $opts);
my $samplesheetfile = shift @ARGV;
my $use .=<<"END";
WIP use: perl $0 $tool -i inputdir -a archivedir samplesheet.csv
Gets all samples/fastqs using the samplesheet and puts em into the archive
dir with the samplesheets. Also does adding samplesheets , checking md5sums and making
the struture read only.
END
die "ERROR: At least one of these missing -p PREFIX . $use." if(not( $opts -> {'p'}));
my $samplesheet = ReadSamplesheet($samplesheetfile);
#my @splitss = SplitByProject($samplesheet);
for my $s (@{$samplesheet}){
warn "INFO: Checking and archiving ".$s -> {sampleName}." to ".$opts -> {'a'} . "\n";
open(my $fh, ">", $opts -> {'a'}."/".".samplesheet.csv" );
print $fh SamplesheetAsString($s);
close $fh;
}
}
#################################
#Subroutines
####
##
#
#
sub ReadSamplesheet {
my $samplesheetf = shift @_;
my $samplesheet;
open( my $samplesheeth,'<', $samplesheetf) or die "Cannot read samplesheet file:'$samplesheetf'";
$_=<$samplesheeth>;
chomp;
my @h = CommaseparatedSplit($_);
#die Dumper(\@h);
while(<$samplesheeth>){
chomp;
my @c = CommaseparatedSplit($_);
#die Dumper(\@c);
if(scalar(@c)==scalar(@h)){
my %d;
my $i=0;
map{$d{$_}=$c[$i]; $i++}(@h);
$c[$i]=join(",",@h);
#ReadFileNameConstructor(\%d);
push(@$samplesheet,\%d);
}else{
die "## ERROR ## Header is not of equal length compared sample line header:".Dumper(\@h)."columns".Dumper(\@c)." ";
}
}
return $samplesheet;
}
sub AnnotateSamplesheet {
my $samplesheet = shift @_;
my $reformatTemplate = shift @_;
#die Dumper($samplesheet)." here";
my $newSamplesheet;
my $id = 1;
for my $sample (@$samplesheet){
my $newSample;
$newSample -> {'sampleName'} = $sample -> {'sampleName'};
#missing:internalId,samplePrep,sequencer,sequencerId,barcode,sequencingStartDate,project,
# controlSampleName,reads3FqGz
$newSample -> {'reads1FqGz'}="something went wrong using samplesheet tool.";
$newSample -> {'internalId'}="$id";$id++;
$newSample -> {'samplePrep'}="oneLibraryPrepPerSampleAssumed";
$newSample -> {'sequencer'}="illumina";#assumed
my $date;@{$date} = CmdRunner('date --iso-8601=date');
chomp($date -> [-1]);
$newSample -> {'sequencingStartDate'}=$date -> [0];
$newSample -> {'project'}="projectNameHere";#lazy find and replace for this keyword in generatescrpts
$newSample -> {'controlSampleName'}=$sample -> {'sampleName'};
$newSample -> {'reads2FqGz'}="";#always present but empty when not found
$newSample -> {'reads3FqGz'}="";
$newSample -> {'barcode'} = "NNNNNN";
my @files;
map{push(@files,$sample -> {$_})if($_ =~ m/^fq\d/)}(keys(%{$sample}));
#die Dumper(@files);
#i put in a sort but this might still give problems based on the sorting of filenames....
for my $file (sort(@files)){
chomp $file;
#Add defaults here when not present in fastq files
#unreadble code.I hope it works!
if($file =~ m/.txt.gz/){#This is very experimental should work for single end sequencing
$newSample -> {'reads1FqGz'} = $file;
my $fqhead;@{$fqhead} = CmdRunner('zcat '.$newSample -> {reads1FqGz}.'|head -n 1');
my @fqheadsplit= split /[\/_\-: \@#]/,($fqhead -> [0]);
chomp($fqheadsplit[-1]);
#@HWI-ST001_0001:1:1111:112345:12345#NNNNNN/1 for read end 1
$newSample -> {'run'} = $fqheadsplit[3];
$newSample -> {'sequencerId'} = $fqheadsplit[2];
$newSample -> {'flowcellId'} = "nofcid";
$newSample -> {'seqType'} = "illumina";
$newSample -> {'lane'} = $fqheadsplit[4];#this should create an uniq list of lanes
$newSample -> {'barcode'}=$fqheadsplit[-2] if($fqheadsplit[-2] =~ m/[ATCGN\+]{6,}/);
$newSample -> {'reads1FqGzMd5'}=Md5Sum($newSample -> {"reads1FqGz"});
}if($file =~ m/_R1\./){
$newSample -> {'reads1FqGz'} = $file;
#zcat $file |head -n 1 should contain @M00000:999:000000000-FLOWCELLIDD:TILE:12345:23456:4567 1:N:0:GTGATTCC+TATAGCCT
my $fqhead;@{$fqhead} = CmdRunner('zcat '.$newSample -> {reads1FqGz}.'|head -n 1');
my @fqheadsplit= split /[: \@]/,($fqhead -> [0]);
chomp($fqheadsplit[-1]);
$newSample -> {'run'} = $fqheadsplit[2];
$newSample -> {'sequencerId'} = $fqheadsplit[1];
$newSample -> {'flowcellId'} = $fqheadsplit[3];
$newSample -> {'seqType'} = $fqheadsplit[3];
$newSample -> {'lane'} = $fqheadsplit[4];#this should create an uniq list of lanes
$newSample -> {'barcode'}=$fqheadsplit[-1] if($fqheadsplit[-1] =~ m/[ATCGN\+]{6,}/);
$newSample -> {'reads1FqGzMd5'}=Md5Sum($newSample -> {"reads1FqGz"});
}elsif($file =~ m/_R2\./){
$newSample -> {'reads2FqGz'} = $file;
my $fqhead;@{$fqhead} = CmdRunner('zcat '.$newSample -> {reads2FqGz}.'|head -n 1');
my @fqheadsplit= split /[: \@]/,($fqhead -> [0]);
$newSample -> {'run'} = $fqheadsplit[2];
$newSample -> {'flowcellId'} = $fqheadsplit[3];
$newSample -> {'seqType'} = $fqheadsplit[3];
$newSample -> {'lane'} = $fqheadsplit[4];
$newSample -> {'reads2FqGzMd5'}=Md5Sum($newSample -> {"reads2FqGz"});
}elsif($file =~ m/_R3\./){#nugene/umi probs
$newSample -> {'reads3FqGz'} = $newSample -> {reads2FqGz};
$newSample -> {'reads3FqGzMd5'} = $newSample -> {reads2FqGzMd5};
$newSample -> {'reads2FqGz'} = $file;
my $fqhead;@{$fqhead} = CmdRunner('zcat '.$newSample -> {reads2FqGz}.'|head -n 1');
my @fqheadsplit= split /[: \@]/,($fqhead -> [0]);
$newSample -> {'run'} = $fqheadsplit[2];
$newSample -> {'flowcellId'} = $fqheadsplit[3];
$newSample -> {'seqType'} = $fqheadsplit[3];
$newSample -> {'lane'} = $fqheadsplit[4];#this should create an uniq list of lanes
$newSample -> {'reads2FqGzMd5'}=Md5Sum($newSample -> {"reads2FqGz"});
}elsif($file =~ m/_umi\./){#umi probes literal no annoying R2 as umi and R2=R3
$newSample -> {'reads3FqGz'} = $file;
my $fqhead;@{$fqhead} = CmdRunner('zcat '.$newSample -> {reads2FqGz}.'|head -n 1');
my @fqheadsplit= split /[: \@]/,($fqhead -> [0]);
$newSample -> {'run'} = $fqheadsplit[2];
$newSample -> {'flowcellId'} = $fqheadsplit[3];
$newSample -> {'seqType'} = $fqheadsplit[3];
$newSample -> {'lane'} = $fqheadsplit[4];#this should create an uniq list of lanes
$newSample -> {'reads3FqGzMd5'}=Md5Sum($newSample -> {"reads3FqGz"});
}elsif($file =~ m/_R4\./){
#Future proofing
$newSample -> {'reads4FqGz'} = $file;
$newSample -> {'reads4FqGzMd5'} = Md5Sum($newSample -> {"reads4FqGz"});
my $fqhead;@{$fqhead} = CmdRunner('zcat '.$newSample -> {reads4FqGz}.'|head -n 1');
my @fqheadsplit= split /[: \@]/,($fqhead -> [0]);
$newSample -> {'run'} = $fqheadsplit[2];
$newSample -> {'flowcellId'} = $fqheadsplit[3];
$newSample -> {'seqType'} = $fqheadsplit[3];
$newSample -> {'lane'} = $fqheadsplit[4];#this should create an uniq list of lanes
}
}
#die Dumper($newSample);
push (@$newSamplesheet, $newSample);
}
return $newSamplesheet;
}
sub ReadSamplesheetIllumina {
my $samplesheetf = shift @_;
my $samplesheet;
open( my $samplesheeth,'<', $samplesheetf) or die "Cannot read samplesheet file:'$samplesheetf'";
my $headerandsettings;
my $line = " ";
while(defined($line = <$samplesheeth>) and not( $line =~ m/\[Data\]/)){
#warn "line " . $line;
$line =~ s/\r?\n\z//;
#$line =~ s/\r|\n|\z//;
chomp $line;
next if($line =~ m/^\[/);
if($line =~ m/\,/){
my @c = CommaseparatedSplit($line);
#warn "###Commaline " . $line ." \n". Dumper(\@c). " ";
#$c[0] =~ s/\r|\n|\z//;
$headerandsettings -> {$c[0]} = $c[1];
}
}
#die "Headerandsettings\n".Dumper($headerandsettings)." ";
$line = <$samplesheeth>;
$line =~ s/\r?\n\z//;
chomp $line;
my @h = CommaseparatedSplit($line);
#die Dumper(\@h);
while(<$samplesheeth>){
s/\r?\n\z//;
chomp;
my @c = CommaseparatedSplit($_);
#die Dumper(\@c);
if(scalar(@c)==scalar(@h)){
my %d = %{$headerandsettings};
$d{'sequencer'}= 'illumina';
$d{'line'}=$.;
my $i=0;
map{$d{$_}=$c[$i]; $i++}(@h);
$c[$i]=join(",",@h);
die "ERROR Invalid sample id: '".$d{'Sample_ID'}."'. This should not contain spaces." if($d{'Sample_ID'} =~ m/ /);
#ReadFileNameConstructor(\%d);
my $ret;
@{$ret} = CmdRunner('ls "$(dirname '."'$samplesheetf'".')"/'.$d{'Sample_Project'}.'/'.$d{'Sample_ID'}.'_*_R[1234]_*.fastq.gz');
if(scalar(@{$ret})){
my @lanes;
for my $file (@{$ret}){
chomp $file;
#unreadble code.I hope it works!
if($file =~ m/_R1_0/){
$d{'reads1FqGz'} = $file;
#zcat $file |head -n 1 should contain @M00000:999:000000000-FLOWCELLIDD:TILE:12345:23456:4567 1:N:0:GTGATTCC+TATAGCCT
my $fqhead;@{$fqhead} = CmdRunner('zcat '.$d{reads1FqGz}.'|head -n 1');
my @fqheadsplit= split /[: \@]/,($fqhead -> [0]);
$d{'run'} = $fqheadsplit[2];
$d{'flowcellId'} = $fqheadsplit[3];
$d{'seqType'} = $fqheadsplit[3];
push @lanes, $fqheadsplit[4];#this should create an uniq list of lanes
}elsif($file =~ m/_R2_0/){
$d{'reads2FqGz'} = $file;
my $fqhead;@{$fqhead} = CmdRunner('zcat '.$d{reads1FqGz}.'|head -n 1');
my @fqheadsplit= split /[: \@]/,($fqhead -> [0]);
$d{'run'} = $fqheadsplit[2];
$d{'flowcellId'} = $fqheadsplit[3];
$d{'seqType'} = $fqheadsplit[3];
}elsif($file =~ m/_R3_0/){#nugene/umi probs
$d{'reads3FqGz'} = $d{reads2FqGz};
$d{'reads2FqGz'} = $file;
my $fqhead;@{$fqhead} = CmdRunner('zcat '.$d{reads1FqGz}.'|head -n 1');
my @fqheadsplit= split /[: \@]/,($fqhead -> [0]);
$d{'run'} = $fqheadsplit[2];
$d{'flowcellId'} = $fqheadsplit[3];
$d{'seqType'} = $fqheadsplit[3];
}elsif($file =~ m/_R4_0/){
#Future proofing
$d{'reads4FqGz'} = $file;
my $fqhead;@{$fqhead} = CmdRunner('zcat '.$d{reads1FqGz}.'|head -n 1');
my @fqheadsplit= split /[: \@]/,($fqhead -> [0]);
$d{'run'} = $fqheadsplit[2];
$d{'flowcellId'} = $fqheadsplit[3];
$d{'seqType'} = $fqheadsplit[3];
}
}
for my $lane (@lanes){
$d{'lane'} = $lane;
for my $fq ('reads1FqGz','reads2FqGz','reads3FqGz'){
my $prettylane = '_L'.sprintf("%03d", $lane).'_';
if(defined($d{$fq})){
$d{$fq} =~ s/_L\d\d\d_/$prettylane/ge;
$d{$fq."Md5"} = Md5Sum($d{$fq});
}if(not(defined($d{$fq}))){
$d{$fq} = '';
}
}
push(@$samplesheet,\%d);
}
}else{
push(@$samplesheet,\%d);
}
}else{
die "## ERROR ## Header is not of equal length compared sample line header:".Dumper(\@h)."columns".Dumper(\@c)." ";
}
}
#die Dumper($samplesheet)." ";
return $samplesheet;
}
sub CommaseparatedSplit {
my $string=pop @_;
#needs to be fixed for citation marks!
warn "Line contains citation marks: this is currently not supported!!. I hope this works. Line=$_" if($string =~ /"|'/);
my $i = index($string,",");
if( $i > -1){
push(@_,substr($string,0,$i));
push(@_,substr($string,$i+1));
@_ = CommaseparatedSplit( @_ );
}else{
push(@_,$string);
return @_;
}
}
sub SamplesheetAsString {
my $self = shift @_;
my $string = '';
#get header values;
my %h;
for my $sample (@$self){
for my $key (keys(%$sample)){
$h{$key}++;
}
}
my @h = sort {$b cmp $a} (keys(%h));
$string.=join(",",@h)."\n";
#warn scalar(@$self);
for my $sample (@$self){
my @c;
for my $h (@h){
if($$sample{$h}){
push (@c,$$sample{$h});
}else{
push (@c,"");
}
}
$string.=join(",",@c)."\n";
}
return $string;
}
sub SamplesheetAsJSONString {
my $self = shift @_;
my $string = '';
#get header values;
my %h;
for my $sample (@$self){
for my $key (keys(%$sample)){
$h{"KEYS"} -> {$key}++ if not $key eq "sampleName";
push(@{$h{"SAMPLENAMES"} -> {$sample -> {'sampleName'}}},$sample) if $key eq "sampleName";
}
}
$string.= '{"samples": [';
#my @h = sort {$b cmp $a} (keys(%h));
#$string.=join(",",@h)."\n";
#warn scalar(@$self);
my $idx = 0;
for my $samplename (keys(%{$h{"SAMPLENAMES"}})){
#die Dumper(%h);
$string.= ' {"name": "'.$h{"SAMPLENAMES"}->{$samplename} -> [0] -> {'sampleName'}.'",
"threeLetterName": "MS1",
"readgroups" : ['."\n";
my $rgidx = 0;
for my $rg (@{$h{"SAMPLENAMES"} -> { $samplename }}){
# my @c;
# for my $h (@h){
# if($$sample{$h}){
# push (@c,$$sample{$h});
# }else{
# push (@c,"");
# }
# }
# $string.=join(",",@c)."\n";
$string.= ' {"identifier": "'.$rg -> {'sampleName'}.'_'.
$rg -> {'lane'}.'_'.$rg -> {'barcode'}.'",
"lane": "'.$rg -> {'lane'}.'",
"barcode2": "NNNNNN",
"fastq1": "'.$rg -> {'reads1FqGz'}.'",'."\n";
$string .= ' "fastq2": "'.$rg -> {'reads2FqGz'}.'",'."\n" if($rg -> {'reads2FqGz'} ne "");
$string .= ' "date": "'.$rg -> {'sequencingStartDate'}.'",
"barcode1": "'.$rg -> {'barcode'}.'",
"run": "'.$rg -> {'run'}.'",
"platform_model" : "HiSeq2xxx",
"sequencer":"'.$rg -> {'sequencerId'}.'",
"platform": "'.$rg -> {'sequencer'}.'",
"flowcell":"'.$rg -> {'flowcellId'}.'",
"sequencing_center": "undef"
}';
$string = $string .',' if(($rgidx+1) < scalar(@{$h{"SAMPLENAMES"} -> { $samplename }}));
$string .= "\n";
$rgidx++;
}
$string .= ' ]'."\n".' }';
$string = $string .',' if(($idx+1) < scalar(keys(%{$h{"SAMPLENAMES"}})));
$string .= "\n";
$idx++;
}
$string.= ']}'."\n";
return $string;
}
sub ReadBaseNameBuilder {
my $self = shift @_;
#140430_SN163_0549_AH78TFADXX_L1_GAGTAGAG_2
#die "columns PREFIX and TARGETPRFIX need to be present. specify on commandline!" if($$self{'PREFIX'} && $$self{'TARGETPRFIX'});
die "Column sequencingStartDate needs to be present. Specify in csv file!".Dumper($self) if(not(exists($$self{'sequencingStartDate'})));
die "Column sequencer needs to be present. Specify in csv file!".Dumper($self) if(not(exists($$self{'sequencer'})));
die "Column run to be present. Specify in csv file!".Dumper($self) if(not(exists($$self{'run'})));
die "Column flowcell needs to be present. Specify in csv file!".Dumper($self) if(not(exists($$self{'flowcell'})));
die "Column lane needs to be present. Specify in csv file!".Dumper($self) if(not(exists($$self{'lane'})));
die "Column barcode needs to be present. Specify in csv file!".Dumper($self) if(not(exists($$self{'barcode'})) && not(exists($$self{'barcode1'})));
my @fqBases=();
#GCC version of fastq files
if(exists($$self{'barcode'})){
push(@fqBases,$$self{'sequencingStartDate'}."_".$$self{'sequencer'}."_".$$self{'run'}."_".$$self{'flowcell'}."_L".$$self{'lane'}."_".$$self{'barcode'});
push(@fqBases,$$self{'sequencingStartDate'}."_".$$self{'sequencer'}."_".'0'x(4- length($$self{'run'})).$$self{'run'}."_".$$self{'flowcell'}."_L".$$self{'lane'}."_".$$self{'barcode'});
}elsif(exists($$self{'barcode1'}) && exists($$self{'barcode2'}) && $$self{'barcode1'} ne "NA" && $$self{'barcode2'} ne "NA"){
push(@fqBases,$$self{'sequencingStartDate'}."_".$$self{'sequencer'}."_".$$self{'run'}."_".$$self{'flowcell'}."_L".$$self{'lane'}."_".$$self{'barcode1'}."-".$$self{'barcode2'});
push(@fqBases,$$self{'sequencingStartDate'}."_".$$self{'sequencer'}."_".'0'x(4- length($$self{'run'})).$$self{'run'}."_".$$self{'flowcell'}."_L".$$self{'lane'}."_".$$self{'barcode1'}."-".$$self{'barcode2'});
}elsif(exists($$self{'barcode1'}) && $$self{'barcode1'} ne "NA"){
push(@fqBases,$$self{'sequencingStartDate'}."_".$$self{'sequencer'}."_".$$self{'run'}."_".$$self{'flowcell'}."_L".$$self{'lane'}."_".$$self{'barcode1'});
push(@fqBases,$$self{'sequencingStartDate'}."_".$$self{'sequencer'}."_".'0'x(4- length($$self{'run'})).$$self{'run'}."_".$$self{'flowcell'}."_L".$$self{'lane'}."_".$$self{'barcode1'});
}else{
push(@fqBases,$$self{'sequencingStartDate'}."_".$$self{'sequencer'}."_".$$self{'run'}."_".$$self{'flowcell'}."_L".$$self{'lane'});
push(@fqBases,$$self{'sequencingStartDate'}."_".$$self{'sequencer'}."_".'0'x(4- length($$self{'run'})).$$self{'run'}."_".$$self{'flowcell'}."_L".$$self{'lane'});
}
#my version
push(@fqBases,"lane".$$self{'lane'}."_".$$self{'barcode'}.'_S*_L00'.$$self{'lane'}."_R1_001");
#default illumina version
#samplename_S5_L001_I1_001.fastq.gz
push(@fqBases,$$self{'externalSampleID'}.'_S*_L00'.$$self{'lane'}."_R1_001");
warn "looking for ". join(', ', @fqBases)." \n";
#lane4_TGTTCCGT_S128_L004_R2_001.fastq.gz
return @fqBases;
#return $self;
}
sub AddReadFileNames {
my $samplesheet = shift @_;
my $prefix = shift @_;
#my $targetprefix = shift @_;
my $samplesheetNew;
@{$samplesheetNew}=();
my $scount=0;
while($scount < scalar(@{$samplesheet})){
my $sample = $samplesheet->[$scount];
my $samplePushed=0;
my @fqbases = ReadBaseNameBuilder($sample);
warn scalar @fqbases;
for my $fqbase (@fqbases){
#warn $prefix."/".$fqbase."";
#warn $prefix."/".$fqbase."_1.fq.gz" if(-e $prefix."/".$fqbase."_1.fq.gz");
my $fqbase2 = $fqbase;
my $fqbase3 = $fqbase;
my $fqbaseI1 = $fqbase;
if(index($fqbase,"_R1_")){
substr($fqbase2,index($fqbase2,"_R1_"),4,"_R2_");
substr($fqbase3,index($fqbase3,"_R1_"),4,"_R3_");
substr($fqbaseI1,index($fqbaseI1,"_R1_"),4,"_I1_");
}
my @exts=('.fq.gz', '.fastq.gz');
#glob or globble?
for my $ext (@exts){
#warn "looking for $fqbase\n$fqbase2\n$fqbase3\n";
if( -e $prefix."/".$fqbase.$ext){
$sample -> {"reads1FqGz"}=$prefix."/".$fqbase.$ext;
$sample -> {"reads1FqGzMd5"}=Md5Sum($sample -> {"reads1FqGz"});
warn "## ".localtime(time())." ## INFO ## Single end read detected. Stored as read1 = ".$$sample{'reads1FqGz'}. "; md5sum = ".$sample -> {'reads1FqGzMd5'};
}elsif((-e $prefix."/".$fqbase."_1".$ext && ! -e $prefix."/".$fqbase."_2".$ext )){
$sample -> {"reads1FqGz"}=$prefix."/".$fqbase."_1".$ext;
$sample -> {"reads1FqGzMd5"}=Md5Sum($sample -> {"reads1FqGz"});
warn "## ".localtime(time())." ## WARN ## Paired end read file name detected but only one end found thus single end assumed. Stored as read1 = ".$$sample{'reads1FqGz'};
}elsif(( ! -e $prefix."/".$fqbase."_1".$ext && -e $prefix."/".$fqbase."_2".$ext )){
$sample -> {"reads1FqGz"}=$prefix."/".$fqbase."_2".$ext;
$sample -> {"reads1FqGzMd5"}=Md5Sum($sample -> {"reads1FqGz"});
warn "## ".localtime(time())." ## WARN ## Paired end read file name detected but only one end found thus single end assumed. Stored as read1 = ".$$sample{'reads1FqGz'};
}elsif(( -e $prefix."/".$fqbase."_1".$ext && -e $prefix."/".$fqbase."_2".$ext )){
$sample -> {"reads1FqGz"}=$prefix."/".$fqbase."_1".$ext;
$sample -> {"reads1FqGzMd5"}=Md5Sum($sample -> {"reads1FqGz"});
$sample -> {"reads2FqGz"}=$prefix."/".$fqbase."_2".$ext;
$sample -> {"reads2FqGzMd5"}=Md5Sum($sample -> {"reads2FqGz"});
warn "## ".localtime(time())." ## INFO ## Paired end read files detected. Stored as read1 = ".$$sample{'reads1FqGz'}." read2 = ".$$sample{'reads2FqGz'};
#warn Dumper($sample);
#illumina raw output rules
#pe with index
}elsif(index($fqbase,"_R1_") && ( -e glob($prefix."/".$fqbase.$ext) && -e glob($prefix."/".$fqbase2.$ext) && -e glob($prefix."/".$fqbase3.$ext) && -e glob($prefix."/".$fqbaseI1.$ext)) ){
$sample -> {"reads1FqGz"}=glob($prefix."/".$fqbase.$ext);
$sample -> {"reads1FqGzMd5"}=Md5Sum($sample -> {"reads1FqGz"});
$sample -> {"reads2FqGz"}=glob($prefix."/".$fqbase3.$ext);
$sample -> {"reads2FqGzMd5"}=Md5Sum($sample -> {"reads2FqGz"});
$sample -> {"reads3FqGz"}=glob($prefix."/".$fqbase2.$ext);
$sample -> {"reads3FqGzMd5"}=Md5Sum($sample -> {"reads3FqGz"});
$sample -> {"reads1IndexFqGz"}=glob($prefix."/".$fqbaseI1.$ext);
$sample -> {"reads1IndexFqGzMd5"}=Md5Sum($sample -> {"reads1IndexFqGz"});
warn "## ".localtime(time())." ## INFO ## Paired end read + index files detected. Stored as read1 = ".$$sample{'reads1FqGz'}." read2 = ".$$sample{'reads2FqGz'};
#warn Dumper($sample);
#pe without index
}elsif(index($fqbase,"_R1_") && ( -e glob($prefix."/".$fqbase.$ext) && -e glob($prefix."/".$fqbase2.$ext) && -e glob($prefix."/".$fqbase3.$ext)) ){
$sample -> {"reads1FqGz"}=glob($prefix."/".$fqbase.$ext);
$sample -> {"reads1FqGzMd5"}=Md5Sum($sample -> {"reads1FqGz"});
$sample -> {"reads2FqGz"}=glob($prefix."/".$fqbase3.$ext);
$sample -> {"reads2FqGzMd5"}=Md5Sum($sample -> {"reads2FqGz"});
$sample -> {"reads3FqGz"}=glob($prefix."/".$fqbase2.$ext);
$sample -> {"reads3FqGzMd5"}=Md5Sum($sample -> {"reads3FqGz"});
$sample -> {"reads1IndexFqGz"}=glob($prefix."/".$fqbaseI1.$ext);
$sample -> {"reads1IndexFqGzMd5"}=Md5Sum($sample -> {"reads1IndexFqGz"});
warn "## ".localtime(time())." ## INFO ## Paired end read files detected. Stored as read1 = ".$$sample{'reads1FqGz'}." read2 = ".$$sample{'reads2FqGz'};
#warn Dumper($sample);
#se with index
}elsif(index($fqbase,"_R1_") && ( -e glob($prefix."/".$fqbase.$ext) && -e glob($prefix."/".$fqbase2.$ext) && -e glob($prefix."/".$fqbaseI1.$ext)) ){
$sample -> {"reads1FqGz"}=glob($prefix."/".$fqbase.$ext);
$sample -> {"reads1FqGzMd5"}=Md5Sum($sample -> {"reads1FqGz"});
$sample -> {"reads2FqGz"}="";
$sample -> {"reads3FqGz"}=glob($prefix."/".$fqbase2.$ext);
$sample -> {"reads3FqGzMd5"}=Md5Sum($sample -> {"reads3FqGz"});
$sample -> {"reads1IndexFqGz"}=glob($prefix."/".$fqbaseI1.$ext);
$sample -> {"reads1IndexFqGzMd5"}=Md5Sum($sample -> {"reads1IndexFqGz"});
warn "## ".localtime(time())." ## INFO ## Single end + index read files detected. Stored as read1 = ".$$sample{'reads1FqGz'}." read2 = ".$$sample{'reads2FqGz'};
#warn Dumper($sample);
#se without index
}elsif(index($fqbase,"_R1_") && ( -e glob($prefix."/".$fqbase.$ext) && -e glob($prefix."/".$fqbase2.$ext) )){
$sample -> {"reads1FqGz"}=glob($prefix."/".$fqbase.$ext);
$sample -> {"reads1FqGzMd5"}=Md5Sum($sample -> {"reads1FqGz"});