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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,148 @@ | ||
| #!/usr/bin/perl | ||
| use warnings; | ||
| use strict; | ||
| use Data::Dumper; | ||
| my %pairs; | ||
| ## for CORNELL RUNS | ||
| ## rename file is different that UCR core | ||
|
|
||
| my $final_dir = $ARGV[0]; | ||
| my $fq_dir = $ARGV[1]; | ||
| my $rename_file = $ARGV[2]; | ||
| ## do a test run or the real thing 0=real thing, 1=test run | ||
| my $test = defined $ARGV[3] ? $ARGV[3] : 0; | ||
| #my $test = 1; | ||
| if (!defined $fq_dir or !defined $final_dir or !defined $rename_file){ | ||
| die "perl rename_files.pl OUTPUT_DIR DIR_OF_FASTQ BARCODE_SAMPLE_FILE | ||
| example usage: | ||
| perl rename_files.pl /home_stajichlab/robb/Wessler-Rice/RIL/Illumina FC153_RIL_1_12 11122012.sample_adapter.list\n"; | ||
| } | ||
| ## head cornell.rename.file | ||
| ##2 6205_N_RILLib60-254_ACTTGA 8 ACTTGA 237 | ||
| ##2 6205_N_RILLib60-254_ATCACG 1 ATCACG 60 | ||
|
|
||
| ## diff from UCR core | ||
| my @files = <$fq_dir/*fastq>; | ||
|
|
||
| ## no need for barcodes hash if i convert in the excel sheet, maybe next time, let the script conver | ||
| my %barcodes; | ||
| my %rename; | ||
| while (my $line = <DATA>){ | ||
| chomp $line; | ||
| if ($line =~ /^\d/){ | ||
| my ($code,$adapter) = split /\s+/ , $line; | ||
| print "($code,$adapter)\n" if $test; | ||
| $barcodes{$code}=$adapter; | ||
| } | ||
| } | ||
|
|
||
| print "opening $rename_file\n" if $test; | ||
| open (IDFILE, $rename_file) or die "Can't open $rename_file\n"; | ||
| while (my $line = <IDFILE>){ | ||
| chomp $line; | ||
| my ($lane,$sample,$code,$adaptor,$RIL) = split /\s+/ , $line; | ||
| print "($lane,$sample,$code,$adaptor,$RIL)\n" if $test; | ||
| #my $adapter = $barcodes{$code}; | ||
| $rename{$sample}{RIL}=$RIL; | ||
| $rename{$sample}{LANE}=$lane | ||
| } | ||
|
|
||
| print "getting ready to rename\n" if $test; | ||
| foreach my $file (@files){ | ||
| #flowcell153_lane5_pair1_ACTGAT.fastq | ||
| chomp $file; | ||
| #my ($fc,$lane,$pair,$barcode) = $file =~ /.+flowcell(\d+)_lane(\d+)_pair(\d)_([ATGC]{6})\.fastq/; | ||
| #6205_N_RILLib60-254_ACTTGA | ||
| #1946_2368_6207_N_RILs95-270_TGACCA_R1.fastq | ||
| #1946_2368_6207_N_RILs95-270_CCGTCC_R2.fastq | ||
| #1945_2368_6206_N_RILLib8-247_28-247_GTGAAA_R1.fastq | ||
| #1943_2368_6204_N_RILLib83-230_TTAGGC_R1.fastq | ||
| my ($one,$two,$sample,$laneID,$lib,$barcode,$pair) = $file =~ /(\d+)_(\d+)_((\d+)_N_(.+)_([ATCG]{6}))_(R\d)\.fastq/; | ||
| print "($one,$two,$sample,$laneID,$lib,$barcode,$pair)\n" if $test; | ||
| if ($pair eq 'R1'){ | ||
| $pair = 1; | ||
| }else { | ||
| $pair = 2; | ||
| } | ||
| if (exists $rename{$sample}){ | ||
| my $strain = $rename{$sample}{RIL}; | ||
| my $lane = $rename{$sample}{LANE}; | ||
| my $mv_dir = "$final_dir/$strain"; | ||
| if (!-d $mv_dir){ | ||
| `mkdir $mv_dir` if !$test; | ||
| } | ||
| my $base = "RIL" . $strain . "_" . $barcode . "_FC082013"."L$lane" ; | ||
| my $newfile=$base."_p$pair.fq" ; | ||
| $pairs{$base}{$pair}="$mv_dir/$newfile"; | ||
| #print "$mv_dir/$newfile\n"; | ||
| if (!-e "$mv_dir/$newfile"){ | ||
| #if (1){ | ||
| `ln -s $file $newfile` if !$test; | ||
| #`rm -f $mv_dir/$newfile` if !$test; | ||
| `ln -s $file $mv_dir/$newfile` if !$test; | ||
| } | ||
| } | ||
| } | ||
| foreach my $strain (keys %pairs){ | ||
| my @toPrint; | ||
| push @toPrint , $strain; | ||
| my $p1 = exists $pairs{$strain}{1} ? $pairs{$strain}{1} : ''; | ||
| my $p2 = exists $pairs{$strain}{2} ? $pairs{$strain}{2} : ''; | ||
| if (defined $p1){ | ||
| push @toPrint , $p1; | ||
| } | ||
| if (defined $p2){ | ||
| push @toPrint , $p2; | ||
| } | ||
| print join (",",@toPrint) , "\n"; | ||
| } | ||
| ## IDs of Illumina barcodes | ||
| __DATA__ | ||
| 1 ATCACG | ||
| 2 CGATGT | ||
| 3 TTAGGC | ||
| 4 TGACCA | ||
| 5 ACAGTG | ||
| 6 GCCAAT | ||
| 7 CAGATC | ||
| 8 ACTTGA | ||
| 9 GATCAG | ||
| 10 TAGCTT | ||
| 11 GGCTAC | ||
| 12 CTTGTA | ||
| 13 AGTCAA | ||
| 14 AGTTCC | ||
| 15 ATGTCA | ||
| 16 CCGTCC | ||
| 17 GTAGAG | ||
| 18 GTCCGC | ||
| 19 GTGAAA | ||
| 20 GTGGCC | ||
| 21 GTTTCG | ||
| 22 CGTACG | ||
| 23 GAGTGG | ||
| 24 GGTAGC | ||
| 25 ACTGAT | ||
| 26 ATGAGC | ||
| 27 ATTCCT | ||
| 28 CAAAAG | ||
| 29 CAACTA | ||
| 30 CACCGG | ||
| 31 CACGAT | ||
| 32 CACTCA | ||
| 33 CAGGCG | ||
| 34 CATGGC | ||
| 35 CATTTT | ||
| 36 CCAACA | ||
| 37 CGGAAT | ||
| 38 CTAGCT | ||
| 39 CTATAC | ||
| 40 CTCAGA | ||
| 41 GACGAC | ||
| 42 TAATCG | ||
| 43 TACAGC | ||
| 44 TATAAT | ||
| 45 TCATTC | ||
| 46 TCCCGA | ||
| 47 TCGAAG | ||
| 48 TCGGCA |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,148 @@ | ||
| #!/usr/bin/perl | ||
| use warnings; | ||
| use strict; | ||
| use Data::Dumper; | ||
| my %pairs; | ||
| ## for CORNELL RUNS | ||
| ## rename file is different that UCR core | ||
|
|
||
| my $final_dir = $ARGV[0]; | ||
| my $fq_dir = $ARGV[1]; | ||
| my $rename_file = $ARGV[2]; | ||
| ## do a test run or the real thing 0=real thing, 1=test run | ||
| my $test = defined $ARGV[3] ? $ARGV[3] : 0; | ||
| #my $test = 1; | ||
| if (!defined $fq_dir or !defined $final_dir or !defined $rename_file){ | ||
| die "perl rename_files.pl OUTPUT_DIR DIR_OF_FASTQ BARCODE_SAMPLE_FILE | ||
| example usage: | ||
| perl rename_files.pl /home_stajichlab/robb/Wessler-Rice/RIL/Illumina FC153_RIL_1_12 11122012.sample_adapter.list\n"; | ||
| } | ||
| ## head cornell.rename.file | ||
| ##2 6205_N_RILLib60-254_ACTTGA 8 ACTTGA 237 | ||
| ##2 6205_N_RILLib60-254_ATCACG 1 ATCACG 60 | ||
|
|
||
| ## diff from UCR core | ||
| my @files = <$fq_dir/*fastq>; | ||
|
|
||
| ## no need for barcodes hash if i convert in the excel sheet, maybe next time, let the script conver | ||
| my %barcodes; | ||
| my %rename; | ||
| while (my $line = <DATA>){ | ||
| chomp $line; | ||
| if ($line =~ /^\d/){ | ||
| my ($code,$adapter) = split /\s+/ , $line; | ||
| print "($code,$adapter)\n" if $test; | ||
| $barcodes{$code}=$adapter; | ||
| } | ||
| } | ||
|
|
||
| print "opening $rename_file\n" if $test; | ||
| open (IDFILE, $rename_file) or die "Can't open $rename_file\n"; | ||
| while (my $line = <IDFILE>){ | ||
| chomp $line; | ||
| my ($lane,$sample,$code,$adaptor,$RIL) = split /\s+/ , $line; | ||
| print "($lane,$sample,$code,$adaptor,$RIL)\n" if $test; | ||
| #my $adapter = $barcodes{$code}; | ||
| $rename{$sample}{RIL}=$RIL; | ||
| $rename{$sample}{LANE}=$lane | ||
| } | ||
|
|
||
| print "getting ready to rename\n" if $test; | ||
| foreach my $file (@files){ | ||
| #flowcell153_lane5_pair1_ACTGAT.fastq | ||
| chomp $file; | ||
| #my ($fc,$lane,$pair,$barcode) = $file =~ /.+flowcell(\d+)_lane(\d+)_pair(\d)_([ATGC]{6})\.fastq/; | ||
| #6205_N_RILLib60-254_ACTTGA | ||
| #1946_2368_6207_N_RILs95-270_TGACCA_R1.fastq | ||
| #1946_2368_6207_N_RILs95-270_CCGTCC_R2.fastq | ||
| #1945_2368_6206_N_RILLib8-247_28-247_GTGAAA_R1.fastq | ||
| #1943_2368_6204_N_RILLib83-230_TTAGGC_R1.fastq | ||
| my ($one,$two,$sample,$laneID,$lib,$barcode,$pair) = $file =~ /(\d+)_(\d+)_((\d+)_N_(.+)_([ATCG]{6}))_(R\d)\.fastq/; | ||
| print "($one,$two,$sample,$laneID,$lib,$barcode,$pair)\n" if $test; | ||
| if ($pair eq 'R1'){ | ||
| $pair = 1; | ||
| }else { | ||
| $pair = 2; | ||
| } | ||
| if (exists $rename{$sample}){ | ||
| my $strain = $rename{$sample}{RIL}; | ||
| my $lane = $rename{$sample}{LANE}; | ||
| my $mv_dir = "$final_dir/$strain"; | ||
| if (!-d $mv_dir){ | ||
| `mkdir $mv_dir` if !$test; | ||
| } | ||
| my $base = "RIL" . $strain . "_" . $barcode . "_FC082013"."L$lane" ; | ||
| my $newfile=$base."_p$pair.fq" ; | ||
| $pairs{$base}{$pair}="$mv_dir/$newfile"; | ||
| #print "$mv_dir/$newfile\n"; | ||
| if (!-e "$mv_dir/$newfile"){ | ||
| #if (1){ | ||
| `ln -s $file $newfile` if !$test; | ||
| #`rm -f $mv_dir/$newfile` if !$test; | ||
| `ln -s $file $mv_dir/$newfile` if !$test; | ||
| } | ||
| } | ||
| } | ||
| foreach my $strain (keys %pairs){ | ||
| my @toPrint; | ||
| push @toPrint , $strain; | ||
| my $p1 = exists $pairs{$strain}{1} ? $pairs{$strain}{1} : ''; | ||
| my $p2 = exists $pairs{$strain}{2} ? $pairs{$strain}{2} : ''; | ||
| if (defined $p1){ | ||
| push @toPrint , $p1; | ||
| } | ||
| if (defined $p2){ | ||
| push @toPrint , $p2; | ||
| } | ||
| print join (",",@toPrint) , "\n"; | ||
| } | ||
| ## IDs of Illumina barcodes | ||
| __DATA__ | ||
| 1 ATCACG | ||
| 2 CGATGT | ||
| 3 TTAGGC | ||
| 4 TGACCA | ||
| 5 ACAGTG | ||
| 6 GCCAAT | ||
| 7 CAGATC | ||
| 8 ACTTGA | ||
| 9 GATCAG | ||
| 10 TAGCTT | ||
| 11 GGCTAC | ||
| 12 CTTGTA | ||
| 13 AGTCAA | ||
| 14 AGTTCC | ||
| 15 ATGTCA | ||
| 16 CCGTCC | ||
| 17 GTAGAG | ||
| 18 GTCCGC | ||
| 19 GTGAAA | ||
| 20 GTGGCC | ||
| 21 GTTTCG | ||
| 22 CGTACG | ||
| 23 GAGTGG | ||
| 24 GGTAGC | ||
| 25 ACTGAT | ||
| 26 ATGAGC | ||
| 27 ATTCCT | ||
| 28 CAAAAG | ||
| 29 CAACTA | ||
| 30 CACCGG | ||
| 31 CACGAT | ||
| 32 CACTCA | ||
| 33 CAGGCG | ||
| 34 CATGGC | ||
| 35 CATTTT | ||
| 36 CCAACA | ||
| 37 CGGAAT | ||
| 38 CTAGCT | ||
| 39 CTATAC | ||
| 40 CTCAGA | ||
| 41 GACGAC | ||
| 42 TAATCG | ||
| 43 TACAGC | ||
| 44 TATAAT | ||
| 45 TCATTC | ||
| 46 TCCCGA | ||
| 47 TCGAAG | ||
| 48 TCGGCA |