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Add the creation of the file MutationSpectraCount-Genomic.txt #15

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Add the creation of the file MutationSpectraCount-Genomic.txt #15

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17 changes: 12 additions & 5 deletions mutspecStat.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
#-----------------------------------#
# Author: Maude #
# Script: mutspecStat.pl #
# Last update: 09/02/17 #
# Last update: 12/06/17 #
#-----------------------------------#

use strict;
Expand Down Expand Up @@ -574,8 +574,10 @@ sub WriteStatistics
my $heatmapCountggplot2 = "$folderFigure/Trinucleotide_Sequence_Context/$k_file/$k_file-HeatmapCount-Genomic.txt";
my $heatmapPercentggplot2 = "$folderFigure/Trinucleotide_Sequence_Context/$k_file/$k_file-HeatmapPercent-Genomic.txt";
my $triNtBarChartggplot2 = "$folderFigure/Trinucleotide_Sequence_Context/$k_file/$k_file-MutationSpectraPercent-Genomic.txt";
# Count of mutations per sequence context
my $triNtBarChartggplot2_count = "$folderFigure/Trinucleotide_Sequence_Context/$k_file/$k_file-MutationSpectraCount-Genomic.txt";

writeTriNtGenomic($ws, $refH_file, $k_file, $colStart_matrixSeqContext, $heatmapCountggplot2, $heatmapPercentggplot2, $triNtBarChartggplot2, \$c_ca6_g, \$c_cg6_g, \$c_ct6_g, \$c_ta6_g, \$c_tc6_g, \$c_tg6_g);
writeTriNtGenomic($ws, $refH_file, $k_file, $colStart_matrixSeqContext, $heatmapCountggplot2, $heatmapPercentggplot2, $triNtBarChartggplot2, $$triNtBarChartggplot2_count, \$c_ca6_g, \$c_cg6_g, \$c_ct6_g, \$c_ta6_g, \$c_tc6_g, \$c_tg6_g);

# For the input matrix for NMF
if($k_file ne "Pool_Data") { push(@{$h_inputNMF{'Sample'}}, $k_file); }
Expand Down Expand Up @@ -2049,7 +2051,7 @@ sub writeDistrByChr
# Trinucleotide sequence context on genomic strand (Panel 1)
sub writeTriNtGenomic
{
my ($ws, $refH_file, $sample, $col, $heatmapCountggplot2, $heatmapPercentggplot2, $triNtBarChartggplot2, $ref_c_ca6_g, $ref_c_cg6_g, $ref_c_ct6_g, $ref_c_ta6_g, $ref_c_tc6_g, $ref_c_tg6_g) = @_;
my ($ws, $refH_file, $sample, $col, $heatmapCountggplot2, $heatmapPercentggplot2, $triNtBarChartggplot2, $$triNtBarChartggplot2_count, $ref_c_ca6_g, $ref_c_cg6_g, $ref_c_ct6_g, $ref_c_ta6_g, $ref_c_tc6_g, $ref_c_tg6_g) = @_;

# Initialise the row of the panel 1
my $row_SeqContext6 = 4;
Expand All @@ -2066,9 +2068,12 @@ sub writeTriNtGenomic
open(HEATMAPPGENOMIC, ">", $heatmapPercentggplot2) or die "$!: $heatmapPercentggplot2\n";
print HEATMAPPGENOMIC "\tC>A\tC>G\tC>T\tT>A\tT>C\tT>G\n";

## Bar plot NMF like
## Bar plot NMF like (percentages)
open(BARPLOTNMFLIKE, ">", $triNtBarChartggplot2) or die "$!: $triNtBarChartggplot2\n";
print BARPLOTNMFLIKE "alteration\tcontext\tvalue\n";
## Bar plot NMF like (counts)
open(COUNTSPECTRA, ">", $triNtBarChartggplot2_count) or die "$!: $triNtBarChartggplot2_count\n";
print COUNTSPECTRA "alteration\tcontext\tvalue\n";


foreach my $k_context (sort keys %{$refH_file->{$sample}{'SeqContextG'}})
Expand Down Expand Up @@ -2099,6 +2104,8 @@ sub writeTriNtGenomic

# For representing the sequence context with a bar plot (NMF like style)
print BARPLOTNMFLIKE $k_mutation,"\t", $k_context,"\t", $percent,"\n";
# Count of mutations per sequence context
print COUNTSPECTRA $k_mutation,"\t",$k_context,"\t",$refH_file->{$sample}{'SeqContextG'}{$k_context}{$k_mutation},"\n";

# Write the count for the heatmap
print HEATMAPCGENOMIC $refH_file->{$sample}{'SeqContextG'}{$k_context}{$k_mutation}."\t";
Expand Down Expand Up @@ -2147,7 +2154,7 @@ sub writeTriNtGenomic
print HEATMAPPGENOMIC "\n";
}
close HEATMAPCGENOMIC; close HEATMAPPGENOMIC;
close BARPLOTNMFLIKE;
close BARPLOTNMFLIKE; close COUNTSPECTRA;


# Write the total number of SBS per mutation type: COUNT
Expand Down