Mercurial > repos > dereeper > sniploid2
diff DrawMapOfOccurences.pl @ 0:e94de0ea3351 draft default tip
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| author | dereeper |
|---|---|
| date | Wed, 11 Sep 2013 09:08:15 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DrawMapOfOccurences.pl Wed Sep 11 09:08:15 2013 -0400 @@ -0,0 +1,656 @@ +#!/usr/bin/perl + +use strict; +use Switch; +use Getopt::Long; +use lib "."; + +my $usage = qq~Usage:$0 <args> +where <args> are: + -c, --count <SNP count SNiPloid output> + -a, --annotation <annotation file in GFF3> + -o, --output_png <output PNG file> + -s, --scale <scale. Default:100000> + -t, --type_analysis <type of analysis: polyploid_diploid or polyploid_polyploid. Default:polyploid_diploid> + -m, --max_nb_chrom <maximum number of chromomsome to display. Default:20> + -n, --nb_min_snp <minimal number of SNP to calculate ratio. Default:10> + -d, --display_cat <display ratio for each category instead of intra-polyploid and inter-diploid (yes/no). Default:no> +~; +$usage .= "\n"; + +my ($snp_count,$annotation,$output_png,$global_scale,$max_nb_chrom,$type_analysis); + +my $global_scale = 10000; +my $max_nb_chrom = 20; +my $nb_min_snp = 10; +my $display_cat = "no"; + + +GetOptions( + "count=s" => \$snp_count, + "annotation=s" => \$annotation, + "output_png=s" => \$output_png, + "scale=s" => \$global_scale, + "max_nb_chrom=s" => \$max_nb_chrom, + "type_analysis=s" => \$type_analysis, + "nb_min_snp=s" => \$nb_min_snp, + "display_cat=s" => \$display_cat +); + + +die $usage + if ( !$snp_count || !$annotation || !$output_png || !$type_analysis); + +my %proportions_categories; +my %ratios; +my %ratios_poly_diploid; +my %nb_snps; +open(my $COUNT,$snp_count); +<$COUNT>; +while(<$COUNT>) +{ + my $line =$_; + chomp($line); + my @infos = split(/\t/,$line); + + + if ($type_analysis eq "polyploid_diploid") + { + my $gene = $infos[0]; + my $nb_snp = $infos[2]; + my $nb_1 = $infos[3]; + my $nb_2 = $infos[4]; + my $nb_3or4 = $infos[5]; + my $nb_3 = $infos[6]; + my $nb_4 = $infos[7]; + my $nb_5 = $infos[8]; + my $nb_other = $infos[9]; + my $nb_heterozygot_diploid = $infos[10]; + my $nb_snp_diploid = $infos[11]; + my $nb_snp_polyploid = $infos[12]; + + $nb_snps{$gene} = $nb_snp; + my $sum = $nb_1 + $nb_2 + $nb_3or4 + $nb_5 + $nb_3 + $nb_4 + $nb_other + $nb_heterozygot_diploid; + + if ($nb_snp >= $nb_min_snp) + { + if ($nb_1) + { + $proportions_categories{$gene}{"1"} = $nb_1/$nb_snp; + } + if ($nb_2) + { + $proportions_categories{$gene}{"2"} = $nb_2/$nb_snp; + } + if ($nb_5) + { + $proportions_categories{$gene}{"5"} = $nb_5/$nb_snp; + } + if ($nb_3or4) + { + $proportions_categories{$gene}{"3or4"} = $nb_3or4/$nb_snp; + } + } + + my $ratio_g1 = $infos[13]; + my $ratio_g2 = $infos[14]; + + if ($ratio_g1) + { + $ratios{$gene} = $ratio_g1; + } + } + + if ($type_analysis eq "polyploid_polyploid") + { + my $gene = $infos[0]; + my $nb_snp = $infos[2]; + my $nb_equal = $infos[3] + $infos[4]; + my $nb_diff = $infos[7]; + $nb_snps{$gene} = $nb_snp; + if ($nb_snp >= $nb_min_snp) + { + if ($nb_equal) + { + $proportions_categories{$gene}{"equal"} = $nb_equal/$nb_snp; + } + if ($nb_diff) + { + $proportions_categories{$gene}{"difference"} = $nb_diff/$nb_snp; + } + } + } + +} +close($COUNT); + + + + +my $max_pos = 0; +my %chrom_sizes; +my $chrom_particule; +my %genes; +my %gene_positions; + +open(my $ANNOT,$annotation); +while(<$ANNOT>) +{ + my $line =$_; + chomp($line); + if (!/^#/ && /gene/) + { + my @infos = split(/\t/,$line); + my $chrom = $infos[0]; + if ($chrom =~/^(\w+_)(\d+)$/) + { + $chrom_particule = $1; + $chrom = $2; + } + + my $attributes = $infos[8]; + my $gene_name; + if ($attributes =~/Name=([^;]+);/) + { + $gene_name = $1; + } + if (!$gene_name && $attributes =~/ID=([^;]+);/) + { + $gene_name = $1; + } + if ($gene_name =~/(.*)_G1/) + { + $gene_name = $1; + } + else + { + next; + } + if (not defined $nb_snps{$gene_name}) + { + next; + } + + my $start = $infos[3]; + my $end = $infos[4]; + my $pos = sprintf("%.0f", ($start + (($end - $start) / 2))); + + $end = $end / $global_scale; + if ($chrom_sizes{$chrom}) + { + if ($end > $chrom_sizes{$chrom}) + { + $chrom_sizes{$chrom} = $end; + if ($end > $max_pos) + { + $max_pos = $end; + } + } + } + else + { + $chrom_sizes{$chrom} = $end; + if ($end > $max_pos) + { + $max_pos = $end; + } + } + $genes{$gene_name} = "$chrom:$pos"; + $gene_positions{$chrom}{$pos}= $gene_name; + } +} +close($ANNOT); + + + +use GD; +use GD::Simple; +use GD::Image; + + + + +#################### +# drawing +#################### + +my $scale = 800 / $max_pos; + +my $margin_left = 80; +my $margin_right = 50; +my $margin_top = 50; +my $margin_legend = 100; +my $margin_bottom = 10; +my $margin_between_chromosomes = 25; +my $margin_between_section = 50; +my $chrom_width = 10; +my $gene_width = 1; + +my $nb_group = 1; + +my $width_of_picture = scalar keys(%gene_positions); +if (scalar keys(%gene_positions) > $max_nb_chrom) +{ + $width_of_picture = $max_nb_chrom; +} + +my $diagram_img = GD::Simple->new(($margin_left + $margin_right + ($max_pos*$scale)), + ($margin_top + ((($chrom_width * $nb_group) + ($margin_between_chromosomes * ($nb_group-1))) * $width_of_picture) + ($margin_between_section * $width_of_picture) + $margin_bottom + $margin_legend) + ); + +my $yellow = $diagram_img->colorAllocate(247,254,46); +my $orange_light = $diagram_img->colorAllocate(250,204,46); +my $red_light = $diagram_img->colorAllocate(254,100,46); +my $red = $diagram_img->colorAllocate(254,46,46); +my $orange = $diagram_img->colorAllocate(254,154,46); + + +# draw chromosomes +my $num_chrom = 0; +my @sorted_chrom = sort {$a <=> $b} keys(%gene_positions); + +my $nombre_genes = 0; +my $y_end; +foreach my $chrom(@sorted_chrom) +{ + if (!$chrom) + { + next; + } + + if ($num_chrom > ($max_nb_chrom - 1)) + { + last; + } + my $ref_hash = $gene_positions{$chrom}; + my %hash = %$ref_hash; + + my $section_size = $chrom_width + (($margin_between_chromosomes + $chrom_width) * ($nb_group - 1)); + + # draw chromosome (X number of groups) + + $diagram_img->fgcolor('black'); + $diagram_img->bgcolor('white'); + $diagram_img->setThickness(1); + my $chrom_chain = $chrom_particule . $chrom; + + $diagram_img->rectangle( $margin_left, + $margin_top + (($section_size + $margin_between_section) * $num_chrom), + $margin_left + ($chrom_sizes{$chrom}*$scale), + $margin_top + $chrom_width + (($section_size + $margin_between_section) * $num_chrom) + ); + + $diagram_img->fgcolor('black'); + $diagram_img->moveTo(5,$margin_top + $chrom_width + (($section_size + $margin_between_section) * $num_chrom) - 1); + $y_end = $margin_top + $chrom_width + (($section_size + $margin_between_section) * ($num_chrom+1)) - 1; + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string($chrom_particule . $chrom); + + + my $previous_x_5; + my $previous_x_1; + my $previous_x_2; + my $previous_x_3or4; + my $previous_y_5; + my $previous_y_1; + my $previous_y_2; + my $previous_y_3or4; + + my $previous_x_equal; + my $previous_x_diff; + my $previous_y_equal; + my $previous_y_diff; + + my $previous_x_snp_diplo; + my $previous_x_snp_poly; + my $previous_y_snp_diplo; + my $previous_y_snp_poly; + + my $previous_x_ratio_diplo_poly; + my $previous_y_ratio_diplo_poly; + + # draw genes + foreach my $pos(sort{$a <=> $b}keys(%hash)) + { + my $gene = $gene_positions{$chrom}{$pos}; + if (not defined $nb_snps{$gene} or $nb_snps{$gene} < $nb_min_snp) + { + next; + } + + if ($type_analysis eq "polyploid_diploid") + { + ##################################################### + # draw ratio (subgenomic contribution) + ##################################################### + my $color = "gray"; + if ($ratios{$gene}) + { + my $ratio_g1 = $ratios{$gene}; + if ($ratio_g1 <= 30) + { + $color = $red; + } + elsif ($ratio_g1 > 30 && $ratio_g1 <= 40) + { + $color = $red_light; + } + elsif ($ratio_g1 > 40 && $ratio_g1 <= 60) + { + $color = $orange; + } + elsif ($ratio_g1 > 60 && $ratio_g1 <= 70) + { + $color = $orange_light; + } + elsif ($ratio_g1 > 70) + { + $color = $yellow; + } + } + + $pos = $pos / $global_scale; + + $diagram_img->fgcolor($color); + $diagram_img->bgcolor($color); + $diagram_img->rectangle( $margin_left + ($pos*$scale) - ($gene_width / 2), + $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1, + $margin_left + ($pos*$scale) + ($gene_width / 2), + $margin_top + $chrom_width + (($section_size + $margin_between_section) * $num_chrom) - 1 + ); + + + + ##################################################### + # draw SNP categories + ##################################################### + + my $proportion_5 = $proportions_categories{$gene}{"5"}; + my $proportion_1 = $proportions_categories{$gene}{"1"}; + my $proportion_2 = $proportions_categories{$gene}{"2"}; + my $proportion_3or4 = $proportions_categories{$gene}{"3or4"}; + my $ratio_poly_diplo = $ratios_poly_diploid{$gene}; + + my $draw = 0; + if (defined $previous_x_5) + { + $draw = 1; + } + + + ####################### + # SNP category 5 + ####################### + if ($draw) + { + $diagram_img->moveTo($previous_x_5,$previous_y_5); + } + $previous_x_5 = $margin_left + ($pos*$scale) - 1; + $diagram_img->setThickness(2); + $diagram_img->fgcolor("red"); + $diagram_img->bgcolor("red"); + $previous_y_5 = $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1 - ($proportion_5 * 20) - 7; + if ($draw) + { + $diagram_img->lineTo($previous_x_5,$previous_y_5); + } + + if ($display_cat eq "yes") + { + ####################### + # SNP category 1 + ####################### + if ($draw) + { + $diagram_img->moveTo($previous_x_1,$previous_y_1); + } + $previous_x_1 = $margin_left + ($pos*$scale) - 1; + $diagram_img->fgcolor("orange"); + $diagram_img->bgcolor("orange"); + $previous_y_1 = $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1 - ($proportion_1 * 20) - 7; + if ($draw) + { + $diagram_img->lineTo($previous_x_1,$previous_y_1); + } + + + ####################### + # SNP category 2 + ####################### + if ($draw) + { + $diagram_img->moveTo($previous_x_2,$previous_y_2); + } + $previous_x_2 = $margin_left + ($pos*$scale) - 1; + $diagram_img->fgcolor("purple"); + $diagram_img->bgcolor("purple"); + $previous_y_2 = $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1 - ($proportion_2 * 20) - 7; + if ($draw) + { + $diagram_img->lineTo($previous_x_2,$previous_y_2); + } + + + ####################### + # SNP category 3 or 4 + ####################### + if ($draw) + { + $diagram_img->moveTo($previous_x_3or4,$previous_y_3or4); + } + $previous_x_3or4 = $margin_left + ($pos*$scale) - 1; + $diagram_img->fgcolor("green"); + $diagram_img->bgcolor("green"); + $previous_y_3or4 = $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1 - ($proportion_3or4 * 20) - 7; + if ($draw) + { + $diagram_img->lineTo($previous_x_3or4,$previous_y_3or4); + } + } + + } + + if ($type_analysis eq "polyploid_polyploid") + { + my $color = "gray"; + $pos = $pos / $global_scale; + + $diagram_img->fgcolor($color); + $diagram_img->bgcolor($color); + $diagram_img->rectangle( $margin_left + ($pos*$scale) - ($gene_width / 2), + $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1, + $margin_left + ($pos*$scale) + ($gene_width / 2), + $margin_top + $chrom_width + (($section_size + $margin_between_section) * $num_chrom) - 1 + ); + + + + my $proportion_equal = $proportions_categories{$gene}{"equal"}; + my $proportion_diff = $proportions_categories{$gene}{"difference"}; + + my $draw = 0; + if (defined $previous_x_equal) + { + $draw = 1; + } + + + ################################################## + # SNP category : equality between 2 polyploids + ################################################## + if ($draw) + { + $diagram_img->moveTo($previous_x_equal,$previous_y_equal); + } + $previous_x_equal = $margin_left + ($pos*$scale) - 1; + $diagram_img->setThickness(2); + $diagram_img->fgcolor("red"); + $diagram_img->bgcolor("red"); + $previous_y_equal = $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1 - ($proportion_equal * 20) - 7; + if ($draw) + { + $diagram_img->lineTo($previous_x_equal,$previous_y_equal); + } + } + + $nombre_genes++; + } + + $num_chrom++; +} + +if ($type_analysis eq "polyploid_polyploid") +{ + $diagram_img->moveTo(5,$y_end); + $diagram_img->setThickness(2); + $diagram_img->fgcolor("red"); + $diagram_img->bgcolor("red"); + $diagram_img->lineTo(25,$y_end); + $diagram_img->fgcolor("black"); + $diagram_img->moveTo(30,$y_end + 5); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("% SNP where P1 = P2"); +} +elsif ($type_analysis eq "polyploid_diploid") +{ + if ($display_cat eq "yes") + { + $diagram_img->moveTo(5,$y_end); + $diagram_img->setThickness(2); + $diagram_img->fgcolor("orange"); + $diagram_img->bgcolor("orange"); + $diagram_img->lineTo(25,$y_end); + $diagram_img->fgcolor("black"); + $diagram_img->moveTo(30,$y_end + 5); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("% SNP type 1"); + + $diagram_img->moveTo(5,$y_end + 20); + $diagram_img->setThickness(2); + $diagram_img->fgcolor("purple"); + $diagram_img->bgcolor("purple"); + $diagram_img->lineTo(25,$y_end + 20); + $diagram_img->fgcolor("black"); + $diagram_img->moveTo(30,$y_end + 25); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("% SNP type 2"); + + $diagram_img->moveTo(5,$y_end + 40); + $diagram_img->setThickness(2); + $diagram_img->fgcolor("green"); + $diagram_img->bgcolor("green"); + $diagram_img->lineTo(25,$y_end + 40); + $diagram_img->fgcolor("black"); + $diagram_img->moveTo(30,$y_end + 45); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("% SNP type 3 or 4"); + + $diagram_img->moveTo(5,$y_end + 60); + $diagram_img->setThickness(2); + $diagram_img->fgcolor("red"); + $diagram_img->bgcolor("red"); + $diagram_img->lineTo(25,$y_end + 60); + $diagram_img->fgcolor("black"); + $diagram_img->moveTo(30,$y_end + 65); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("% SNP type 5"); + } + else + { + $diagram_img->moveTo(5,$y_end); + $diagram_img->setThickness(2); + $diagram_img->fgcolor("red"); + $diagram_img->bgcolor("red"); + $diagram_img->lineTo(25,$y_end); + $diagram_img->fgcolor("black"); + $diagram_img->moveTo(30,$y_end + 5); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("% SNP Class 5 per gene (SNP Intra-Diploids = SNP Intra-Polyploid)"); + } + + $diagram_img->moveTo(5,$y_end + 30); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("Estimate of subgenomic contribution to the transcriptome for each gene (%G2)"); + + + $diagram_img->moveTo(25,$y_end + 45); + $diagram_img->setThickness(10); + $diagram_img->fgcolor($red); + $diagram_img->bgcolor($red); + $diagram_img->lineTo(30,$y_end + 45); + $diagram_img->fgcolor("black"); + $diagram_img->moveTo(35,$y_end + 50); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("0-30%"); + + $diagram_img->moveTo(95,$y_end + 45); + $diagram_img->setThickness(10); + $diagram_img->fgcolor($red_light); + $diagram_img->bgcolor($red_light); + $diagram_img->lineTo(100,$y_end + 45); + $diagram_img->fgcolor("black"); + $diagram_img->moveTo(105,$y_end + 50); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("30-40%"); + + $diagram_img->moveTo(165,$y_end + 45); + $diagram_img->setThickness(10); + $diagram_img->fgcolor($orange); + $diagram_img->bgcolor($orange); + $diagram_img->lineTo(170,$y_end + 45); + $diagram_img->fgcolor("black"); + $diagram_img->moveTo(175,$y_end + 50); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("40-60%"); + + $diagram_img->moveTo(235,$y_end + 45); + $diagram_img->setThickness(10); + $diagram_img->fgcolor($orange_light); + $diagram_img->bgcolor($orange_light); + $diagram_img->lineTo(240,$y_end + 45); + $diagram_img->fgcolor("black"); + $diagram_img->moveTo(245,$y_end + 50); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("60-70%"); + + $diagram_img->moveTo(305,$y_end + 45); + $diagram_img->setThickness(10); + $diagram_img->fgcolor($yellow); + $diagram_img->bgcolor($yellow); + $diagram_img->lineTo(310,$y_end + 45); + $diagram_img->fgcolor("black"); + $diagram_img->moveTo(315,$y_end + 50); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("70-100%"); + + $diagram_img->moveTo(25,$y_end + 60); + $diagram_img->setThickness(10); + $diagram_img->fgcolor("gray"); + $diagram_img->bgcolor("gray"); + $diagram_img->lineTo(30,$y_end + 60); + $diagram_img->fgcolor("black"); + $diagram_img->moveTo(35,$y_end + 65); + $diagram_img->fontsize(12); + $diagram_img->font('Times'); + $diagram_img->string("No ratio information, no SNP class 5 in this gene"); + +} + + +open( DIAGRAM_PICT, ">$output_png" ); +binmode(DIAGRAM_PICT); +print DIAGRAM_PICT $diagram_img->png; +close DIAGRAM_PICT;