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b9abc72
add todo
Jun 20, 2019
b9c8f4d
add todo
Jun 20, 2019
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5 changes: 3 additions & 2 deletions README.md
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Expand Up @@ -54,8 +54,9 @@ SamFixCigar.jar of jvarkit will convert M to X/= in cigar of sam file, if do thi
```

#### ToDo:<br>
&nbsp;&nbsp;&nbsp;&nbsp; support Hi-C data/reads mapping
&nbsp;&nbsp;&nbsp;&nbsp; support julia/python api to call clustersploter
&nbsp;&nbsp;&nbsp;&nbsp; support GC plot and defined subtrack for gff file,like read_mapping subtrack<br>
&nbsp;&nbsp;&nbsp;&nbsp; support Hi-C data/reads mapping<br>
&nbsp;&nbsp;&nbsp;&nbsp; support julia/python api to call clustersploter<br>
&nbsp;&nbsp;**2018-12-28**:<br>
&nbsp;&nbsp;&nbsp;&nbsp;1. add gtf fomrat, not only gff format<br>
&nbsp;&nbsp;&nbsp;&nbsp;2. add blat_spl and mummer4 fomrat, not only blast_m8 or paf format<br>
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14 changes: 8 additions & 6 deletions src/myth.pm
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Expand Up @@ -66,7 +66,7 @@ sub shift_tracks_x(){
}

sub show_segment_strand(){
my ($info, $id_line_x, $id_line_y, $id_line_height, $id_line_width, $reverse)=@_;
my ($info, $id_line_x, $id_line_y, $id_line_height, $id_line_width, $reverse,$font_family)=@_;
die "error: display_segment_strand=$info format error, should like display_segment_strand=5:5,3:3,color:black,fontsize:5\n" if($info!~ /^5:(.*),3:(.*),color:(.*),fontsize:([\d\.]+)$/);
my ($five,$three,$color,$fsize)=($1, $2, $3, $4);
return "" if(!$five || !$three);
Expand All @@ -81,8 +81,8 @@ sub show_segment_strand(){
$five=$three_tmp;
$three=$five_tmp;
}
my $left="<text class='myth' x=\"$five_x\" y=\"$five_y\" style=\"font-family:Times New Roman;font-size:${fsize}px;fill:$color;text-anchor:end;alignment-baseline:middle\" >$five</text>\n";
my $right="<text class='myth' x=\"$three_x\" y=\"$three_y\" style=\"font-family:Times New Roman;font-size:${fsize}px;fill:$color;text-anchor:start;alignment-baseline:middle\" >$three</text>\n";
my $left="<text class='myth' x=\"$five_x\" y=\"$five_y\" style=\"font-family:$font_family;font-size:${fsize}px;fill:$color;text-anchor:end;alignment-baseline:middle\" >$five</text>\n";
my $right="<text class='myth' x=\"$three_x\" y=\"$three_y\" style=\"font-family:$font_family;font-size:${fsize}px;fill:$color;text-anchor:start;alignment-baseline:middle\" >$three</text>\n";
return "$left $right";
}

Expand Down Expand Up @@ -610,6 +610,7 @@ sub draw_genes(){
my $feature_shift_x=&get_para("feature_shift_x", $feature_id, $conf);
my $label_text_alignment_baseline=&get_para("label_text_alignment_baseline", $feature_id, $conf);
my $feature_popup_title=&get_para("feature_popup_title", $feature_id, $conf);
my $font_family = $conf->{font_family};
if($feature_popup_title){
my @kvs=split(/;/, $feature_popup_title);
$feature_popup_title="\n";
Expand Down Expand Up @@ -862,7 +863,7 @@ sub draw_genes(){
}

## draw label of feature
$orders->{$order_f_label}.= "<text class='myth' x=\"$label_x\" y=\"$label_y\" style=\"font-family:Times New Roman;font-size:${index_label_size}px;fill:$index_label_col;text-anchor:$label_text_anchor;$label_text_alignment_baseline$feature_label_autowidth\" transform=\"rotate($index_label_angle $label_x $label_y)\" >$index_label_content</text>\n" if($display_feature_label!~ /no/i && $display_feature_label!~ /no,no/i ); # label of feature
$orders->{$order_f_label}.= "<text class='myth' x=\"$label_x\" y=\"$label_y\" style=\"font-family:$font_family;font-size:${index_label_size}px;fill:$index_label_col;text-anchor:$label_text_anchor;$label_text_alignment_baseline$feature_label_autowidth\" transform=\"rotate($index_label_angle $label_x $label_y)\" >$index_label_content</text>\n" if($display_feature_label!~ /no/i && $display_feature_label!~ /no,no/i ); # label of feature
}
# check this feature if is in crossing_link
#print "ssfeature_id is $feature_id\n";
Expand Down Expand Up @@ -974,7 +975,7 @@ sub draw_genes(){

## draw label of feature
die "die:label_y is $label_y, id is $feature_id\n" if(!$label_y);
$orders->{$order_f_label}.= "<text class='myth' x=\"$label_x\" y=\"$label_y\" style=\"font-family:Times New Roman;font-size:${index_label_size}px;fill:$index_label_col;text-anchor:$label_text_anchor;$label_text_alignment_baseline$feature_label_autowidth\" transform=\"rotate($index_label_angle $label_x $label_y)\" >$index_label_content</text>\n" if($display_feature_label!~ /no/i && $display_feature_label!~ /no,no/i); # label of feature
$orders->{$order_f_label}.= "<text class='myth' x=\"$label_x\" y=\"$label_y\" style=\"font-family:$font_family;font-size:${index_label_size}px;fill:$index_label_col;text-anchor:$label_text_anchor;$label_text_alignment_baseline$feature_label_autowidth\" transform=\"rotate($index_label_angle $label_x $label_y)\" >$index_label_content</text>\n" if($display_feature_label!~ /no/i && $display_feature_label!~ /no,no/i); # label of feature
}
# check this feature if is in crossing_link
#print "feature_id is $feature_id\n";
Expand Down Expand Up @@ -1077,7 +1078,7 @@ sub draw_genes(){


## draw label of feature
$orders->{$order_f_label}.= "<text class='myth' x=\"$label_x\" y=\"$label_y\" style=\"font-family:Times New Roman;font-size:${index_label_size}px;fill:$index_label_col;text-anchor:$label_text_anchor;$label_text_alignment_baseline$feature_label_autowidth\" transform=\"rotate($index_label_angle $label_x $label_y)\" >$index_label_content</text>\n" if($display_feature_label!~ /no/i && $display_feature_label!~ /no,no/i); # label of feature
$orders->{$order_f_label}.= "<text class='myth' x=\"$label_x\" y=\"$label_y\" style=\"font-family:$font_family;font-size:${index_label_size}px;fill:$index_label_col;text-anchor:$label_text_anchor;$label_text_alignment_baseline$feature_label_autowidth\" transform=\"rotate($index_label_angle $label_x $label_y)\" >$index_label_content</text>\n" if($display_feature_label!~ /no/i && $display_feature_label!~ /no,no/i); # label of feature
}
# check this feature if is in crossing_link
if(exists $conf->{crossing_link2}->{features}->{$feature_id}){
Expand Down Expand Up @@ -1161,6 +1162,7 @@ sub read_conf(){

sub default_setting(){
my ($skip_not_exists, %conf) = @_;
$conf{font_family} ||="Times New Roman";
$conf{svg_width_height} ||= '600,1500';
#$conf{anchor_positon_ratio} ||= 1;
$conf{feature_keywords} ||=",";
Expand Down
11 changes: 5 additions & 6 deletions src/plot.genome.featureCluster.pl
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Expand Up @@ -17,11 +17,10 @@

die "
perl $0 [options]:
* --list <str> two formats: [sample gff genome seq_id1 seq_draw_start1 seq_draw_end1 genome seq_id2 seq_draw_start2 seq_draw_end2 ...]
or [sample gff genome]no seq_id mean full length of whole gff
* --list <str> [track_name gene.gff genome.fa seq_id1 seq_draw_start1 seq_draw_end1 seq_id2 seq_draw_start2 seq_draw_end2 ...]
* --prefix <str>
* --outdir <str>
* --conf <str>
* --conf <str>

writed by myth
" unless($list && $prefix && $outdir && $conf);
Expand Down Expand Up @@ -233,7 +232,7 @@
#reversed_block{$sample}{$block_index}
my @block_region=&get_real_feature_region($reverse_block_flag, $start_once, $end_once, $start_once, $end_once, "+", $gff{$sample}{scf}{$scf[0]}, "block"); # "$start-$end", $start, $end, $strand);
$orders{$track_order}.="<g class='myth'><title>$scf[0]:$block_region[0]</title>\n<rect x=\"$id_line_x\" y=\"$id_line_y\" width=\"$id_line_width\" height=\"$id_line_height\" style=\"$conf{track_style}\" /></g>\n";
$orders{$track_order}.=&show_segment_strand($conf{display_segment_strand}, $id_line_x, $id_line_y, $id_line_height, $id_line_width, $reverse_block_flag);
$orders{$track_order}.=&show_segment_strand($conf{display_segment_strand}, $id_line_x, $id_line_y, $id_line_height, $id_line_width, $reverse_block_flag, $conf{font_family});

if($display_segment_name_flag=~ /yes/i){
my $segment_baseline;
Expand Down Expand Up @@ -955,7 +954,7 @@ ()
$tick_label=&format_scale($tick_label);
$tick_label.="bp" if($tick == 0);
$orders{$conf{scale_order}}.="<line x1=\"$tick_x\" y1=\"$tick_y1\" x2=\"$tick_x\" y2=\"$tick_y2\" style=\"stroke:$conf{scale_color};stroke-width:$conf{scale_width};opacity:$conf{scale_tick_opacity}\"/>\n"; # ticks
$orders{$conf{scale_order}}.= "<text class='myth' x=\"$tick_x\" y=\"$tick_label_y\" style=\"font-size:${font_size}px;fill:$conf{scale_color};text-anchor:middle;font-family:Times New Roman;\">$tick_label</text>\n"; # label of feature
$orders{$conf{scale_order}}.= "<text class='myth' x=\"$tick_x\" y=\"$tick_label_y\" style=\"font-size:${font_size}px;fill:$conf{scale_color};text-anchor:middle;font-family:$conf{font_family};\">$tick_label</text>\n"; # label of feature

}
print "cluster_width_ratio $cluster_width_ratio*$svg_width % $unit_scale\n";
Expand All @@ -965,7 +964,7 @@ ()
my $last_tick_label=&format_scale($max_length+$scale_start-1);
$last_tick_label.="bp";

$orders{$conf{scale_order}}.= "<text class='myth' x=\"$x_end_scale\" y=\"$tick_label_y\" style=\"font-size:${font_size}px;fill:$conf{scale_color};text-anchor:middle;font-family:Times New Roman\">$last_tick_label</text>\n"; # label of feature
$orders{$conf{scale_order}}.= "<text class='myth' x=\"$x_end_scale\" y=\"$tick_label_y\" style=\"font-size:${font_size}px;fill:$conf{scale_color};text-anchor:middle;font-family:$conf{font_family}\">$last_tick_label</text>\n"; # label of feature

}

Expand Down