Trying to show the gaps of each seq on bio::Graphics after converting clustalw

Question

I want a box representing each sequence, positioned as they are in the alignment and with gaps shown as breaks in the each box.

I've been having trouble for a while with this and have been trying to get this on my own, but I can't. I'm trying to display the gaps using Bio::Graphics after retrieving my sequences from an alignment file.

I removed the exit portion. I was trying to format the code for this website and accidentally put the exit there. The input fill is a custalw file which is an alignment file with sequences on it. The sequences have "-" that represent gaps.

The command is ./aln.pl test-bioaln.aln > ll.png
My expected output would be a .png file with sequences that are aligned and show gaps as a different color.

The input file is:

CLUSTAL W (1.81) multiple sequence alignment
JD1:1:102:1601:ORFJ00027      ------------------------------atgtataaacaacaatattttatttct--c
94a:1:107:117:orf00001        ------------------------------atgtataaacaacaatattttatttct-ac
118a:1:106:158122218:orf00020 ------------------------------atgtataaacaacaatattttatttct-gc
B31:1:100:4091:ORFB0018       ------------------------------atgtataaacaacaatattttatttctggc
72a:1:105:32:orf00022         ------------------------------atgtataaacaacaatattttatttctggc
64b:1:110:473:orf00001        ------------------------------atgtataaacaacaatattttatttctggc
29805:1:108:171:orf00001      ------------------------------atgtataaacaacaatattttatttctggc
BOL26:1:111:60:orf00001       ------------------------------atgtataaacaacaatattttatttctggc
CA-11.2A:1:109:33:orf00001    ------------------------------atgtataaacaacaatattttatttctggc
WI91-23:1:112:493:orf00001    ------------------------------atgtataaacaacaatattttatttctggc
297:1:103:411:ORFB00012       ttggatagattttatacaaagaaggtaataatgtataaacaacaatattttatttctggc
N40:1:101:1716:ORFK00021      ------------------------------atgtataaacaacaatattttatttctggc
ZS7:1:113:22:orf00001         ------------------------------atgtataaacaacaatattttatttctggc
                                                            ******************************
JD1:1:102:1601:ORFJ00027      aaggtgcaaggtgttggttttagatttttcacagagcaaatagcaaataatatgaaacta
94a:1:107:117:orf00001        aaggtacaaggtgttggttttagattttttacagagcaaatagcaaataatatgaaacta
118a:1:106:158122218:orf00020 aaggtacaaggtgttggttttagattttttacagagcaaatagcaaataatatgaaacta
B31:1:100:4091:ORFB0018       aaggtgcaaggtgttggttttagatttttcacagagcaaatagcaaataatatgaaacta
72a:1:105:32:orf00022         aaggtacaaggtgttggttttagattttttacagagcaaatagcaaataatatgaaacta
64b:1:110:473:orf00001        aaggtgcaaggtgttggttttagatttttcacagagcaaatagcaaataatatgaaacta
29805:1:108:171:orf00001      aaggtgcaaggtgttggttttagatttttcacagagcaaatagcaaataatatgaaacta
BOL26:1:111:60:orf00001       aaggtacaaggtgttggttttagattttttacagagcaaatagcaaataatatgaaacta
CA-11.2A:1:109:33:orf00001    aaggtacaaggtgttggttttagattttttacagagcaaatagcaaataatatgaaacta
WI91-23:1:112:493:orf00001    aaggtgcaaggtgttggttttagatttttcacagagcaaatagcaaataatatgaaacta
297:1:103:411:ORFB00012       aaggtacaaggtgttggttttagattttttacagagcaaatagcaaataatatgaaacta
N40:1:101:1716:ORFK00021      aaggtgcaaggtgttggttttagatttttcacagagcaaatagcaaataatatgaaacta
ZS7:1:113:22:orf00001         aaggtacaaggtgttggttttagattttttacagagcaaatagcaaataatatgaaacta
                              ***** *********************** ******************************
JD1:1:102:1601:ORFJ00027      aaaggatttgtaaaaaatctcaacgatggaagggtagaaattgtagctttctttaatact
94a:1:107:117:orf00001        aaaggatttgtaaaaaatctaaacgatggaagggtagaaattgtagctttctttaatact
118a:1:106:158122218:orf00020 aaaggatttgtaaaaaatctaaacgatggaagggtagaaattgtagctttctttaatact
B31:1:100:4091:ORFB0018       aaaggatttgtaaaaaatctcaacgatggaagggtagaaattgtagctttctttaatact
72a:1:105:32:orf00022         aaaggatttgtaaaaaatctaaacgatggaagggtagaaattgtagctttctttaatact
64b:1:110:473:orf00001        aaaggatttgtaaaaaatctcaacgatggaagggtagaaattgtagctttctttaatact
29805:1:108:171:orf00001      aaaggatttgtaaaaaatctcaacgatggaagggtagaaattgtagctttctttaatact
BOL26:1:111:60:orf00001       aaaggatttgtaaaaaatctcaacgatggaagggtagaaattgtagctttctttaatact
CA-11.2A:1:109:33:orf00001    aaaggatttgtaaaaaatctaaacgatggaagggtagaaattgtagctttctttaatact
WI91-23:1:112:493:orf00001    aaaggatttgtaaaaaatctcaacgatggaagggtagaaattgtagctttctttaatact
297:1:103:411:ORFB00012       aaaggatttgtaaaaaatctaaacgatggaagggtagaaattgtagctttctttaatact
N40:1:101:1716:ORFK00021      aaaggatttgtaaaaaatctcaacgatggaagggtagaaattgtagctttctttaatact
ZS7:1:113:22:orf00001         aaaggatttgtaaaaaatctcaacgatggaagggtagaaattgtagctttctttaatact
                              ******************** ***************************************
JD1:1:102:1601:ORFJ00027      aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattaaa
94a:1:107:117:orf00001        aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattgaa
118a:1:106:158122218:orf00020 aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattgaa
B31:1:100:4091:ORFB0018       aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattaaa
72a:1:105:32:orf00022         aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattgaa
64b:1:110:473:orf00001        aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattaaa
29805:1:108:171:orf00001      aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattgaa
BOL26:1:111:60:orf00001       aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattaaa
CA-11.2A:1:109:33:orf00001    aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattgaa
WI91-23:1:112:493:orf00001    aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattgaa
297:1:103:411:ORFB00012       aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattgaa
N40:1:101:1716:ORFK00021      aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattgaa
ZS7:1:113:22:orf00001         aaagaacaaatgaaaaaatttgaaaaattattaaatgggaataagtattcaaacattaaa
                              ********************************************************* **
JD1:1:102:1601:ORFJ00027      aacattgaaaaaatagttttagatgaaaattatccttttcaatttaatgattttaaaatt
94a:1:107:117:orf00001        aacattgaaaaaatagttttagatgaaaattatccttttcaatttaatgattttaaaatt
118a:1:106:158122218:orf00020 aacattgaaaaaatagttttagatgaaaattatccttttcaatttaatgattttaaaatt
B31:1:100:4091:ORFB0018       aacattgaaaaaatagttttagatgaaaattatccttttcaatttaatgattttaaaatt
72a:1:105:32:orf00022         aacattgaaaaaatagttttagatgaaaattatccttttcaatttaatgattttaaaatt
64b:1:110:473:orf00001        aacattgaaaaaatagttttagatgaaaattatccttttcaatttaatgattttaaaatt
29805:1:108:171:orf00001      aacattgaaaaaatagctttagatgaaaattatccttttcaatttaatgattttaaaatt
BOL26:1:111:60:orf00001       aacattgaaaaaatagttttagatgaaaattatccttttcaatttaatgattttaaaatt
CA-11.2A:1:109:33:orf00001    aacattgaaaaaatagttttagatgaaaattatccttttcaatttaatgattttaaaatt
WI91-23:1:112:493:orf00001    aacattgaaaaaatagctttagatgaaaattatccttttcaatttaatgattttaaaatt
297:1:103:411:ORFB00012       aacattgaaaaaatagttttagatgaaaattatccttttcaatttaatgattttaaaatt
N40:1:101:1716:ORFK00021      aacattgaaaaaatagctttagatgaaaattatccttttcaatttaatgattttaaaatt
ZS7:1:113:22:orf00001         aacattgaaaaaatagttttagatgaaaattatccttttcaatttaatgattttaaaatt
                              **************** *******************************************
JD1:1:102:1601:ORFJ00027      tattat
94a:1:107:117:orf00001        tattat
118a:1:106:158122218:orf00020 tattat
B31:1:100:4091:ORFB0018       tattat
72a:1:105:32:orf00022         tattat
64b:1:110:473:orf00001        tattat
29805:1:108:171:orf00001      tattat
BOL26:1:111:60:orf00001       tattat
CA-11.2A:1:109:33:orf00001    tattat
WI91-23:1:112:493:orf00001    tattat
297:1:103:411:ORFB00012       tattat
N40:1:101:1716:ORFK00021      tattat
ZS7:1:113:22:orf00001         tattat
                              ******

Here's the code:

#!/usr/bin/perl
use Bio::AlignIO;
use Bio::Graphics::Panel;
my $line = shift @ARGV;
my $in = Bio::AlignIO->new(-file=>$line,-format=>"clustalw");
while($aln = $in->next_aln()){
    foreach $seqobj($aln->each_seq()){
        my $seq = $seqobj->seq;
        my $id = $seqobj->id;
        my $length = $seqobj->length;
        my $seqobj = Bio::SeqFeature::Generic->new(-start =>1, -end=>$length,-display_name=>$id);
        push (@seq, $seqobj);
    }
    foreach $seq(@seq){
        my @features = $seq->get_SeqFeatures;
        my %sorted_features;
        for my $f (@features) {
            my $tag = "-";
            push @{$sorted_features{$tag}},$f;
        }
    my <span class="math-container">$panel = Bio::Graphics::Panel-&gt;new(
        -length    =&gt; $</span>seq-&gt;length,
        -key_style =&gt; 'between',
        -width     =&gt; 800,
        -pad_left  =&gt; 10,
        -pad_right =&gt; 10,
    );
    <span class="math-container">$panel-&gt;add_track(generic =&gt; Bio::SeqFeature::Generic-&gt;new(-start=&gt;1,
            -end=&gt;$</span>seq-&gt;length),
        -glyph  =&gt; 'generic',
        -bgcolor =&gt; 'blue',
        -label  =&gt; 1,
    );

    my @colors = qw(cyan orange blue purple green chartreuse magenta yellow aqua);
    my <span class="math-container">$idx    = 0;
    for my $</span>tag (sort keys my %sorted_features) {
        my <span class="math-container">$features = $</span>sorted_features{<span class="math-container">$tag};
        $</span>panel-&gt;add_track(<span class="math-container">$features,
            -glyph    =&gt;  'generic',
            -bgcolor  =&gt;  $</span>colors[<span class="math-container">$idx++ % @colors],
            -fgcolor  =&gt; 'black',
            -font2color =&gt; 'red',
            -key      =&gt; "$</span>{tag}s&quot;,
            -bump     =&gt; +1,
            -height   =&gt; 8,
            -label    =&gt; 1,
            -description =&gt; 1,
        );
    }
    print $panel-&gt;png;

}

}

Unfortunately, $seq->get_SeqFeatures never returns anything. I'm not sure why it doesn't since there should be features on it coming from the Bio::SimpleAlign object. Maybe I should set some new parameters?

Trying to show the gaps of each seq on bio::Graphics after converting clustalw

0 Answers0