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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Modified help for \"get Indels\" tool, and made some small changes to the perl script.
This commit is contained in:
Guruprasad Anada
@@ -1,4 +1,4 @@
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<tool id="indels_3way" name="Fetch Indels" version="1.0.1">
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<tool id="indels_3way" name="Fetch Indels" version="1.0.2">
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<description> from 3-way alignments</description>
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<command interpreter="perl">
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parseMAF_smallIndels.pl $input1 $out_file1 $outgroup
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@@ -30,7 +30,14 @@
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**What it does**
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This tool estimates the indel type and length for each of the 3-way alignments in the input MAF file.
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This tool consists of the first module from the computational pipeline to identify indels as described in Kvikstad et al., 2007. Note that the generated output does not include subsequent filtering steps.
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Deletions in a particular species are identified as one or more consecutive gap columns within an alignment block, given that the orthologous positions in the other two species contain nucleotides of
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equal length.
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Similarly, insertions in a particular species are identified as one or more consecutive nucleotide columns within an alignment block, given that the orthologous positions in the other two
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species contain gaps.
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*Kvikstad E. M. et al. (2007). A Macaques-Eye View of Human Insertions and Deletions: Differences in Mechanisms. PLoS Computational Biology 3(9):e176*
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-----
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@@ -163,7 +163,7 @@ sub get_sequences_within_block{
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sub get_indels_within_block{
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my (@sequences) = @_;
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my $line1 = my $line2 = my $line3 = "";
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my @line1 = my @line2 = my @line3 = ();
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my @line1 = my @line2 = my @line3 = ();
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my $score = 0;
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my $start1 = my $align_length1 = my $end1 = my $seq_length1 = 0;
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my $start2 = my $align_length2 = my $end2 = my $seq_length2 = 0;
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@@ -182,7 +182,7 @@ sub get_indels_within_block{
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my @array_return = ();
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my $test1 = 0;
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my $line1_stat = my $line2_stat = my $line3_stat = "";
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# process 3-way blocks only
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if (scalar(@sequences) == 3){
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$line1 = $sequences[0];
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@@ -194,143 +194,128 @@ sub get_indels_within_block{
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# check order of sequences and assign uniformly seq1= human, seq2 = chimp, seq3 = macaque
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if ($line1 =~ m/$outgroup/){
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$line1_stat = "out";
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$line2_stat = "in";
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$line3_stat = "in";}
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$line2=~ s/^\s*//;
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$line2 =~ s/\s+/\t/g;
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@line2 = split(/\t/, $line2);
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if (($ingroup1 eq "") || ($line2[1] =~ m/$ingroup1/)){
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$line2_stat = "in1";
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$line3_stat = "in2";
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}
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else{
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$line3_stat = "in1";
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$line2_stat = "in2"; }
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}
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elsif ($line2 =~ m/$outgroup/){
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$line2_stat = "out";
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$line1_stat = "in";
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$line3_stat = "in";}
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$line1=~ s/^\s*//;
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$line1 =~ s/\s+/\t/g;
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@line1 = split(/\t/, $line1);
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if (($ingroup1 eq "") || ($line1[1] =~ m/$ingroup1/)){
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$line1_stat = "in1";
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$line3_stat = "in2";
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}
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else{
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$line3_stat = "in1";
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$line1_stat = "in2"; }
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}
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elsif ($line3 =~ m/$outgroup/){
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$line3_stat = "out";
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$line1_stat = "in";
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$line2_stat = "in";}
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$line1=~ s/^\s*//;
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$line1 =~ s/\s+/\t/g;
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@line1 = split(/\t/, $line1);
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if (($ingroup1 eq "") || ($line1[1] =~ m/$ingroup1/)){
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$line1_stat = "in1";
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$line2_stat = "in2";
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}
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else{
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$line2_stat = "in1";
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$line1_stat = "in2"; }
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}
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#print "# l1 = $line1_stat\n";
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#print "# l2 = $line2_stat\n";
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#print "# l3 = $line3_stat\n";
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if ($line1_stat eq "in"){
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$line1=~ s/^\s*//;
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$line1 =~ s/\s+/\t/g;
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@line1 = split(/\t/, $line1);
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$end1 =($line1[2]+$line1[3]-1);
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$seq1 = $line1[1].":".$line1[3];
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$ingroup1 = (split(/\./, $seq1))[0];
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$start1 = $line1[2];
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$align_length1 = $line1[3];
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$orient1 = $line1[4];
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$seq_length1 = $line1[5];
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$sequence1 = $line1[6];
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$test1 = length($sequence1);
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my $total_length1 = $test1+$start1;
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my @array1 = ($start1,$end1,$orient1,$seq_length1);
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($start1_plus, $end1_plus) = convert_coords(@array1);
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}
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elsif ($line1_stat eq "out"){
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$line1=~ s/^\s*//;
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$line1 =~ s/\s+/\t/g;
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@line1 = split(/\t/, $line1);
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$end3 =($line1[2]+$line1[3]-1);
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$seq3 = $line1[1].":".$line1[3];
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$start3 = $line1[2];
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$align_length3 = $line1[3];
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$orient3 = $line1[4];
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$seq_length3 = $line1[5];
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$sequence3 = $line1[6];
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my $test3 = length($sequence3);
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my $total_length3 = $test3+$start3;
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my @array3 = ($start3,$end3,$orient3,$seq_length3);
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($start3_plus, $end3_plus) = convert_coords(@array3);
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}
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if (($line1_stat eq "in") && ($line2_stat eq "in")){
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$line2=~ s/^\s*//;
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$line2 =~ s/\s+/\t/g;
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@line2 = split(/\t/, $line2);
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$end2 =($line2[2]+$line2[3]-1);
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$seq2 = $line2[1].":".$line2[3];
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$ingroup2 = (split(/\./, $seq2))[0];
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$start2 = $line2[2];
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$align_length2 = $line2[3];
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$orient2 = $line2[4];
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$seq_length2 = $line2[5];
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$sequence2 = $line2[6];
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my $test2 = length($sequence2);
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my $total_length2 = $test2+$start2;
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my @array2 = ($start2,$end2,$orient2,$seq_length2);
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($start2_plus, $end2_plus) = convert_coords(@array2);
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}
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elsif (($line1_stat eq "in") && ($line2_stat eq "out")){
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$line2=~ s/^\s*//;
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$line2 =~ s/\s+/\t/g;
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@line2 = split(/\t/, $line2);
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$end3 =($line2[2]+$line2[3]-1);
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$seq3 = $line2[1].":".$line2[3];
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$start3 = $line2[2];
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$align_length3 = $line2[3];
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$orient3 = $line2[4];
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$seq_length3 = $line2[5];
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$sequence3 = $line2[6];
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my $test3 = length($sequence3);
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my $total_length3 = $test3+$start3;
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my @array3 = ($start3,$end3,$orient3,$seq_length3);
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($start3_plus, $end3_plus) = convert_coords(@array3);
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}
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elsif ($line1_stat eq "out"){
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$line2=~ s/^\s*//;
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$line2 =~ s/\s+/\t/g;
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@line2 = split(/\t/, $line2);
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$end1 =($line2[2]+$line2[3]-1);
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$seq1 = $line2[1].":".$line2[3];
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$ingroup1 = (split(/\./, $seq1))[0];
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$start1 = $line2[2];
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$align_length1 = $line2[3];
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$orient1 = $line2[4];
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$seq_length1 = $line2[5];
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$sequence1 = $line2[6];
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$test1 = length($sequence1);
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my $total_length1 = $test1+$start1;
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my @array1 = ($start1,$end1,$orient1,$seq_length1);
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($start1_plus, $end1_plus) = convert_coords(@array1);
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}
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my $linei1 = my $linei2 = my $lineo = "";
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my @linei1 = my @linei2 = my @lineo = ();
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if ((($line1_stat eq "in") or ($line2_stat eq "in")) && ($line3_stat eq "in")){
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$line3=~ s/^\s*//;
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$line3 =~ s/\s+/\t/g;
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@line3 = split(/\t/, $line3);
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$end2 =($line3[2]+$line3[3]-1);
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$seq2 = $line3[1].":".$line3[3];
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$ingroup2 = (split(/\./, $seq2))[0];
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$start2 = $line3[2];
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$align_length2 = $line3[3];
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$orient2 = $line3[4];
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$seq_length2 = $line3[5];
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$sequence2 = $line3[6];
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my $test2 = length($sequence2);
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my $total_length2 = $test2+$start2;
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my @array2 = ($start2,$end2,$orient2,$seq_length2);
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($start2_plus, $end2_plus) = convert_coords(@array2);
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}
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elsif ($line3_stat eq "out"){
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$line3=~ s/^\s*//;
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$line3 =~ s/\s+/\t/g;
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@line3 = split(/\t/, $line3);
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$end3 =($line3[2]+$line3[3]-1);
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$seq3 = $line3[1].":".$line3[3];
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$start3 = $line3[2];
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$align_length3 = $line3[3];
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$orient3 = $line3[4];
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$seq_length3 = $line3[5];
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$sequence3 = $line3[6];
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my $test3 = length($sequence3);
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my $total_length3 = $test3+$start3;
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my @array3 = ($start3,$end3,$orient3,$seq_length3);
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($start3_plus, $end3_plus) = convert_coords(@array3);
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}
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#print "# l1 = $ingroup1\n";
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if ($line1_stat eq "out"){
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$lineo = $line1;
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}
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elsif ($line1_stat eq "in1"){
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$linei1 = $line1;
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}
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else{
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$linei2 = $line1;
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}
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if ($line2_stat eq "out"){
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$lineo = $line2;
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}
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elsif ($line2_stat eq "in1"){
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$linei1 = $line2;
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}
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else{
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$linei2 = $line2;
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}
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if ($line3_stat eq "out"){
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$lineo = $line3;
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}
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elsif ($line3_stat eq "in1"){
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$linei1 = $line3;
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}
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else{
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$linei2 = $line3;
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}
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$linei1=~ s/^\s*//;
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$linei1 =~ s/\s+/\t/g;
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@linei1 = split(/\t/, $linei1);
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$end1 =($linei1[2]+$linei1[3]-1);
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$seq1 = $linei1[1].":".$linei1[3];
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$ingroup1 = (split(/\./, $seq1))[0];
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$start1 = $linei1[2];
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$align_length1 = $linei1[3];
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$orient1 = $linei1[4];
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$seq_length1 = $linei1[5];
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$sequence1 = $linei1[6];
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$test1 = length($sequence1);
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my $total_length1 = $test1+$start1;
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my @array1 = ($start1,$end1,$orient1,$seq_length1);
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($start1_plus, $end1_plus) = convert_coords(@array1);
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$linei2=~ s/^\s*//;
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$linei2 =~ s/\s+/\t/g;
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@linei2 = split(/\t/, $linei2);
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$end2 =($linei2[2]+$linei2[3]-1);
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$seq2 = $linei2[1].":".$linei2[3];
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$ingroup2 = (split(/\./, $seq2))[0];
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$start2 = $linei2[2];
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$align_length2 = $linei2[3];
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$orient2 = $linei2[4];
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$seq_length2 = $linei2[5];
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$sequence2 = $linei2[6];
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my $test2 = length($sequence2);
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my $total_length2 = $test2+$start2;
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my @array2 = ($start2,$end2,$orient2,$seq_length2);
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($start2_plus, $end2_plus) = convert_coords(@array2);
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$lineo=~ s/^\s*//;
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$lineo =~ s/\s+/\t/g;
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@lineo = split(/\t/, $lineo);
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$end3 =($lineo[2]+$lineo[3]-1);
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$seq3 = $lineo[1].":".$lineo[3];
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$start3 = $lineo[2];
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$align_length3 = $lineo[3];
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$orient3 = $lineo[4];
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$seq_length3 = $lineo[5];
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$sequence3 = $lineo[6];
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my $test3 = length($sequence3);
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my $total_length3 = $test3+$start3;
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my @array3 = ($start3,$end3,$orient3,$seq_length3);
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($start3_plus, $end3_plus) = convert_coords(@array3);
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#print "# l1 = $ingroup1\n";
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#print "# l2 = $ingroup2\n";
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#print "# l3 = $outgroup\n";
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@@ -592,7 +577,7 @@ for ($counter2 = 0; $counter2 < @seq3_delete_startOnly; $counter2++){
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}
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for ($counter3 = 0; $counter3 < @seq2_insert_startOnly; $counter3++){
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$final_line3 = join("\t",($seq2_insert_startOnly[$counter3],$seq2_insert_lengths[$counter3]));
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$final_line3 = join("\t",($seq2_insert_startOnly[$counter3],$seq2_insert_lengths[$counter3]));
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push(@final3,$final_line3);
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}
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