Difference between revisions of "DbSNP Silent Mutations Parser"
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| + | <code> |
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#!/usr/bin/perl |
#!/usr/bin/perl |
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| Line 146: | Line 147: | ||
print "|} \n"; |
print "|} \n"; |
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} |
} |
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| + | </code> |
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Revision as of 23:14, 16 June 2011
- !/usr/bin/perl
if ($#ARGV < 2){
print "wrong arguments!\n";
exit();
}
$out_format=$ARGV[0];
$inFile = $ARGV[1];
$mRNA_fasta = $ARGV[2];
if ($out_format ne "list" && $out_format ne "wiki" && $out_format ne "map"){
print "wrong output type!\n";
exit();
}
$mRNA_seq = "";
open(RNA, '<'.$mRNA_fasta) || die "Can not open file $inFile: $!";
while (<RNA>){
if(!/^>/){
chomp($_);
$mRNA_seq = $mRNA_seq . $_;
}
}
close(RNA);
@mRNA_array = split(//, $mRNA_seq);
$codon_pos = 0;
@codon = ();
$frame = 1;
$pos = 1;
foreach(@mRNA_array){
$codon[$codon_pos] = $codon[$codon_pos] . $_;
if ($frame == 3){
$frame = 1;
$codon_pos++;
} else {
$frame++;
}
}
$rs = "";
$i=0;
$ref_allele ="";
$mut_allele ="";
$ref_frame = "";
$mut_frame = "";
$ref_residue = "";
$mut_residue = "";
$ref_aa_pos = "";
$mut_aa_pos = "";
$ref_aa_pos_plus_1 = "";
$mut_aa_pos_plus_1 = "";
if($out_format eq "wiki"){
print '{| border="1"'."\n";
print "|-\n";
print "! Identifier\n";
print "! AA-Position\n";
print "! Reference Triplet\n";
print "! Mutated Triplet\n";
print "! Reference Allele\n";
print "! Mutated Allele\n";
print "! Frame\n";
print "! Reference Residue\n";
print "! Mutated Residue\n";
}
$pref_rs ="-1";
open(IN, '<'.$inFile) || die "Can not open file $inFile: $!";
while (<IN>){
if(/^(rs\d+)/){
$rs = $1;
}
if(/^LOC.+fxn-class=reference.+allele=(\w).+frame=(\d).+residue=(\w).+aa_position=(\d+)/){
$ref_allele = $1;
$ref_frame = $2;
$ref_residue = $3;
$ref_aa_pos = $4;
$ref_aa_pos_plus_1 = $ref_aa_pos + 1;
}
if(/^LOC.+fxn-class=synonymous-codon.+allele=(\w).+frame=(\d).+residue=(\w).+aa_position=(\d+)/){
$mut_allele = $1;
$mut_frame = $2;
$mut_residue = $3;
$mut_aa_pos = $4;
$mut_aa_pos_plus_1 = $mut_aa_pos + 1;
}
if (/^\s/){
$ref_triplet= $codon[$ref_aa_pos];
$mut_triplet= $ref_triplet;
if($mut_frame == 1){
$mut_triplet=~ s/(\w)(\w)(\w)/$mut_allele$2$3/;
} elsif($mut_frame == 2){
$mut_triplet=~ s/(\w)(\w)(\w)/$1$_mut_allele$3/;
} elsif($mut_frame == 3){
$mut_triplet=~ s/(\w)(\w)(\w)/$1$2$mut_allele/;
} else {
print "lol";
}
if($out_format eq "wiki" && $prev_rs ne $rs){
print "|-\n";
print "| $rs\n";
print "| $mut_aa_pos_plus_1\n";
print "| $ref_triplet\n";
print "| $mut_triplet\n";
print "| $ref_allele\n";
print "| $mut_allele\n";
print "| $mut_frame \n";
print "| $ref_residue \n";
print "| $mut_residue \n";
} elsif($out_format eq "map" && $prev_rs ne $rs){
print "$rs,silent,$ref_residue$mut_aa_pos_plus_1$mut_residue,$ref_triplet-$mut_triplet\n";
} elsif ($out_format eq "list" && $prev_rs ne $rs){
print "$rs triplet=$ref_triplet/$mut_triplet allele=$ref_allele/$mut_allele frame=$ref_frame/$mut_frame ";
print "residue=$ref_residue/$mut_residue aa_pos=$ref_aa_pos_plus_1/$mut_aa_pos_plus_1 \n";
}
$prev_rs = $rs;
}
}
close(IN);
if($out_format eq "wiki"){
print "|} \n";
}
