Re: Alignment and matrix generation

Do you expect the output like the following?

1       A       20.0    C       0.0     G       0.0     T       0.0
2       A       0.0     C       0.0     G       0.0     T       20.0
3       A       0.0     C       0.0     G       20.0    T       0.0
4       A       0.0     C       0.0     G       20.0    T       0.0
5       A       0.0     C       0.0     G       20.0    T       0.0
...
115     A       0.0     C       0.0     G       0.0     T       100.0
116     A       0.0     C       20.0    G       80.0    T       0.0
117     A       0.0     C       0.0     G       60.0    T       40.0
118     A       60.0    C       0.0     G       40.0    T       0.0
119     A       0.0     C       80.0    G       0.0     T       20.0
120     A       0.0     C       0.0     G       0.0     T       100.0
[download]

It was generated by the following script:

#!/usr/bin/perl
use strict;
use warnings;
use Syntax::Construct qw{ // };

my ($startpos, $endpos, $count);
my %occurrences;
while (<DATA>) {
    if (/^\s+ ([0-9]+) \s+ ([0-9]+) \s*$/x) {
        ($startpos, $endpos) = ($1, $2);
        $count = 0;

    } elsif (/\s+ ([-actg]+) \s*$/x) {
        ++$count;
        my @nucleotides = split //, $1;
        for my $pos (0 .. $#nucleotides) {
            ++$occurrences{ $nucleotides[$pos] }[$startpos + $pos]
                unless '-' eq $nucleotides[$pos];
        }
    }
}

for my $pos (1 .. $endpos) {
    print "$pos\t";
    for my $nucleotide (sort keys %occurrences) {
        printf "%s\t%0.1f\t", uc $nucleotide,
            100 * ($occurrences{$nucleotide}[$pos] // 0) / $count;
    }
    print "\n";
}

__DATA__
CLUSTAL O(1.2.1) multiple sequence alignment

                                   1                                  
+                        60 
gnl|hbvcds|AB014370_PreC_P-A       -----------------------------------
+-------------------------
gnl|hbvcds|AB064314_PreC_P-A       -----------------------------------
+-------------------------
gnl|hbvcds|AB014384_C_P-C          -----------------------------------
+-------------------------
gnl|hbvcds|AB014385_C_P-C          -----------------------------------
+-------------------------
gnl|hbvcds|AB048701_PreS1_P-D      atggggcagaatctttccaccagcaatcctctggg
+attctttcccgaccatcagttggat
gnl|hbvcds|AB078031_PreS1_P-D      atggggcagaatctttccaccagcaaccctctggg
+attctttcccgaccaccagttggat
gnl|hbvcds|AB030513_S_P-A          -----------------------------------
+-------------------------
gnl|hbvcds|AB064314_S_P-A          -----------------------------------
+-------------------------
gnl|hbvcds|AB194947_PreS2_P-E      -----------------------------------
+-------------------------
gnl|hbvcds|AB194948_PreS2_P-E      -----------------------------------
+-------------------------

                                   61                                 
+                        120
gnl|hbvcds|AB014370_PreC_P-A       tagagtctcctgagcattgctcacctcaccatact
+gcactcaggcaagccattctctgct
gnl|hbvcds|AB064314_PreC_P-A       tagagtctcctgagcattgctcacctcaccatacg
+gcactcaggcaagccattctctgct
gnl|hbvcds|AB014384_C_P-C          tagagtctccggaacattgttcacctcaccataca
+gcactcaggcaagctattctgtgtt
gnl|hbvcds|AB014385_C_P-C          tagagtctccggaacattgttcacctcaccataca
+gcactcaggcaagctattctgtgtt
gnl|hbvcds|AB048701_PreS1_P-D      gggtttttcttgttgacaagaatcctcacaatacc
+gcagagtctagactcgtggtggact
gnl|hbvcds|AB078031_PreS1_P-D      gggtttttcttgttgacaagaatcctcacaatacc
+gcagagtctagactcgtggtggact
gnl|hbvcds|AB030513_S_P-A          gggtttttcttgttgacaagaatcctcacaatacc
+gcagagtctagactcgtggtggact
gnl|hbvcds|AB064314_S_P-A          gggtttttcttgttgacaagaatcctcacaatacc
+gcagagtctagactcgtggtggact
gnl|hbvcds|AB194947_PreS2_P-E      gggtttttcttgttgacaaaaatcctcacaatacc
+gcagagtctagactcgtggtggact
gnl|hbvcds|AB194948_PreS2_P-E      gggtttttcttgttgacaaaaatcctcacaatacc
+gcagagtctagactcgtggtggact
                                     *  * **  *   *       ****** **** 
+***        *    *  *    *
[download]

لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

Comment on Re: Alignment and matrix generation Select or Download Code

Replies are listed 'Best First'.
Re^2: Alignment and matrix generation by newtoperlprog (Sexton) on Mar 30, 2015 at 16:44 UTC
Dear Choroba, Thank you for your time and helping me with the code to develop matrix for the data. However, the data file should not be having number 1 , 60 , this was provided by me for the clarification that its 60 column wide. Actual data file is like this: CLUSTAL O(1.2.1) multiple sequence alignment + gnl\|hbvcds\|AB014370_PreC_P-A ----------------------------------- +------------------------- gnl\|hbvcds\|AB064314_PreC_P-A ----------------------------------- +------------------------- gnl\|hbvcds\|AB014384_C_P-C ----------------------------------- +------------------------- gnl\|hbvcds\|AB014385_C_P-C ----------------------------------- +------------------------- gnl\|hbvcds\|AB048701_PreS1_P-D atggggcagaatctttccaccagcaatcctctggg +attctttcccgaccatcagttggat gnl\|hbvcds\|AB078031_PreS1_P-D atggggcagaatctttccaccagcaaccctctggg +attctttcccgaccaccagttggat gnl\|hbvcds\|AB030513_S_P-A ----------------------------------- +------------------------- gnl\|hbvcds\|AB064314_S_P-A ----------------------------------- +------------------------- gnl\|hbvcds\|AB194947_PreS2_P-E ----------------------------------- +------------------------- gnl\|hbvcds\|AB194948_PreS2_P-E ----------------------------------- +------------------------- + + gnl\|hbvcds\|AB014370_PreC_P-A tagagtctcctgagcattgctcacctcaccatact +gcactcaggcaagccattctctgct gnl\|hbvcds\|AB064314_PreC_P-A tagagtctcctgagcattgctcacctcaccatacg +gcactcaggcaagccattctctgct gnl\|hbvcds\|AB014384_C_P-C tagagtctccggaacattgttcacctcaccataca +gcactcaggcaagctattctgtgtt gnl\|hbvcds\|AB014385_C_P-C tagagtctccggaacattgttcacctcaccataca +gcactcaggcaagctattctgtgtt gnl\|hbvcds\|AB048701_PreS1_P-D gggtttttcttgttgacaagaatcctcacaatacc +gcagagtctagactcgtggtggact gnl\|hbvcds\|AB078031_PreS1_P-D gggtttttcttgttgacaagaatcctcacaatacc +gcagagtctagactcgtggtggact gnl\|hbvcds\|AB030513_S_P-A gggtttttcttgttgacaagaatcctcacaatacc +gcagagtctagactcgtggtggact gnl\|hbvcds\|AB064314_S_P-A gggtttttcttgttgacaagaatcctcacaatacc +gcagagtctagactcgtggtggact gnl\|hbvcds\|AB194947_PreS2_P-E gggtttttcttgttgacaaaaatcctcacaatacc +gcagagtctagactcgtggtggact gnl\|hbvcds\|AB194948_PreS2_P-E gggtttttcttgttgacaaaaatcctcacaatacc +gcagagtctagactcgtggtggact * * ** * * **** +* * * * * [download] Please let me know where I can modify the code to incorporate the changes. Regards	[reply] [d/l]
Re^3: Alignment and matrix generation by choroba (Cardinal) on Mar 30, 2015 at 20:59 UTC
Just few changes: --- 1.pl 2015-03-30 22:58:28.434954333 +0200 +++ 2.pl 2015-03-30 22:58:11.261833250 +0200 @@ -3,16 +3,18 @@ use warnings; use Syntax::Construct qw{ // }; -my ($startpos, $endpos, $count); +my $endpos = 0; +my ($startpos, $count); my %occurrences; while (<DATA>) { - if (/^\s+ ([0-9]+) \s+ ([0-9]+) \s$/x) { - ($startpos, $endpos) = ($1, $2); + if (/^ +$/) { + $startpos = $endpos + 1; $count = 0; } elsif (/\s+ ([-actg]+) \s$/x) { ++$count; my @nucleotides = split //, $1; + $endpos = $endpos + length $1 if $startpos == $endpos + 1; for my $pos (0 .. $#nucleotides) { ++$occurrences{ $nucleotides[$pos] }[$startpos + $pos] unless '-' eq $nucleotides[$pos]; [download] لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ	[reply] [d/l]
Re^4: Alignment and matrix generation by newtoperlprog (Sexton) on Mar 31, 2015 at 15:45 UTC
Dear Choroba Thank you for your time. I modified the code as per your suggestions but it seems that the code is skipping the first block of alignment and rest the occurrences of nucleotides as percentages are wrong. I am attaching the code and the data file for the same #!/usr/bin/perl use strict; use warnings; use Syntax::Construct qw{ // }; my $endpos = 0; my ($startpos, $count); my %occurrences; my $file = $ARGV[0]; open(DATA, $file); while (<DATA>) { if (/^CLUSTAL./) {next;} if (/^ +$/) { $startpos = $endpos + 1; $count = 0; } elsif (/\s+ ([-actg]+) \s$/x) { ++$count; my @nucleotides = split //, $1; $endpos = $endpos + length $1 if $startpos == $endpos + 1; for my $pos (0 .. $#nucleotides) { ++$occurrences{ $nucleotides[$pos] }[$startpos + $pos] unless '-' eq $nucleotides[$pos]; } } } for my $pos (1 .. $endpos) { print "$pos\t"; for my $nucleotide (sort keys %occurrences) { printf "%s\t%0.1f\t", uc $nucleotide, 100 * ($occurrences{$nuc +leotide}[$pos] // 0) / $count; } print "\n"; } [download] Data file CLUSTAL O(1.2.1) multiple sequence alignment gnl\|hbvcds\|AB014370_PreC_P-A ----------------------------------- +------------------------- gnl\|hbvcds\|AB064314_PreC_P-A ----------------------------------- +------------------------- gnl\|hbvcds\|AB014384_C_P-C ----------------------------------- +------------------------- gnl\|hbvcds\|AB014385_C_P-C ----------------------------------- +------------------------- gnl\|hbvcds\|AB048701_PreS1_P-D atggggcagaatctttccaccagcaatcctctggg +attctttcccgaccatcagttggat gnl\|hbvcds\|AB078031_PreS1_P-D atggggcagaatctttccaccagcaaccctctggg +attctttcccgaccaccagttggat gnl\|hbvcds\|AB030513_S_P-A ----------------------------------- +------------------------a gnl\|hbvcds\|AB064314_S_P-A ----------------------------------- +------------------------c gnl\|hbvcds\|AB194947_PreS2_P-E ----------------------------------- +------------------------g gnl\|hbvcds\|AB194948_PreS2_P-E ----------------------------------- +------------------------g + gnl\|hbvcds\|AB014370_PreC_P-A tagagtctcctgagcattgctcacctcaccatact +gcactcaggcaagccattctctgct gnl\|hbvcds\|AB064314_PreC_P-A tagagtctcctgagcattgctcacctcaccatacg +gcactcaggcaagccattctctgct gnl\|hbvcds\|AB014384_C_P-C tagagtctccggaacattgttcacctcaccataca +gcactcaggcaagctattctgtgtt gnl\|hbvcds\|AB014385_C_P-C tagagtctccggaacattgttcacctcaccataca +gcactcaggcaagctattctgtgtt gnl\|hbvcds\|AB048701_PreS1_P-D gggtttttcttgttgacaagaatcctcacaatacc +gcagagtctagactcgtggtggact gnl\|hbvcds\|AB078031_PreS1_P-D gggtttttcttgttgacaagaatcctcacaatacc +gcagagtctagactcgtggtggact gnl\|hbvcds\|AB030513_S_P-A gggtttttcttgttgacaagaatcctcacaatacc +gcagagtctagactcgtggtggact gnl\|hbvcds\|AB064314_S_P-A gggtttttcttgttgacaagaatcctcacaatacc +gcagagtctagactcgtggtggact gnl\|hbvcds\|AB194947_PreS2_P-E gggtttttcttgttgacaaaaatcctcacaatacc +gcagagtctagactcgtggtggact gnl\|hbvcds\|AB194948_PreS2_P-E gggtttttcttgttgacaaaaatcctcacaatacc +gcagagtctagactcgtggtggact * * ** * * **** +* * * * * [download] Regards	[reply] [d/l] [select]
Re^5: Alignment and matrix generation by choroba (Cardinal) on Mar 31, 2015 at 15:57 UTC
Re^6: Alignment and matrix generation by newtoperlprog (Sexton) on Apr 01, 2015 at 14:12 UTC