-
Notifications
You must be signed in to change notification settings - Fork 49
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Add the script postprocessing the output of trust4.
- Loading branch information
Showing
1 changed file
with
134 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,134 @@ | ||
| #!/usr/bin/env perl | ||
|
|
||
| use strict ; | ||
| use warnings ; | ||
|
|
||
| die "usage: ./trust-simplerepo.pl xxx_cdr3.out [OPTIONS]\n" if ( @ARGV == 0 ) ; | ||
| my %cdr3 ; | ||
|
|
||
| # Copied from http://www.wellho.net/resources/ex.php4?item=p212/3to3 | ||
| my %DnaToAa = ( | ||
| 'TCA' => 'S', # Serine | ||
| 'TCC' => 'S', # Serine | ||
| 'TCG' => 'S', # Serine | ||
| 'TCT' => 'S', # Serine | ||
| 'TTC' => 'F', # Phenylalanine | ||
| 'TTT' => 'F', # Phenylalanine | ||
| 'TTA' => 'L', # Leucine | ||
| 'TTG' => 'L', # Leucine | ||
| 'TAC' => 'Y', # Tyrosine | ||
| 'TAT' => 'Y', # Tyrosine | ||
| 'TAA' => '_', # Stop | ||
| 'TAG' => '_', # Stop | ||
| 'TGC' => 'C', # Cysteine | ||
| 'TGT' => 'C', # Cysteine | ||
| 'TGA' => '_', # Stop | ||
| 'TGG' => 'W', # Tryptophan | ||
| 'CTA' => 'L', # Leucine | ||
| 'CTC' => 'L', # Leucine | ||
| 'CTG' => 'L', # Leucine | ||
| 'CTT' => 'L', # Leucine | ||
| 'CCA' => 'P', # Proline | ||
| 'CCC' => 'P', # Proline | ||
| 'CCG' => 'P', # Proline | ||
| 'CCT' => 'P', # Proline | ||
| 'CAC' => 'H', # Histidine | ||
| 'CAT' => 'H', # Histidine | ||
| 'CAA' => 'Q', # Glutamine | ||
| 'CAG' => 'Q', # Glutamine | ||
| 'CGA' => 'R', # Arginine | ||
| 'CGC' => 'R', # Arginine | ||
| 'CGG' => 'R', # Arginine | ||
| 'CGT' => 'R', # Arginine | ||
| 'ATA' => 'I', # Isoleucine | ||
| 'ATC' => 'I', # Isoleucine | ||
| 'ATT' => 'I', # Isoleucine | ||
| 'ATG' => 'M', # Methionine | ||
| 'ACA' => 'T', # Threonine | ||
| 'ACC' => 'T', # Threonine | ||
| 'ACG' => 'T', # Threonine | ||
| 'ACT' => 'T', # Threonine | ||
| 'AAC' => 'N', # Asparagine | ||
| 'AAT' => 'N', # Asparagine | ||
| 'AAA' => 'K', # Lysine | ||
| 'AAG' => 'K', # Lysine | ||
| 'AGC' => 'S', # Serine | ||
| 'AGT' => 'S', # Serine | ||
| 'AGA' => 'R', # Arginine | ||
| 'AGG' => 'R', # Arginine | ||
| 'GTA' => 'V', # Valine | ||
| 'GTC' => 'V', # Valine | ||
| 'GTG' => 'V', # Valine | ||
| 'GTT' => 'V', # Valine | ||
| 'GCA' => 'A', # Alanine | ||
| 'GCC' => 'A', # Alanine | ||
| 'GCG' => 'A', # Alanine | ||
| 'GCT' => 'A', # Alanine | ||
| 'GAC' => 'D', # Aspartic Acid | ||
| 'GAT' => 'D', # Aspartic Acid | ||
| 'GAA' => 'E', # Glutamic Acid | ||
| 'GAG' => 'E', # Glutamic Acid | ||
| 'GGA' => 'G', # Glycine | ||
| 'GGC' => 'G', # Glycine | ||
| 'GGG' => 'G', # Glycine | ||
| 'GGT' => 'G', # Glycine | ||
| ); | ||
|
|
||
| # read in the input | ||
| open FP1, $ARGV[0] ; | ||
| my $totalCnt = 0 ; | ||
| while ( <FP1> ) | ||
| { | ||
| chomp ; | ||
| my @cols = split ; | ||
| my $key = join( "\t", ( $cols[2], $cols[3], $cols[4], $cols[7] ) ) ; | ||
| if ( defined $cdr3{ $key } ) | ||
| { | ||
| my $val = \@{ $cdr3{ $key } } ; | ||
| $val->[0] = $cols[8] if ( $cols[8] > $val->[0] ) ; | ||
| $val->[1] += $cols[9] ; | ||
| } | ||
| else | ||
| { | ||
| @{ $cdr3{ $key } } = ( $cols[8], $cols[9] ) ; | ||
| } | ||
| $totalCnt += $cols[9] ; | ||
| } | ||
| close FP1 ; | ||
|
|
||
| # Output what we collected. | ||
| print( "#count\tfrequency\tCDR3nt\tCDR3aa\tV\tD\tJ\tC\n" ) ; | ||
| foreach my $key ( sort { $cdr3{$b}[1] <=> $cdr3{$a}[1] } keys %cdr3 ) | ||
| { | ||
| my @val = @{ $cdr3{ $key } } ; | ||
| my @info = split /\t/, $key ; | ||
| my $aa = "" ; | ||
| if ( $val[0] == 0 ) | ||
| { | ||
| $aa = "partial" ; | ||
| } | ||
| else | ||
| { | ||
| if ( length( $info[3] ) % 3 != 0 ) | ||
| { | ||
| $aa = "Out_of_frame" ; | ||
| } | ||
| else | ||
| { | ||
| my $len = length( $info[3] ) ; | ||
| my $s = uc( $info[3] ) ; | ||
| for ( my $i = 0 ; $i < $len ; $i += 3 ) | ||
| { | ||
| if ( !defined $DnaToAa{ substr( $s, $i, 3 ) } ) | ||
| { | ||
| $aa = "?" ; | ||
| } | ||
| else | ||
| { | ||
| $aa .= $DnaToAa{ substr( $s, $i, 3 ) } ; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| printf( "%.2f\t%e\t%s\t%s\t%s\t*\t%s\t%s\n", $val[1], $val[1] / $totalCnt, $info[3], $aa, $info[0], $info[1], $info[2] ) ; | ||
| } |