Re: sequence composition

[Shawn H Corey]

On 10-12-01 02:58 PM, Mariano Loza Coll wrote:

gi|61499|emb|CAA24495.1| src [Avian sarcoma virus]

MGSSKSKPKDPSQRRRSLEPPDSTHHGGFPASQTPNKTAAPDTHRTPSRSFGTVATEPKLFGGFNTSDTV
TSPQRAGALAGGVTTFVALYDYESWIETDLSFKKGERLQIVNNTEGNWWLAHSLTTGQTGYIPSNYVAPS
DSIQAEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSG
GFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGE
VWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVIEYMSKGSLLDFL
KGEMGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQ
GAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMGNGEVLDRVERGYRMPCPPECPES
LHDLMCQCWRRDPEERPTFEYLQAQLLPACVLEVAE

Try:

#!/usr/bin/perl

use strict;
use warnings;

my %counts_of = ();
my $total = 0;

while( <DATA> ){
  next if m{ \A \> }msx;
  chomp;
  for my $aminoacid ( split //, $_ ){
    $counts_of{$aminoacid} ++;
    $total ++;
  }
}

for my $aminoacid ( sort keys %counts_of ){
  printf "%3s %7.2f\n", $aminoacid, $counts_of{$aminoacid} / $total * 100;
}

__DATA__
> gi|61499|emb|CAA24495.1| src [Avian sarcoma virus]
MGSSKSKPKDPSQRRRSLEPPDSTHHGGFPASQTPNKTAAPDTHRTPSRSFGTVATEPKLFGGFNTSDTV
TSPQRAGALAGGVTTFVALYDYESWIETDLSFKKGERLQIVNNTEGNWWLAHSLTTGQTGYIPSNYVAPS
DSIQAEEWYFGKITRRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSG
GFYITSRTQFSSLQQLVAYYSKHADGLCHRLTNVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGE
VWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVIEYMSKGSLLDFL
KGEMGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQ
GAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMGNGEVLDRVERGYRMPCPPECPES
LHDLMCQCWRRDPEERPTFEYLQAQLLPACVLEVAE



--
Just my 0.00000002 million dollars worth,
  Shawn

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as it is about coding.

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