Hi,

I'm trying to write a perl script which reads multiple fasta entries from one input file and give me the number of each amino acid for each entry. But for some reason, perl is reading all the contents of the file as one entry and is giving me the total number of each amino acids in the file as a whole. I am attaching my scripts and files below. Please help.

----------------------------------------------------------------------input file------------------------------------------------------------------

>sp|P09153|TFAE_ECOLI Prophage tail fiber assembly protein homolog Tfa
+E OS=Escherichia coli (strain K12) OX=83333 GN=tfaE PE=1 SV=2
MHKAILNSDLIATKAGDVTVYNYDGETREYISTSNEYLAVGVGIPACSCLDAPGTHKAGY
AICRSADFNSWEYVPDHRGETVYSTKTGESKEIKAPGDYPENTTTIAPLSPYDKWDGEKW
VTDTEAQHSAAVDAAEAQRQSLIDAAMASISLIQLKLQAGRKLTQAETTRLNAVLDYIDA
VTATDTSTAPDVIWPELPEA

>sp|P20605|FIC_ECOLI Probable protein adenylyltransferase Fic OS=Esche
+richia coli (strain K12) OX=83333 GN=fic PE=1 SV=1
MSDKFGEGRDPYLYPGLDIMRNRLNIRQQQRLEQAAYEMTALRAATIELGPLVRGLPHLR
TIHRQLYQDIFDWAGQLREVDIYQGDTPFCHFAYIEKEGNALMQDLEEEGYLVGLEKAKF
VERLAHYYCEINVLHPFRVGSGLAQRIFFEQLAIHAGYQLSWQGIEKEAWNQANQSGAMG
DLTALQMIFSKVVSEAGESE

>sp|P0ADH5|FIMB_ECOLI Type 1 fimbriae regulatory protein FimB OS=Esche
+richia coli (strain K12) OX=83333 GN=fimB PE=3 SV=1
MKNKADNKKRNFLTHSEIESLLKAANTGPHAARNYCLTLLCFIHGFRASEICRLRISDID
LKAKCIYIHRLKKGFSTTHPLLNKEVQALKNWLSIRTSYPHAESEWVFLSRKGNPLSRQQ
FYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYTASN
AGRFYGIWDRARGRQRHAVL
[download]

---------------------------------------------------------------------------end of input file-------------------------------------------------------------------------

----------------------------------------------------------------------------------perl script---------------------------------------------------------------

print "This script will count the number of amino acids\n\n";
use strict;
use warnings;

#variables
my $A=0;
my $C=0;
my $D=0;
my $E=0;
my $F=0;
my $G=0;
my $H=0;
my $I=0;
my $K=0;
my $L=0;
my $M=0;
my $N=0;
my $P=0;
my $Q=0;
my $R=0;
my $S=0;
my $T=0;
my $V=0;
my $W=0;
my $Y=0;
my @prot;
my $prot_filename;
my $line;
my $sequence;
my $aa;
open (my $out_file, '>', 'aa_report.txt');

print "PLEASE ENTER THE FILENAME OF THE PROTEIN SEQUENCE: ";
chomp($prot_filename=<STDIN>);

open(PROTFILE,$prot_filename) or die "unable to open the file";
@prot=<PROTFILE>;
close PROTFILE;


foreach $line (@prot) {

# discard blank line
if ($line =~ /^\s*$/) {
next;

# # discard comment line
} elsif($line =~ /^\s*#/) {
next;

# discard fasta header line
} elsif($line =~ /^>/) {
next;

# keep line, add to sequence string
} else {
$sequence .= $line;
}
}

# remove non-sequence data (in this case, whitespace) from $sequence s
+tring
$sequence =~ s/\s//g;
@prot=split("",$sequence); #splits string into an array
print " \nThe original PROTEIN file is:\n$sequence \n";

while(@prot){
$aa = shift (@prot);
if($aa =~/[A]/ig){
$A++;
}
if($aa=~/[C]/ig){
$C++;
}
if($aa=~/[D]/ig){
$D++;
}
if($aa=~/[E]/ig){
$E++;
}
if($aa=~/[F]/ig){
$F++;
}
if($aa=~/[G]/ig){
$G++;
}
if($aa=~/[H]/ig){
$H++;
}
if($aa=~/[I]/ig){
$I++;
}
if($aa=~/[K]/ig){
$K++;
}
if($aa=~/[L]/ig){
$L++;
}
if($aa=~/[M]/ig){
$M++;
}
if($aa=~/[N]/ig){
$N++;
}
if($aa=~/[P]/ig){
$P++;
}
if($aa=~/[Q]/ig){
$Q++;
}
if($aa=~/[R]/ig){
$R++;
}
if($aa=~/[S]/ig){
$S++;
}
if($aa=~/[T]/ig){
$T++;
}
if($aa=~/[V]/ig){
$V++;
}
if($aa=~/[W]/ig){
$W++;
}
if($aa=~/[Y]/ig){
$Y++;
}
}

print "\n";
print $out_file "A=$A C=$C D=$D E=$E F=$F G=$G H=$H I=$I K=$K L=$L M=$
+M N=$N P=$P Q=$Q R=$R S=$S T=$T V=$V W=$W Y=$Y ";
print "\n";
print "done";
[download]

---------------------------------------------------------------end of perl script----------------------------------------------------------------------------

------------------------------------------------------------------------output generated in aa_report.txt------------------------------------------------------------

A=61 C=10 D=31 E=40 F=18 G=41 H=23 I=39 K=28 L=57 M=11 N=24 P=21 Q=27 
+R=37 S=36 T=35 V=23 W=11 Y=27
[download]

-----------------------------------------------------------------------end of output generated in aa_report.txt------------------------------------------------------

I want it to read the three entries in the input file as 3 separate entries and generate separate output for them in the output file. I am guessing it will be a loop or something like that but I'm not sure. Please help.

2019-02-25 Athanasius added code tags