Question

I use this same bit of code with different files a couple times through-out the program without problems:

#if the info is part of a file
if($proteinIn =~  m/\.txt$/i){
    my $input_file = catfile('..', dataset => $proteinIn);

    open my $protein_file, '<', $input_file
        or die "couldn't open '$input_file': $!";
    while (my $protLine = <$protein_file>) {
        print $protLine."\n";
        $protLine =~ s/\s+\z//; # remove all trailing space
        $protein{$protLine} = 1;
    }
    close $protein_file;
}

When reading in a file containing this

Q5KDZ7_CRYNJ
Q2U9C0_ASPOR
Q2U048_ASPOR
G2Q3M9_THIHA
G2QAZ2_THIHA

the print statement “print $protLine.”\n”;” only prints the last line. In this case:

G2QAZ2_THIHA

the other example of this in my program reads every line of the files given

foreach my $tempFile(@fileList){
    my $input_file = catfile('..', dataset => $tempFile);

    open my $ps_file, '<', $input_file
        or die "couldn't open '$input_file': $!";
    while (my $line = <$ps_file>) {
        $line =~ s/\s+\z//; # remove all trailing space

        my @curLine = split /\t/, $line;
<the rest of the program>

The files opened by this code contain lines like:

>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1 MAFSAEDVLKEYDRRRRMEALLLSLYYPNDRKLLDYKEWSPPRVQVECPKAPVEWNNPPSEKGLIVGHFSGIKYKGEKAQASEVDVNKMCCWVSKFKDAMRRYQGIQTCKIPGKVLSDLDAKIKAYNLTVEGVEGFVRYSRVTKQHVAAFLKELRHSKQYENVNLIHYILTDKRVDIQHLEKDLVKDFKALVESAHRMRQGHMINVKYILYQLLKKHGHGPDGPDILTVKTGSKGVLYDDSFRKIYTDLGWKFTPL    FRG3G

Why is the first example of the code only printing the last line of the file?

Edit: Response to comment that problem is upstream in code; luckily my problem is near the beginning so here is everything before the problem code

When running the code, I used the command “perl regProt.pl “” “truePool.txt” “uniprot_sprot.dat” “fungi”

#!/usr/bin/env perl
use strict;
use File::Spec::Functions qw( catfile );

#use warnings;
#@author David Dziak

#A program for quick regex functions on uniprot data to test protein signatures
#my $max = 325783;
#my $cur = 0;
my $annotation;
my $fingerprint = $ARGV[0];
unless($fingerprint){
    $fingerprint = "[GASRK][KRVSG][RKVI][KRVI]x[ASCR]x[AST]x(0,45)[GATF]xxx[VLI]N[GKND]x(11,12)[RKL]x(16,18)[NDA]x(6)[GS]GGx(10)[AG][LIVM][GAS][KR][GASN][VLI]";#prosite s9

    #$fingerprint = "[GS]Gx(2)[GSA][QK]x(2)[SA]x(3)[GSA]x[GSTAV][KR][GSALVD][LIFV]";#prosite s9
    #$fingerprint = "[STDNQ]G[KRNQMHSI]x(6)[LIVM]x(4)[LIVMC][GSD]x(2)[LFI][GAS][DE][FYM]x(2)[ST]";#prosite s19
    #$fingerprint = "[RKHN][KSTR]X(3)[AVSCR]X(6)GXGX(0,23)X(25)GGGX(2)[GAS][QRKS]X(0,50)X(20)[APS]RX(5)[VSTA]XR";#s9
    #$fingerprint = "[GAR][RKHG][RKHNT][KSTR]X(3)[AVSCR][RASTHKQLP]X(5)[GPSTND]X[GPSTKDQ]X(4)[NDVGIT]X(0,60)G[GS]GX(2)[GSA][QRS]X(0,70)[QTRA][FWYETK][STAVH][KY][RK]";#s9
    #$fingerprint = "[RGWCKT]X(5)PX(3)[GARDENS]X(4)[VIL][HYF]XGX(7)[LIVMP]X(7)x[LFI][GASR][DEA][FYME]";#s19
}
$annotation .= $fingerprint;
#protein name to search
my $proteinIn = $ARGV[1];
my %protein;
#if the info is part of a file
if($proteinIn =~  m/\.txt$/i){
    my $input_file = catfile('..', dataset => $proteinIn);

Answer 1

I’m betting that your file for some reason has lines separated by \r, not \n.

Try putting at the top:

use Data::Dumper;
$Data::Dumper::Useqq=1;

and replacing the print with:

print Data::Dumper::Dumper($protLine);