Under the assumption that the strings you are looking for are always the values of the /locus_tag, it is better to load the values you are searching for into a hash to use the exists function in addition to a regex. So you could loop over your second file, extract the value of the /locus_tag and if it exists in the hash, print the next line.

use strict;
use warnings;

my %hashOfVals;
open(my $tmp, "<", "NC_001903.gbk.txt") || die "Could not open $!";
undef @hashOfVals{map {chomp; $_} <$tmp>};
close($tmp);

open(my $tmpFile, "<", "cp26_diffexpr.txt") || die "Could not open $!"
+;
my @arrayFromCSV = <$tmpFile>;
chomp @arrayFromCSV;
close($tmpFile);

for (0..$#arrayFromCSV-1) {
    print "$1: $arrayFromCSV[$_+1]\n" 
        if $arrayFromCSV[$_] =~ /locus_tag="(.*)"/ and exists $hashOfV
+als{$1};
}
[download]

Thanks for the reply! The code compiled and ran, but produced no output. I ran into the same problem with the C-style for loops (deleted now from the code, copied and pasted below). I wasn't completely sure if my problem was a regex issue, a problem in the implementation, or something simple I missed?

for (my $j=0; $j<$#arrayFromCSV; $j++) {
    for (my $i=0; $i<$#wkArray; $i++) {
        if ("$arrayFromCSV[$j]" =~ /$wkArray[$i]/g) {
            print "$wkArray[$i+1]\n";
             }
        }
    }
[download]

As it is, your code assumes that the two input files have matching elements in matching order. Do you know that the two files are already sorted in the same way, and actually have matching contents?

It looks like you tried to include sample data in your post. Please edit that to put "code" tags around the data. In fact, you could include an adequate sample of data as part of your posted code, like this:

(start with a <code> tag, of course, or just <c>)
# your sample code
# goes here… (but please just include what you're actually using)

# when it's time to read the sample data in your code, do this:
while (<DATA>) {
    # do stuff with the sample data
}

# more code… enough to exit cleanly with coherent output…

__DATA__
your sample data
goes here…
(don't forget the closing "code" tag…)
[download]

Thanks! Sorry the data files weren't formatted better, I'll fix that now. The first file is essentially a list of strings, and the second is a list of line-by-line strings.

Ok, I got it to work (many thank again to hdb, Kenosis, and graff). I found a format from the NCBI called a GFF file worked much better for parsing. However, I couldn't get the suggested hash function to work, so my updated question is how would I get this to work using a hash instead and more resemble a Perl script than a cobbled Perl/C/something construct? As it stands, it functions, but it's inefficient and not elegant. (Truncated) Sample files also attached. EDIT: I made one more modification, I finally got the hang of using a hash.

##gff-version 3
#!gff-spec-version 1.20
#!processor NCBI annotwriter
##sequence-region NC_001903.1 1 26498
##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2
+24326
NC_001903.1    RefSeq    region    1    26498    .    +    .    ID=id0
+;Name=cp26;Dbxref=taxon:224326;Is_circular=true;gbkey=Src;genome=plas
+mid;mol_type=genomic DNA;plasmid-name=cp26;strain=B31
NC_001903.1    RefSeq    gene    46    324    .    +    .    ID=gene0;
+Name=BB_B01;Dbxref=GeneID:1194411;gbkey=Gene;locus_tag=BB_B01
NC_001903.1    RefSeq    CDS    46    324    .    +    0    ID=cds0;Na
+me=NP_046987.2;Parent=gene0;Note=catalyzes the hydrolysis of acylphos
+phate;Dbxref=Genbank:NP_046987.2,GeneID:1194411;gbkey=CDS;product=acy
+lphosphatase;protein_id=NP_046987.2;transl_table=11
NC_001903.1    RefSeq    gene    308    751    .    -    .    ID=gene1
+;Name=BB_B02;Dbxref=GeneID:1194420;gbkey=Gene;locus_tag=BB_B02
NC_001903.1    RefSeq    CDS    308    751    .    -    0    ID=cds1;N
+ame=NP_046988.1;Parent=gene1;Note=hypothetical protein%3B identified 
+by Glimmer%3B putative;Dbxref=Genbank:NP_046988.1,GeneID:1194420;gbke
+y=CDS;product=hypothetical protein;protein_id=NP_046988.1;transl_tabl
+e=11
NC_001903.1    RefSeq    gene    837    2186    .    -    .    ID=gene
+2;Name=BB_B03;Dbxref=GeneID:1194419;gbkey=Gene;locus_tag=BB_B03
NC_001903.1    RefSeq    CDS    837    2186    .    -    0    ID=cds2;
+Name=NP_046989.1;Parent=gene2;Note=hypothetical protein%3B identified
+ by Glimmer%3B putative;Dbxref=Genbank:NP_046989.1,GeneID:1194419;gbk
+ey=CDS;product=hypothetical protein;protein_id=NP_046989.1;transl_tab
+le=11
NC_001903.1    RefSeq    gene    2476    3798    .    -    .    ID=gen
+e3;Name=BB_B04;Dbxref=GeneID:1194410;gbkey=Gene;locus_tag=BB_B04
NC_001903.1    RefSeq    CDS    2476    3798    .    -    0    ID=cds3
+;Name=NP_046990.2;Parent=gene3;Note=similar to GB:U07818 PID:466474 S
+P:Q45400 percent identity: 36.93%3B identified by sequence similarity
+%3B putative;Dbxref=Genbank:NP_046990.2,GeneID:1194410;gbkey=CDS;prod
+uct=chitibiose transporter protein ChbC;protein_id=NP_046990.2;transl
+_table=11
NC_001903.1    RefSeq    gene    4084    4431    .    +    .    ID=gen
+e4;Name=BB_B05;Dbxref=GeneID:1194409;gbkey=Gene;locus_tag=BB_B05
NC_001903.1    RefSeq    CDS    4084    4431    .    +    0    ID=cds4
+;Name=NP_046991.1;Parent=gene4;Note=similar to SP:P46319 PID:895750 P
+ID:1783268 GB:AL009126 percent identity: 27.62%3B identified by seque
+nce similarity%3B putative;Dbxref=Genbank:NP_046991.1,GeneID:1194409;
+gbkey=CDS;product=chitibiose transporter protein ChbA;protein_id=NP_0
+46991.1;transl_table=11
NC_001903.1    RefSeq    gene    4482    4757    .    +    .    ID=gen
+e5;Name=BB_B06;Dbxref=GeneID:1194408;gbkey=Gene;locus_tag=BB_B06
NC_001903.1    RefSeq    CDS    4482    4757    .    +    0    ID=cds5
+;Name=NP_046992.2;Parent=gene5;Note=similar to SP:P46318 PID:895748 P
+ID:1783266 GB:AL009126 percent identity: 46.32%3B identified by seque
+nce similarity%3B putative;Dbxref=Genbank:NP_046992.2,GeneID:1194408;
+gbkey=CDS;product=chitibiose transporter protein ChbB;protein_id=NP_0
+46992.2;transl_table=11
NC_001903.1    RefSeq    gene    4769    5866    .    +    .    ID=gen
+e6;Name=BB_B07;Dbxref=GeneID:1194407;gbkey=Gene;locus_tag=BB_B07
NC_001903.1    RefSeq    CDS    4769    5866    .    +    0    ID=cds6
+;Name=NP_046993.1;Parent=gene6;Note=similar to GB:M88764 SP:Q09090 PI
+D:469166 PID:1199570 percent identity: 21.29%3B identified by sequenc
+e similarity%3B putative;Dbxref=Genbank:NP_046993.1,GeneID:1194407;gb
+key=CDS;product=alpha3-beta1 integrin-binding protein;protein_id=NP_0
+46993.1;transl_table=11
NC_001903.1    RefSeq    gene    5888    6517    .    -    .    ID=gen
+e7;Name=BB_B08;Dbxref=GeneID:1194418;gbkey=Gene;locus_tag=BB_B08;pseu
+do=true
NC_001903.1    RefSeq    gene    6677    7714    .    +    .    ID=gen
+e8;Name=BB_B09;Dbxref=GeneID:1194417;gbkey=Gene;locus_tag=BB_B09
NC_001903.1    RefSeq    CDS    6677    7714    .    +    0    ID=cds7
+;Name=NP_046995.1;Parent=gene8;Note=hypothetical protein%3B identifie
+d by Glimmer%3B putative;Dbxref=Genbank:NP_046995.1,GeneID:1194417;gb
+key=CDS;product=hypothetical protein;protein_id=NP_046995.1;transl_ta
+ble=11
NC_001903.1    RefSeq    gene    7836    8765    .    +    .    ID=gen
+e9;Name=BB_B10;Dbxref=GeneID:1194406;gbkey=Gene;locus_tag=BB_B10
NC_001903.1    RefSeq    CDS    7836    8765    .    +    0    ID=cds8
+;Name=NP_046996.1;Parent=gene9;Note=similar to GP:1655797 percent ide
+ntity: 33.68%3B identified by sequence similarity%3B putative;Dbxref=
+Genbank:NP_046996.1,GeneID:1194406;gbkey=CDS;product=hypothetical pro
+tein;protein_id=NP_046996.1;transl_table=11
NC_001903.1    RefSeq    gene    8781    9299    .    +    .    ID=gen
+e10;Name=BB_B11;Dbxref=GeneID:1194405;gbkey=Gene;locus_tag=BB_B11;pse
+udo=true
NC_001903.1    RefSeq    gene    9275    10036    .    +    .    ID=ge
+ne11;Name=BB_B12;Dbxref=GeneID:1194404;gbkey=Gene;locus_tag=BB_B12
NC_001903.1    RefSeq    CDS    9275    10036    .    +    0    ID=cds
+9;Name=NP_046998.1;Parent=gene11;Note=similar to GP:2182756 percent i
+dentity: 46.00%3B identified by sequence similarity%3B putative;Dbxre
+f=Genbank:NP_046998.1,GeneID:1194404;gbkey=CDS;product=hypothetical p
+rotein;protein_id=NP_046998.1;transl_table=11
NC_001903.1    RefSeq    gene    10104    10652    .    +    .    ID=g
+ene12;Name=BB_B13;Dbxref=GeneID:1194403;gbkey=Gene;locus_tag=BB_B13
NC_001903.1    RefSeq    CDS    10104    10652    .    +    0    ID=cd
+s10;Name=NP_046999.1;Parent=gene12;Note=similar to GB:U03641 PID:4582
+18 percent identity: 42.59%3B identified by sequence similarity%3B pu
+tative;Dbxref=Genbank:NP_046999.1,GeneID:1194403;gbkey=CDS;product=hy
+pothetical protein;protein_id=NP_046999.1;transl_table=11
NC_001903.1    RefSeq    gene    10920    11417    .    -    .    ID=g
+ene13;Name=BB_B14;Dbxref=GeneID:1194402;gbkey=Gene;locus_tag=BB_B14
[download]

BB_B10
BB_B29
BB_B18
BB_B13
BB_B14
BB_B12
BB_B04
BB_B16
BB_B22
BB_B17
BB_B27
BB_B19
BB_B07
BB_B23
BB_B09
BB_B02
BB_B28
BB_B24
BB_B03
BB_B05
BB_B06
[download]

 
#!/usr/bin/perl -w
use Data::Dumper;

my @arrayOfVals;
open(my $tmp, "<", "/Users/bioinformatics/Desktop/NC_001903.gff.txt") 
+|| die "Could not open $!";

LINE: while (<$tmp>) {
    chomp;
    next LINE if /^#/; # discard header, unneeded and will interfere
    push(@arrayOfVals, $_);
}
close($tmp);
# input each line as an array

my @tmpArray;
open (my $arrVal, "<", "/Users/bioinformatics/Desktop/cp26_dff.txt") |
+| die "Could not open $!";
while (<$arrVal>) {
    chomp;
    push(@tmpArray, $_);
}
close($arrVal);
# same as above, each line of file is match string in array

my @tmpDictKeyArray;
my @tmpDictValueArray;

for (my $k=0; $k<$#arrayOfVals; $k++) {
    $gffCompare = $arrayOfVals[$k];
    $gffDescription = $arrayOfVals[$k+1];
    # rationale: $gffCompare is the compare String, 
    # and the information I need will always follow one entry after in
+ the array
    # if match is TRUE, then entry+1 will display the information
    for (my $j=0; $j<$#tmpArray; $j++) {
        $tmpArrayVal = $tmpArray[$j];
        if ($gffCompare =~ /$tmpArrayVal/) {
            if ($gffCompare =~ /.*;locus_tag=(.*)/) {
                push(@tmpDictKeyArray, $1);
                # Assign to array for hash
                } 
            if ($gffDescription =~ /.*;Name=(.*);protein_/) {
                push(@tmpDictValueArray, $1);
                # see above
                
            }
        }
    }
}

my %hashArray;
@hashArray{@tmpDictKeyArray} = @tmpDictValueArray;

print Dumper(\%hashArray);
[download]

Here is a version which may help. You do not need the next LINE bit, and the C-style loop hides a bug - you never test for the last item in @tmpArray (BB_B06).

my @arrayOfVals;
open(my $tmp, "<", "/Users/bioinformatics/Desktop/NC_001903.gff.txt") 
+or die "Could not open $!";
while (<$tmp>) {
    chomp;
    next if /^#/; # discard header, unneeded and will interfere
    push(@arrayOfVals, $_);
}
close($tmp);

my %hashOfKeys;
open (my $arrVal, "<", "/Users/bioinformatics/Desktop/cp26_dff.txt") o
+r die "Could not open $!";
while (<$arrVal>) {
    chomp;
    $hashOfKeys{$_} = 1;
}
close($arrVal);

my %hash;

for my $k (0 .. $#arrayOfVals -1) {
    if ($arrayOfVals[$k] =~ /.*;locus_tag=(.*)/) {
        next unless $hashOfKeys{$1};
        my $key = $1;
        if ($arrayOfVals[$k+1] =~ /.*;Name=(.*);protein_/) {
            $hash{$key} = $1;
        }
    }
}
print Dumper(\%hash);
[download]

It's evident that you're attempting to search a GenBank file. What, specifically, are you trying to find in that file, i.e., in which GenBank field?

Thanks for the reply! I have a list (technically a spreadsheet that I made a list) of bacterial genes from an RNASeq sequencing run. I've isolated a sublist of strings that correspond to gene names that I am interested in investigating further, but I need to get information on them from the GenBank file, nothing too elaborate, basically Gene Name, GeneBank ID or GeneID, and a brief description. Initially I set up a simple script to type in the name to search (see the commented out STDIN section), which matched the pattern to the string in the GeneBank file-I just copied and pasted the lines I needed-but when I realized there were way too many for this to be feasible, I tried the current approach of inputing the list of genes from the RNASeq run as search patterns to match.