Hello! I have a problem (repeated in comments). I have a search string $mystring that I am searching for a matching string against a NCBI text file, nothing complicated, basic regex. The only slight modification is when I find a match, I need the string immediately following the match, not the match itself. The problem is I'm stuck. I've narrowed it down to maybe a regex issue? But basically, the files, basic text files, load, but the input from the search pattern (it's in the code as a CSV because initially I set it as such but got fed up fighting with Text::CSV so I just used text instead) doesn't seem to recognize each line of the array as a string. When I do an if loop to debug, Perl doesn't seem to recognize search patterns as strings. Below are sample text copied and pasted. I'd greatly appreciate any help! Thanks and Happy Mardi Gras!! 


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]
                     /locus_tag="BB_B01"
                     /db_xref="GeneID:1194411"
     CDS             46..324
                     /locus_tag="BB_B01"
                     /note="catalyzes the hydrolysis of acylphosphate"
                     /codon_start=1
                     /transl_table=11
                     /product="acylphosphatase"
                     /protein_id="NP_046987.2"
                     /db_xref="GI:364556794"
                     /db_xref="GeneID:1194411"
                     /translation="MYKQQYFISGKVQGVGFRFFTEQIANNMKLKGFVK
+NLNDGRVEI
                     VAFFNTKEQMKKFEKLLNGNKYSNIKNIEKIVLDENYPFQFNDFKIYY"
     misc_feature    46..321
                     /locus_tag="BB_B01"
                     /note="acylphosphatase; Provisional; Region: PRK1
+4432"
                     /db_xref="CDD:184678"
     gene            complement  308..751  
                     /locus_tag="BB_B02"
                     /db_xref="GeneID:1194420"
     CDS             complement  308..751  
                     /locus_tag="BB_B02"
                     /note="hypothetical protein; identified by Glimme
+r;
                     putative"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="NP_046988.1"
                     /db_xref="GI:11497029"
                     /db_xref="GeneID:1194420"
                     /translation="MKIGPHYFFKKILKSNDNRTIYISYLYDRLASVKP
+AGEWLRIYF
                     KDSKRGKKYFILFNRNSSNGSFISCSFLKTSCNCGLDIKFSDGNLNIFC
+RNRKSLEFL
                     KFKVEHFFRTSVSCYKNNNSYVHNIKPKNKVKVLVKREASPNNKF"
     gene            complement  837..2186  
                     /locus_tag="BB_B03"
                     /db_xref="GeneID:1194419"
     CDS             complement  837..2186  
                     /locus_tag="BB_B03"
                     /note="hypothetical protein; identified by Glimme
+r;
                     putative"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="NP_046989.1"
                     /db_xref="GI:11497028"
                     /db_xref="GeneID:1194419"
                     /translation="MPPKVKIKNDFEIFRKELEILYKKYLNNELSYLKL
+KEKLKILAE
                     NHKAILFRKDKFTNRSIILNLSKTRKIIKEYINLSVIERIRRDNTFLFF
+WKSRRIKEL
                     KNIGIKDRKKIEELIFSNQMNDEKSYFQYFIDLFVTPKWLNDYAHKYKI
+EKINSYRKE
                     QIFVKINLNTYIEIIKLLLNQSRDIRLKFYGVLMAIGRRPVEVMKLSQF
+YIADKNHIR
                     MEFIAKKRENNIVNEVVFPVFADPELIINSIKEIRYMEQTENLTKEIIS
+SNLAYSYNR
                     LFRQIFNNIFAPEESVYFCRAIYCKFSYLAFAPKNMEMNYWITKVLGHE
+PNDITTAFH
                     YNRYVLDNLDDKADNSLLTLLNQRIYTYVRRKATYSTLTMDRLESLIKE
+HHIFDDNYI
                     KTLIVIKNLMLKDNLETLAMVRGLNVKIRKAFKATYGYNYNYIKLTEYL
+SIIFNYKL"
     gene            complement  2476..3798  
                     /locus_tag="BB_B04"
                     /db_xref="GeneID:1194410"
     CDS             complement  2476..3798  
                     /locus_tag="BB_B04"

[download]
 
#!/usr/bin/perl -w
use Text::CSV;

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

while (<$tmp>) {
    chomp;
    push(@arrayOfVals, $_);
}
close($tmp);

my @arrayFromCSV;
open(my $tmpFile, "<", "/Users/bioinformatics/Desktop/cp26_diffexpr.tx
+t") || die "Could not open $!";

while (<$tmpFile>) {
    chomp;
    push(@arrayFromCSV, $_);
}
close($tmpFile);

foreach(@arrayFromCSV) {
    if ($_ eq "BB_B10") {
        print "MAtch!!\n";
    } else {print "$_\n";}
}

my @wkArray = @arrayOfVals;
my @secArrayFromCSV = @arrayFromCSV;


 while (my $matchCheck = shift @wkArray) {            
        $csvVal = shift(@secArrayFromCSV);
        if ( $csvVal =~ /$matchCheck/) {
            my $geneValue = shift(@wkArray);
             print "$geneValue\n";
        } else {
            print "no match";
            }
}

[download]

In reply to Need Help with Maybe a Regex Issue by sharkbait

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