Re^2: remove part of string (DNA)

[Generoso]

Some minor improvements.

#!/usr/bin/perl
#
use strict;
use warnings;
# forward (F) barcodes

my @forward = ("AGCCTAAGCT",
               "TCAAGTTAGC",
               "AGCCTGGCAT",
               "ACGGTCCATG",
               "ACTTGCCGAT",
               "ACGGTGGATC",
               "ATCCGCCTAG",
               "ATGGCGGTAC");

# reverse (R) barcodes

my @reverse = ("AGCTTAGGCT",
               "TAGCCTAAGC",
               "AGCTTGCCAT",
               "ACGTTCAATG",
               "ACTGGCGGAT",
               "ACGTTGAATC",
               "ATCGGCAAGT",
               "ATGCCGTTAC");

my @dnsstr1 = ();
my $fr= 0;
# read first header
$dnsstr1[0] = <DATA>;
foreach my $line(<DATA>) { 
#read rest of lines in the dan sequece
if ($line =~ /^>/) { 
# it is not a foward or a revers itentify as other
    print "Other\n" if $fr == 0;
    print @dnsstr1,"\n";
    @dnsstr1 = ();
    $fr = 0;
    push @dnsstr1,$line;
    }
else {push @dnsstr1,$line;
#check if it is a forward
    foreach my $f (@forward){
    if ($line =~  $f) { $fr =1; print "Forward\n";}}
#check if it is a reverse
    foreach my $f (@reverse){
    if ($line =~  $f) { $fr =2; print "Reverse\n";}}
}
} 
# print last dns string
print "Other\n" if $fr == 0;
print @dnsstr1,"\n";

__DATA__
>HSBGPG Human gene for bone gla protein (BGP)
GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAG
+AGGGT
AGCTTAGGCTCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAG
+ACACC
ATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGT
+GCCCC
CACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCC
+CTTTG
GCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGC
+AGAGG
GAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGG
+TGAAC
CAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGAT
+GGACC
TGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCT
+GTCTG
GCCATCAGGAAGGCCAGCCTGCTCCCCACCTGATCCTCCCAAACCCAGAGCCACCTGATGCCTGCCCCTC
+TGCTC
CACAGCCTTTGTGTCCAAGCAGGAGGGCAGCGAGGTAGTGAAGAGACCCAGGCGCTACCTGTATCAATGG
+CTGGG
GTGAGAGAAAAGGCAGAGCTGGGCCAAGGCCCTGCCTCTCCGGGATGGTCTGTGGGGGAGCTGCAGCAGG
+GAGTG
GCCTCTCTGGGTTGTGGTGGGGGTACAGGCAGCCTGCCCTGGTGGGCACCCTGGAGCCCCATGTGTAGGG
+AGAGG
AGGGATGGGCATTTTGCACGGGGGCTGATGCCACCACGTCGGGTGTCTCAGAGCCCCAGTCCCCTACCCG
+GATCC
CCTGGAGCCCAGGAGGGAGGTGTGTGAGCTCAATCCGGACTGTGACGAGTTGGCTGACCACATCGGCTTT
+CAGGA
GGCCTATCGGCGCTTCTACGGCCCGGTCTAGGGTGTCGCTCTGCTGGCCTGGCCGGCAACCCCAGTTCTG
+CTCCT
CTCCAGGCACCCTTCTTTCCTCTTCCCCTTGCCCTTGCCCTGACCTCCCAGCCCTATGGATGTGGGGTCC
+CCATC
ATCCCAGCTGCTCCCAAATAAACTCCAGAAG
>HSGLTH1 Human theta 1-globin gene
CCACTGCACTCACCGCACCCGGCCAATTTTTGTGTTTTTAGTAGAGACTAAATACCATATAGTGAACACC
+TAAGA
CGGGGGGCCTTGGATCCAGGGCGATTCAGAGGGCCCCGGTCGGAGCTGTCGGAGATTGAGCGCGCGCGGT
+CCCGG
GATCTCCGACGAGGCCCTGGACCCCCGGGCGGCGAAGCTGCGGCGCGGCGCCCCCTGGAGGCCGCGGGAC
+CCCTG
GCCGGTCCGCGCAGGCGCAGCGGGGTCGCAGGGCGCGGCGGGTTCCAGCGCGGGGATGGCGCTGTCCGCG
+GAGGA
CCGGGCGCTGGTGCGCGCCCTGTGGAAGAAGCTGGGCAGCAACGTCGGCGTCTACACGACAGAGGCCCTG
+GAAAG
GTGCGGCAGGCTGGGCGCCCCCGCCCCCAGGGGCCCTCCCTCCCCAAGCCCCCCGGACGCGCCTCACCCA
+CGTTC
CTCTCGCAGGACCTTCCTGGCTTTCCCCGCCACGAAGACCTACTTCTCCCACCTGGACCTGAGCCCCGGC
+TCCTC
ACAAGTCAGAGCCCACGGCCAGAAGGTGGCGGACGCGCTGAGCCTCGCCGTGGAGCGCCTGGACGACCTA
+CCCCA
CGCGCTGTCCGCGCTGAGCCACCTGCACGCGTGCCAGCTGCGAGTGGACCCGGCCAGCTTCCAGGTGAGC
+GGCTG
CCGTGCTGGGCCCCTGTCCCCGGGAGGGCCCCGGCGGGGTGGGTGCGGGGGGCGTGCGGGGCGGGTGCAG
+GCGAG
TGAGCCTTGAGCGCTCGCCGCAGCTCCTGGGCCACTGCCTGCTGGTAACCCTCGCCCGGCACTACCCCGG
+AGACT
TCAGCCCCGCGCTGCAGGCGTCGCTGGACAAGTTCCTGAGCCACGTTATCTCGGCGCTGGTTTCCGAGTA
+CCGCT
GAACTGTGGGTGGGTGGCCGCGGGATCCCCAGGCGACCTTCCCCGTGTTTGAGTAAAGCCTCTCCCAGGA
+GCAGC
CTTCTTGCCGTGCTCTCTCGAGGTCAGGACGCGAGAGGAAGGCGC
>seq1
AGCCTAAGCTASTPGHTIIYEAVCLHNDRTTIP
>seq2 optional comment
ASQKRPSQRHGSKYLATASTMDHARHGFLPRHRDTGILDSIGRFFGGDRGAPK
NMYKDSHHPARTAHYGSLPQKSHGRTQDENPVVHFFKNIVTPRTPPPSQGKGR
KSAHKGFKGVDAQGTLSKIFKLGGRDSRSGSPMARRELVISLIVES

Results

perl "D:\Citi Midleware\db\perl\perl5data.pl" stocks 10 5
Process started >>>
Reverse
>HSBGPG Human gene for bone gla protein (BGP)
GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAG
+AGGGT
AGCTTAGGCTCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAG
+ACACC
ATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGT
+GCCCC
CACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCC
+CTTTG
GCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGC
+AGAGG
GAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGG
+TGAAC
CAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGAT
+GGACC
TGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCT
+GTCTG
GCCATCAGGAAGGCCAGCCTGCTCCCCACCTGATCCTCCCAAACCCAGAGCCACCTGATGCCTGCCCCTC
+TGCTC
CACAGCCTTTGTGTCCAAGCAGGAGGGCAGCGAGGTAGTGAAGAGACCCAGGCGCTACCTGTATCAATGG
+CTGGG
GTGAGAGAAAAGGCAGAGCTGGGCCAAGGCCCTGCCTCTCCGGGATGGTCTGTGGGGGAGCTGCAGCAGG
+GAGTG
GCCTCTCTGGGTTGTGGTGGGGGTACAGGCAGCCTGCCCTGGTGGGCACCCTGGAGCCCCATGTGTAGGG
+AGAGG
AGGGATGGGCATTTTGCACGGGGGCTGATGCCACCACGTCGGGTGTCTCAGAGCCCCAGTCCCCTACCCG
+GATCC
CCTGGAGCCCAGGAGGGAGGTGTGTGAGCTCAATCCGGACTGTGACGAGTTGGCTGACCACATCGGCTTT
+CAGGA
GGCCTATCGGCGCTTCTACGGCCCGGTCTAGGGTGTCGCTCTGCTGGCCTGGCCGGCAACCCCAGTTCTG
+CTCCT
CTCCAGGCACCCTTCTTTCCTCTTCCCCTTGCCCTTGCCCTGACCTCCCAGCCCTATGGATGTGGGGTCC
+CCATC
ATCCCAGCTGCTCCCAAATAAACTCCAGAAG

Other
>HSGLTH1 Human theta 1-globin gene
CCACTGCACTCACCGCACCCGGCCAATTTTTGTGTTTTTAGTAGAGACTAAATACCATATAGTGAACACC
+TAAGA
CGGGGGGCCTTGGATCCAGGGCGATTCAGAGGGCCCCGGTCGGAGCTGTCGGAGATTGAGCGCGCGCGGT
+CCCGG
GATCTCCGACGAGGCCCTGGACCCCCGGGCGGCGAAGCTGCGGCGCGGCGCCCCCTGGAGGCCGCGGGAC
+CCCTG
GCCGGTCCGCGCAGGCGCAGCGGGGTCGCAGGGCGCGGCGGGTTCCAGCGCGGGGATGGCGCTGTCCGCG
+GAGGA
CCGGGCGCTGGTGCGCGCCCTGTGGAAGAAGCTGGGCAGCAACGTCGGCGTCTACACGACAGAGGCCCTG
+GAAAG
GTGCGGCAGGCTGGGCGCCCCCGCCCCCAGGGGCCCTCCCTCCCCAAGCCCCCCGGACGCGCCTCACCCA
+CGTTC
CTCTCGCAGGACCTTCCTGGCTTTCCCCGCCACGAAGACCTACTTCTCCCACCTGGACCTGAGCCCCGGC
+TCCTC
ACAAGTCAGAGCCCACGGCCAGAAGGTGGCGGACGCGCTGAGCCTCGCCGTGGAGCGCCTGGACGACCTA
+CCCCA
CGCGCTGTCCGCGCTGAGCCACCTGCACGCGTGCCAGCTGCGAGTGGACCCGGCCAGCTTCCAGGTGAGC
+GGCTG
CCGTGCTGGGCCCCTGTCCCCGGGAGGGCCCCGGCGGGGTGGGTGCGGGGGGCGTGCGGGGCGGGTGCAG
+GCGAG
TGAGCCTTGAGCGCTCGCCGCAGCTCCTGGGCCACTGCCTGCTGGTAACCCTCGCCCGGCACTACCCCGG
+AGACT
TCAGCCCCGCGCTGCAGGCGTCGCTGGACAAGTTCCTGAGCCACGTTATCTCGGCGCTGGTTTCCGAGTA
+CCGCT
GAACTGTGGGTGGGTGGCCGCGGGATCCCCAGGCGACCTTCCCCGTGTTTGAGTAAAGCCTCTCCCAGGA
+GCAGC
CTTCTTGCCGTGCTCTCTCGAGGTCAGGACGCGAGAGGAAGGCGC

Forward
>seq1
AGCCTAAGCTASTPGHTIIYEAVCLHNDRTTIP

OTher
>seq2 optional comment
ASQKRPSQRHGSKYLATASTMDHARHGFLPRHRDTGILDSIGRFFGGDRGAPK
NMYKDSHHPARTAHYGSLPQKSHGRTQDENPVVHFFKNIVTPRTPPPSQGKGR
KSAHKGFKGVDAQGTLSKIFKLGGRDSRSGSPMARRELVISLIVES 


<<< Process finished.
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