#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

=cut
Open fasta with multiple fasta sequences. Select those sequences
based on an identifier and then reverse complement them.
=cut
# Set record separator
$/ = '>';
#open(my $in, "C:\Documents and Settings\mydir\Desktop\rev_comp\13414_
+fasta");
open(my $out, ">C:/Documents and Settings/mydir/Desktop/rev_comp/13414
+_fasta_rev_comp");


while(<DATA>){
    if(my $line =~m/LacZ|SD/){
        
            next $line;
            my $revcom = reverse $line;
            # Next substitute all bases by their complements,
            # A->T, T->A, G->C, C->G
            $revcom =~ s/A/T/g;
            $revcom =~ s/T/A/g;
            $revcom =~ s/G/C/g;
            $revcom =~ s/C/G/g;
            # Make a new copy of the DNA
            $revcom = reverse $line;
            # The Perl translate/transliterate command:
            $revcom =~ tr/ACGTacgt/TGCAtgca/;
            #print Dumper($/, $line);
        #}
    }
}
#close $in;
close $out;

__DATA__
>AM_13414L3_LacZ.SEE.rc_G01_2009-05-01.ab1   1368      0   1368  ABI
TTTTTCCCCCAACAAAGGGGAGGGTGGGCGGCTAGTCTGTTCAGCTGTGT
CACACCGGGATTCTCCCAATCTCTCCTCTGCAGGACCACTGGATCATTTA
AATCGGTACCCATCTTCTTAGTGGGCAGACCCAGCTGGCCTTCAGACTGC
TTGCTGTTCCTGGCCCGGTCTTGCTATTTATACATGTAAGAGGATCAGGA
AGTCCCTGGGGTACAGCTCATAATGCCCTCCTTTGACTACATAACACCCA
ACATGCTAGTTCTAAGAGAGGGAACAGTGTGCAGTGGGAAGTGGAGGGCA
AAGGTGACTTGGGGCTTTCCAAAGTTCAAATTGATTCAGAGAGAGTAAAT
ATTTCCAGAAGGATTTCTCCTTTTATAAAATTCATTCACTCCTTTAGCTC
TGACCACAGGGTGGGAGTGAGGGATCCTTCTAGACCCCTGATGAGAGGTT
AGCTTGGAGGACGCTGGCTTATGCTCATTGACAGCTGACCGACAGATATA
GATTATAAAAGTAAACTTATATGTCTTGCCAGAGATATATAAAATTGTTG
TCAACTCCTTCTTTAATTATTTTTCTTTAATTTTTAAAGATTTATTTTAT
ATCCATGTTTTGCCTGCATGTGTGTATGTCTACCACATACATGCAGTGCT
GTGCAGGTCAGAAGAGGGTGTTAAATTCCCTGGTACTAGAGTTACAGATG
GTTGTGAGCCATCATGTGGATGCTGAGAACTGAAGCCAGCAAGTGTCCTT
AACCGCTGAGCCAACTCTCCAGCCCCTTTAGATATTTTTAATATACTTTA
ACATCAGAGGAAAAAAAAATCTTTAGAACGTCTGTCAGAAGAAACATCTA
AGGCTGGTTGGGGTGGTGTTCACCACTTGGTGTCAGCACTTGGGAGCCAG
AGGCAGGTGTGTGTGTGTGTTTGAGGCCAGTCTGGTCTACACACTCAGTT
ATCCAATCTCCGTGAGTTTGTGAATGTTTGCTGTTCATTTGGGGTTTTAG
TCTGATGTGGTCAAATAGAATAGGAAGAGAGGGCTAAAGACCCACCTTAC
TGGTTTAAAGCACTTGTTGCTTTTTTAAAAAACCAAGTTTAATTCTTTCG
GAGTTTCATTAGCCCTTTTTCTATTAGGGAGGGACCCCTTTTTTCTTGAT
TTATAAAGGACCCCTTTGCTTGGCAATTCTGTTTTTGGGCTGGAGGGTCC
AGGTTTTCCAAACTTTGGGAAATGCCTTTCCACCCTTTCTGTTCCCCTGA
TGGACAATTTCCTGCCCCATGAATTTAATGGGTTTCTCTTTTATGGCTTT
TTAAACATTTTTTTTTTGTTTTTTAAAAACTTTTTTCCTTTTAAACTTTT
TATTTTATAATTTGAAAA
>AM_13414L3_SD_F01_2009-05-01.ab1   1397      0   1397  ABI
AATTTAAAGCATACTGTAAATACTACTAACTAAAGGGCAAAATAGGGCAT
CAGTTTTCTTTGGAATTGGAATTATAGATAGTTTGAGCTGCCATCTAAGT
GGGAATTGAACCCAGGTCCTCTGGAAGAGCAGCAGGTGCTCTTAACCACC
AAGCCATCTCTCCAGACCTTGCCCATTTATCTCAATCAAATATTATGTGT
AGTCATTGAGGTCAGCTTCAGACCTTCCAGGCATCTGAGTTTTCAGATGA
CTGGGGTTGGCACAGACAAGTTTCCCCTCTGTGACAAAGCCAGATATGCC
ACTTTAAAGTGGAACAGAAAAAAAAATGTTTATATACCTATAAAAATAAA
CACTTAGAGCCACTTAGGTGGTCACTGGGGAAGACCAAAGAAAGTAGCTG
GCAGTTCACACCCTTCTCTGCTAGCATAACTTCGTATAGCATACATTATA
CGAAGTTATCTAGGGGCTGCAGGTCGAGGTCTGATGGAATTAGAACTTGG
CAAAACAATACTGAGAATGAAGTGTATGTGGAACAGAGGCTGCTGATCTC
GTTCTTCAGGCTATGAAACTGACACATTTGGAAACCACAGTACTTAGAAC
CACAAAGTGGGAATCAAGAGAAAAACAATGATCCCACGAGAGATCTATAG
ATCTATAGATCATGAGTGGGAGGAATGAGCTGGCCCTTAATTTGGTTTTG
CTTGTTTAAATTATGATATCCAACTATGAAACATTATCATAAAGCAATAG
TAAAGAGCCTTCAGTAAAGAGCAGGCATTTATCTAATCCCACCCCACCCC
CACCCCCGTAGCTCCAATCCTTCCATTCAAAATGTAGGTACTCTGTTCTC
ACCCTTCTTAACAAAGTATGACAGGAAAAACTTCCATTTTAGTGGACATC
TTTATTGTTTAATAGATCATCAATTTCTGCAGACTTACAGCGGATCCCCT
CAGAAGAACTCGTCAAAGAAGCGATAGAAGGCGATGCGCTGCGAATCGGG
AGCGGCGATACCCGTAAGCACGAGGAAACGGTCAGCCCATTCGCCGCCAA
GCTCTTCAGCAATATCACGGGTAGCCAACGCTATGTTCTGATAGCGGTCC
CCCACACCCAGCCGGCCACAGTCGATGAATCCAGAAAAACGGGCCTTTTT
CACCCTGAATATCGGCAAGCAGGCATTCGCCTGGGGTAACGACGAGTTCC
TTCGCCGTCGGGCATGCCCGCCCTTGAGCCCGGGCGAACAGTTTCGGCTG
GCCCCGAGCCCCCTGATGCTTCTTTCTTCCAAATTCATCCTGGTTCAAAC
AGAACCCGGCTTTCCCATCCCCAATAACCTGGCCTTCCTTTCGGATGCGG
AATGTTTTTCCCTTTGGGGGGGTCAAAAAGGGGGCACGGGGAGCCCN
>AM_13414L3_SU_E01_2009-05-01.ab1   1447      0   1447  ABI
CTCCAGCCTACCCTCTATCCAGGGGNTCTAGAGGATCCCTCACTCCCACC
CTGTGGTCAGAGCTAAAGGAGTGAATGAATTTTATAAAAGGAGAAATCCT
TCTGGAAATATTTACTCTCTCTGAATCAATTTGAACTTTGGAAAGCCCCA
AGTCACCTTTGCCCTCCACTTCCCACTGCACACTGTTCCCTCTCTTAGAA
CTAGCATGTTGGGTGTTATGTAGTCAAAGGAGGGCATTATGAGCTGTACC
CCAGGGACTTCCTGATCCTCTTACATGTATAAATAGCAAGACCGGGCCAG
GAACAGCAAGCAGTCTGAAGGCCAGCTGGGTCTGCCCACTAAGAAGATGG
GTACCGATTTAAATGATCCAGTGGTCCTGCAGAGGAGAGATTGGGAGAAT
CCCGGTGTGACACAGCTGAACAGACTAGCCGCCCACCCTCCCTTTGCTTC
TTGGAGAAACAGTGAGGAAGCTAGGACAGACAGACCAAGCCAGCAACTCA
GATCTTTGAACGGGGAGTGGAGATTTGCCTGGTTTCCGGCACCAGAAGCG
GTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGT
CGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCA
ACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAAT
CCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACA
GGAAGGCCAGACGCGAATTATTTTTGATGGCGTTAACTCGGCGTTTCATC
TGTGGTGCAACGGGCGCTGGGTCGGTTACGGCCAGGACAGTCGTTTGCCG
TCTGAATTTGACCTGAGCGCATTTTTACGCGCCCGGAGAAAACCGCCCTG
CGGTGATGGTGCTGCGCTGGAGTGACGGGCGTTATCTGGAAGATCAGGAT
ATGTGGCGGATGAGCGGCATTTTTCCGTGACGTCTTGTTGCTGCATAAAC
CGACTACCCAAATCAAACGATTTCCATGTTGCCACTCGCTTTAAATGATG
ATTTTCACCCCGCCTGTACTGGAGGCTGAAATTTCAAAATGGCGGGGAGT
TGCGGGACTACCCTCCGGGTAAACAGTTTCTTTTATGGCAGGGGTGAAAA
CCCAAGGCCGCCCACCGGCCCCGCGGCCCTTTTCGGCCGGGGAAAATTAT
CCGATGAAGCGGGGTGGTTTATTGCCCAATCCGCGTCCAACCTACCTTCT
GAAAAGGCCCAAAAACCCCGAAAACTGGTGGAGCCCCCCAAAAATTCCCC
AAAATTTTTTTTTCTTTGGGGGGGGGGGTTGAAACCTGCACCCCCCCCCC
CCCAACGGGCACCCCTTTTTATTTTGAAAAAACCAAAAAACCCCTGCCCG
ACTGCTCCCCGGGTTTTTTCCCCCGCGGGAGGAGGGGGCCGGAGAAA
>AM_13414L3_pgK.Neo.2fw_H01_2009-05-01.ab1   1387      0   1387  ABI
AAGTTCTAATTCATCGNANCTCGCCTGCAGCCCCTAGATAACTTCGTATA
ATGTATGCTATACGAAGTTATGCTAGCAGAGAAGGGTGTGAACTGCCAGC
TACTTTCTTTGGTCTTCCCCAGTGACCACCTAAGTGGCTCTAAGTGTTTA
TTTTTATAGGTATATAAACATTTTTTTTTCTGTTCCACTTTAAAGTGGCA
TATCTGGCTTTGTCACAGAGGGGAAACTTGTCTGTGCCAACCCCAGTCAT
CTGAAAACTCAGATGCCTGGAAGGTCTGAAGCTGACCTCAATGACTACAC
ATAATATTTGATTGAGATAAATGGGCAAGGTCTGGAGAGATGGCTTGGTG
GTTAAGAGCACCTGCTGCTCTTCCAGAGGACCTGGGTTCAATTCCCACTT
AGATGGCAGCTCAAACTATCTATAATTCCAATTCCAAAGAAAACTGATGC
CCTATTTTGCCCTTTAGTTAGTAGTATTTACAGTATTCTTTATAAATTCA
CCTTGACATGACCATCTTGAGCTACAGCCATCCTAACTGCCTCAGAATCA
CTCAAGTTCTTCCACTCGGTTTCCCAGCGGATTATAAGTGGATAAACTGT
GAGAGTGGTCTGTGGGACTTTGGAATGTGTCTGGTTCTGATAGTCACTTA
TGGCAACCCGGGTACATTCAACTAGGATGAAATAAATTCTGCCTTAGCCC
AGTAGTATGTCTGTGTTTGTAAGGACCCAGCTGATTTTCCCACCACCCCT
CCATCAGTAAGCCACTAATAAAGTGCATCTATGCAGCCACAGGTCTGTCT
GCCTCTTTTGCTTCAGTTTCCTAGGACTATGGGCTGAAATTGGGCTGTTA
GGGAGAAAGCATCTCACTCGCTTTTATTGAATCTGCAGTGGAAAAGAAAC
AGAGGGAGTCAGGTAACTTTGAATATTTTCTTCAAAACAAAAGATATCAT
GGTACAATTTTTTTTAAATTTTTTGTTTGTTTGTTTTTGTTTTTCGAGAC
AGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCA
AGTTGGCCTCCAACTCAGAAATCCGCCTGCCTCTGCCTCCTGAGTGCTGG
GATTAAAGGCGTGCGCCCCCACCCCCCCGCCCCATGGTCAATTTTTAAAT
TTTCCCAAAAATTATTTTTTCCCAAGGTAGACTTCTTTTTAAAGGTGGTT
TTTTTACCCCCTTTTGAAAAGAAAACATTAAAGGGGATTCTTCCAAAATT
TTGTGAAAGTTTTCCCCGTTTCGAATAAAAAACCCCCCTTTTCCTTTTCC
GGGGATCTCCACCCTGGGTGACACTTGGTTTTTTTTACCCCCCCCCCCCT
GGCCGGTTTTTTTTTTACCTGGGGGGCCTTGGGTTTA
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