#!/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 the first header > $dnsstr1[0] = ; foreach my $line() { #Read rest of lines until nest header if ($line =~ /^>/) { print "Revese\n" if $fr == 0; print @dnsstr1,"\n"; @dnsstr1 = (); $fr = 0; push @dnsstr1,$line; } else {push @dnsstr1,$line; # check if dna string is in the Forward ones foreach my $f (@forward){ if ($line =~ $f) { $fr =1; print "Forward\n";}} } #print $line; } #print the last dna string print "Revese\n" if $fr == 0; print @dnsstr1,"\n"; __DATA__ >HSBGPG Human gene for bone gla protein (BGP) GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT ATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACC ATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCC CACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCCCTTTG GCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGCAGAGG GAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGGTGAAC CAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGATGGACC TGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCTGTCTG GCCATCAGGAAGGCCAGCCTGCTCCCCACCTGATCCTCCCAAACCCAGAGCCACCTGATGCCTGCCCCTCTGCTC CACAGCCTTTGTGTCCAAGCAGGAGGGCAGCGAGGTAGTGAAGAGACCCAGGCGCTACCTGTATCAATGGCTGGG GTGAGAGAAAAGGCAGAGCTGGGCCAAGGCCCTGCCTCTCCGGGATGGTCTGTGGGGGAGCTGCAGCAGGGAGTG GCCTCTCTGGGTTGTGGTGGGGGTACAGGCAGCCTGCCCTGGTGGGCACCCTGGAGCCCCATGTGTAGGGAGAGG AGGGATGGGCATTTTGCACGGGGGCTGATGCCACCACGTCGGGTGTCTCAGAGCCCCAGTCCCCTACCCGGATCC CCTGGAGCCCAGGAGGGAGGTGTGTGAGCTCAATCCGGACTGTGACGAGTTGGCTGACCACATCGGCTTTCAGGA GGCCTATCGGCGCTTCTACGGCCCGGTCTAGGGTGTCGCTCTGCTGGCCTGGCCGGCAACCCCAGTTCTGCTCCT CTCCAGGCACCCTTCTTTCCTCTTCCCCTTGCCCTTGCCCTGACCTCCCAGCCCTATGGATGTGGGGTCCCCATC ATCCCAGCTGCTCCCAAATAAACTCCAGAAG >HSGLTH1 Human theta 1-globin gene CCACTGCACTCACCGCACCCGGCCAATTTTTGTGTTTTTAGTAGAGACTAAATACCATATAGTGAACACCTAAGA CGGGGGGCCTTGGATCCAGGGCGATTCAGAGGGCCCCGGTCGGAGCTGTCGGAGATTGAGCGCGCGCGGTCCCGG GATCTCCGACGAGGCCCTGGACCCCCGGGCGGCGAAGCTGCGGCGCGGCGCCCCCTGGAGGCCGCGGGACCCCTG GCCGGTCCGCGCAGGCGCAGCGGGGTCGCAGGGCGCGGCGGGTTCCAGCGCGGGGATGGCGCTGTCCGCGGAGGA CCGGGCGCTGGTGCGCGCCCTGTGGAAGAAGCTGGGCAGCAACGTCGGCGTCTACACGACAGAGGCCCTGGAAAG GTGCGGCAGGCTGGGCGCCCCCGCCCCCAGGGGCCCTCCCTCCCCAAGCCCCCCGGACGCGCCTCACCCACGTTC CTCTCGCAGGACCTTCCTGGCTTTCCCCGCCACGAAGACCTACTTCTCCCACCTGGACCTGAGCCCCGGCTCCTC ACAAGTCAGAGCCCACGGCCAGAAGGTGGCGGACGCGCTGAGCCTCGCCGTGGAGCGCCTGGACGACCTACCCCA CGCGCTGTCCGCGCTGAGCCACCTGCACGCGTGCCAGCTGCGAGTGGACCCGGCCAGCTTCCAGGTGAGCGGCTG CCGTGCTGGGCCCCTGTCCCCGGGAGGGCCCCGGCGGGGTGGGTGCGGGGGGCGTGCGGGGCGGGTGCAGGCGAG TGAGCCTTGAGCGCTCGCCGCAGCTCCTGGGCCACTGCCTGCTGGTAACCCTCGCCCGGCACTACCCCGGAGACT TCAGCCCCGCGCTGCAGGCGTCGCTGGACAAGTTCCTGAGCCACGTTATCTCGGCGCTGGTTTCCGAGTACCGCT GAACTGTGGGTGGGTGGCCGCGGGATCCCCAGGCGACCTTCCCCGTGTTTGAGTAAAGCCTCTCCCAGGAGCAGC CTTCTTGCCGTGCTCTCTCGAGGTCAGGACGCGAGAGGAAGGCGC >seq1 AGCCTAAGCTASTPGHTIIYEAVCLHNDRTTIP >seq2 optional comment ASQKRPSQRHGSKYLATASTMDHARHGFLPRHRDTGILDSIGRFFGGDRGAPK NMYKDSHHPARTAHYGSLPQKSHGRTQDENPVVHFFKNIVTPRTPPPSQGKGR KSAHKGFKGVDAQGTLSKIFKLGGRDSRSGSPMARRELVISLIVES #### perl "D:\Citi Midleware\db\perl\perl5data.pl" stocks 10 5 Process started >>> Revese >HSBGPG Human gene for bone gla protein (BGP) GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT ATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACC ATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCC CACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCCCTTTG GCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGCAGAGG GAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGGTGAAC CAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGATGGACC TGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCTGTCTG GCCATCAGGAAGGCCAGCCTGCTCCCCACCTGATCCTCCCAAACCCAGAGCCACCTGATGCCTGCCCCTCTGCTC CACAGCCTTTGTGTCCAAGCAGGAGGGCAGCGAGGTAGTGAAGAGACCCAGGCGCTACCTGTATCAATGGCTGGG GTGAGAGAAAAGGCAGAGCTGGGCCAAGGCCCTGCCTCTCCGGGATGGTCTGTGGGGGAGCTGCAGCAGGGAGTG GCCTCTCTGGGTTGTGGTGGGGGTACAGGCAGCCTGCCCTGGTGGGCACCCTGGAGCCCCATGTGTAGGGAGAGG AGGGATGGGCATTTTGCACGGGGGCTGATGCCACCACGTCGGGTGTCTCAGAGCCCCAGTCCCCTACCCGGATCC CCTGGAGCCCAGGAGGGAGGTGTGTGAGCTCAATCCGGACTGTGACGAGTTGGCTGACCACATCGGCTTTCAGGA GGCCTATCGGCGCTTCTACGGCCCGGTCTAGGGTGTCGCTCTGCTGGCCTGGCCGGCAACCCCAGTTCTGCTCCT CTCCAGGCACCCTTCTTTCCTCTTCCCCTTGCCCTTGCCCTGACCTCCCAGCCCTATGGATGTGGGGTCCCCATC ATCCCAGCTGCTCCCAAATAAACTCCAGAAG Revese >HSGLTH1 Human theta 1-globin gene CCACTGCACTCACCGCACCCGGCCAATTTTTGTGTTTTTAGTAGAGACTAAATACCATATAGTGAACACCTAAGA CGGGGGGCCTTGGATCCAGGGCGATTCAGAGGGCCCCGGTCGGAGCTGTCGGAGATTGAGCGCGCGCGGTCCCGG GATCTCCGACGAGGCCCTGGACCCCCGGGCGGCGAAGCTGCGGCGCGGCGCCCCCTGGAGGCCGCGGGACCCCTG GCCGGTCCGCGCAGGCGCAGCGGGGTCGCAGGGCGCGGCGGGTTCCAGCGCGGGGATGGCGCTGTCCGCGGAGGA CCGGGCGCTGGTGCGCGCCCTGTGGAAGAAGCTGGGCAGCAACGTCGGCGTCTACACGACAGAGGCCCTGGAAAG GTGCGGCAGGCTGGGCGCCCCCGCCCCCAGGGGCCCTCCCTCCCCAAGCCCCCCGGACGCGCCTCACCCACGTTC CTCTCGCAGGACCTTCCTGGCTTTCCCCGCCACGAAGACCTACTTCTCCCACCTGGACCTGAGCCCCGGCTCCTC ACAAGTCAGAGCCCACGGCCAGAAGGTGGCGGACGCGCTGAGCCTCGCCGTGGAGCGCCTGGACGACCTACCCCA CGCGCTGTCCGCGCTGAGCCACCTGCACGCGTGCCAGCTGCGAGTGGACCCGGCCAGCTTCCAGGTGAGCGGCTG CCGTGCTGGGCCCCTGTCCCCGGGAGGGCCCCGGCGGGGTGGGTGCGGGGGGCGTGCGGGGCGGGTGCAGGCGAG TGAGCCTTGAGCGCTCGCCGCAGCTCCTGGGCCACTGCCTGCTGGTAACCCTCGCCCGGCACTACCCCGGAGACT TCAGCCCCGCGCTGCAGGCGTCGCTGGACAAGTTCCTGAGCCACGTTATCTCGGCGCTGGTTTCCGAGTACCGCT GAACTGTGGGTGGGTGGCCGCGGGATCCCCAGGCGACCTTCCCCGTGTTTGAGTAAAGCCTCTCCCAGGAGCAGC CTTCTTGCCGTGCTCTCTCGAGGTCAGGACGCGAGAGGAAGGCGC Forward >seq1 AGCCTAAGCTASTPGHTIIYEAVCLHNDRTTIP Revese >seq2 optional comment ASQKRPSQRHGSKYLATASTMDHARHGFLPRHRDTGILDSIGRFFGGDRGAPK NMYKDSHHPARTAHYGSLPQKSHGRTQDENPVVHFFKNIVTPRTPPPSQGKGR KSAHKGFKGVDAQGTLSKIFKLGGRDSRSGSPMARRELVISLIVES <<< Process finished. ================ READY ================