Perl: Search a pattern across array elements

Question

I am a Perl newbie, stuck with another bioinformatics problem that requires some help and input.

The problem in brief:

1. I have a file, which has over 40,000 unique DNA sequences. By unique, I mean unique sequence id. I am attaching a portion of it at the end of my post to help you show what it looks like.

2. I need to divide each of the 40,000 sequences into 3 parts. So if a particular sequence is 999 character long, each of the 3 parts would have 333 characters.

3. I need to look for the following pattern through each of the 3 individual parts:

   $gpat = [G]{3,5}; $npat = [A-Z]{1,25};
   $pattern = $gpat.$npat.$gpat.$npat.$gpat.$npat.$gpat;

4. If $pattern appears in the first of the 3 parts, increase the counter of 'beginning', if $pattern occurs in the 2nd of the 3 parts, increase counter of 'middle' and lastly if the $pattern appears in the 3rd part, increase counter of 'end'.

5. Print the counters of 'beginning','middle' and 'end' i.e basically summation of 'beginning','middle','end' for each of the sequences.

   Say in 1st sequence, the values are like '2','5','3' respectively and in 2nd sequence, the values are '4','1','6', the final count should be '7,6,9'.

The issues I am having:

1. If a particular sequence is split into 3 parts, potential $pattern is lost. eg say on a sequence like :

gggatgtcgatgcatggggatgcatcgatgcggggactagctagcgggatgctacgatggggatgatgataatatcgcggcgcatatatgctagtctatatatta

a split into 3 parts produces following 3 sub-parts,each of 35 character length:

gggatgtcgatgcatggggatgcatcgatgcgggg
actagctagcgggatgctacgatggggatgatgat
aatatcgcggcgcatatatgctagtctatatatta

Hence, $pattern gets split into the first 2 parts. Is there anyway to say "If $pattern begins in 1st part and ends in 2nd part", increase count of "beginning" ?

##UPDATE## The following issue has been resolved thanks to the code suggested by Cupidvogel

2.How do I divide a sequence into 3 parts if its length is not divisible by 3? I tried using int, but then the last part is 1-2 characters short.

The following is the code I have written so far.

It reads in the file, displays the header name and sequence, the length into which each sequence will be divided and finally the sequence split into 3 parts which works fine provided the sequence length is divisible by 3, for those which aren't, the final 3rd part is 1-2 characters short.

#Take Filename from user
print "Please enter file name : ";
$in =<>;
chomp $in;


open (FASTA,"$in") or die ;
while (<FASTA>)
{
$/=">";
@array = split '\n', $_;
$header=shift @array; # Header of the fasta sequence
print "\n\nNext sequence: \n";
print $header,"\n";


$seq= join '', @array; # sequence
$seq=~s/\s//g;
$seq=~s/\*//g;
$seq=~s/>//g;
print $seq,"\n\n";

$num = int(length($seq)/3);
@arr = unpack("A$num A$num A*",$seq);
print " New method gives this :", @arr;
print "\nThe first element is :", $arr[0]; 
print "\nThe second element is :",$arr[1]; 
print "\nThe third element is :",$arr[2] ;



#The following lines of code were originally written to split...
#...the sequence into 3 parts, albeit unsuccessfully                    
#my $split = (length $seq)/3;
#print $split,"\n\n";

#my $int = int $split;
#print $int,"\n\n";


#my @array2 = $seq =~ /(.{$int})/g;
#print join (" ", @array2),"\n\n";

#print $array2[0],"\n",$array2[1],"\n",$array2[2];


}


exit;

I have been trying the code I have written so far with the following sample file : sample.fa

>ABC_123 2
atgtcgatcgatcggcgggcatgcgcgcgcggatg
atatatagcgcgcgctatatagcgcgactctacgc
atgctgctgactagctatagtcgctgactgcgcgt
gggaaaaagggcccgggccccgttttggggatcta
ggggatagctgatgctagcatgcatgctgactgca
>DEF_456 4
gggatgtcgatgcatggggatgcatcgatgcgggg
actagctagcgggatgctacgatggggatgatgat
aatatcgcggcgcatatatgctagtctatatatta
>GHI_789 1
atagctgctagtcgatcggcgcgggtatcgatcgg
ggatcgatcgatcggggatcgatcgggggatcgat

The actual input file looks like the following:

>NR_037701 1
aggagctatgaatattaatgaaagtggtcctgatgcatgcatattaaaca
tgcatcttacatatgacacatgttcaccttggggtggagacttaatattt
aaatattgcaatcaggccctatacatcaaaaggtctattcaggacatgaa
ggcactcaagtatgcaatctctgtaaacccgctagaaccagtcatggtcg
gtgggctccttaccaggagaaaattaccgaaatcactcttgtccaatcaa
agctgtagttatggctggtggagttcagttagtcagcatctggtggagct
gcaagtgttttagtattgtttatttagaggccagtgcttatttagctgct
agagaaaaggaaaacttgtggcagttagaacatagtttattcttttaagt
gtagggctgcatgacttaacccttgtttggcatggccttaggtcctgttt
gtaatttggtatcttgttgccacaaagagtgtgtttggtcagtcttatga
cctctattttgacattaatgctggttggttgtgtctaaaccataaaaggg
aggggagtataatgaggtgtgtctgacctcttgtcctgtcatggctggga
actcagtttctaaggtttttctggggtcctctttgccaagagcgtttcta
ttcagttggtggaggggacttaggattttatttttagtttgcagccaggg
tcagtacatttcagtcacccccgcccagccctcctgatcctcctgtcatt
cctcacatcctgtcattgtcagagattttacagatatagagctgaatcat
ttcctgccatctcttttaacacacaggcctcccagatctttctaacccag
gacctacttggaaaggcatgctgggtctcttccacagactttaagctctc
cctacaccagaatttaggtgagtgctttgaggacatgaagctattcctcc
caccaccagtagccttgggctggcccacgccaactgtggagctggagcgg
gagggaggagtacagacatggaattttaattctgtaatccagggcttcag
ttatgtacaacatccatgccatttgatgattccaccactccttttccatc
tcccagaagcctgctttttaatgcccgcttaatattatcagagccgagcc
tggaatcaaactgcctctttcaaaacctgccactatatcctggctttgtg
acctcagccaagttgcttgactattctcagtctcagtttctgcacctgtc
aaatagggtttatgttaacctaactttcagggctgtcaggattaaatgag
catgaaccacataaaatgtttggtgtatagtaagtgtacagtaaatactt
ccattatcagtccctgcaattctatttttcttccttctctacacagcccc
tgtctggctttaaaatgtcctgccctgctttttatgagtggataccccca
gccctatgtggattagcaagttaagtaatgacactcagagacagttccat
ctttgtccataacttgctctgtgatccagtgtgcatcactcaaacagact
atctcttttctcctacaaaacagacagctgcctctcagataatgttgggg
gcataggaggaatgggaagcccgctaagagaacagaagtcaaaaacagtt
gggttctagatgggaggaggtgtgcgtgcacatgtatgtttgtgtttcag
gtcttggaatctcagcaggtcagtcacattgcagtgtgtcgcttcacctg
gctccctcttttaaagattttccttccctctttccaactccctgggtcct
ggatcctccaacagtgtcagggttagatgccttttatgggccacttgcat
tagtgtcctgatagaggcttaatcactgctcagaaactgccttctgccca
ctggcaaagggaggcaggggaaatacatgattctaattaatggtccaggc
agagaggacactcagaatttcaggactgaagagtatacatgtgtgtgatg
gtaaatgggcaaaaatcatcccttggcttctcatgcataatgcatgggca
cacagactcaaaccctctctcacacacatacacatatacattgttattcc
acacacaaggcataatcccagtgtccagtgcacatgcatacacgcacaca
ttcccttcctaggccactgtattgctttcctagggcatcttcttataaga
caccagtcgtataaggagcccaccccactcatctgagcttatcaaccaat
tacattaggaaagactgtatttcctagtaaggtcacattcagtagtactg
agggttgggacttcaacacagctttttgggggatcataattcaacccatg
acagccactgagattattatatctccagagaataaatgtgtggagttaaa
aggaagatacatgtggtacaaggggtggtaaggcaagggtaaaaggggag
ggaggggattgaactagacacagacacatgagcaggactttggggagtgt
gttttatatctgtcagatgcctagaacagcacctgaaatatgggactcaa
tcattttagtccccttctttctataagtgtgtgtgtgcggatatgtgtgc
tagatgttcttgctgtgttaggaggtgataaacatttgtccatgttatat
aggtggaaagggtcagactactaaattgtgaagacatcatctgtctgcat
ttattgagaatgtgaatatgaaacaagctgcaagtattctataaatgttc
actgttattagatattgtatgtctttgtgtccttttattcatgaattctt
gcacattatgaagaaagagtccatgtggtcagtgtcttacccggtgtagg
gtaaatgcacctgatagcaataacttaagcacacctttataatgacccta
tatggcagatgctcctgaatgtgtgtttcgagctagaaaatccgggagtg
gccaatcggagattcgtttcttatctataatagacatctgagcccctggc
ccatcccatgaaacccaggctgtagagaggattgaggccttaagttttgg
gttaaatgacagttgccaggtgtcgctcattagggaaaggggttaagtga
aaatgctgtataaactgcatgatgtttgcaggcagttgtggttttcctgc
ccagcctgccaccaccgggccatgcggatatgttgtccagcccaacacca
caggaccatttctgtatgtaagacaattctatccagcccgccacctctgg
actccctcccctgtatgtaagccctcaataaaaccccacgtctcttttgc
tggcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
aaa
>NM_198399 1
aacagattttaactctgaaaagccatttccagtgtctatagactattgtg
agcctggagaagtagcatttagttgggatagcttcactagagctgcctgc
caaagacttccttccacaggatcttgtcgcaccagcaactgacaggagct
tgggagctcgggagcttgggagagggcttatgtttttaataatgtagctg
tcagttcgaagcctggaaatgttgaccctcaaagggcataaaatcttgtt
attttaatttgcatctgggagaatgtctgagcaaggagacctgaatcagg
caatagcagaggaaggagggactgagcaggagacggccactccagagaac
ggcattgttaaatcagaaagtctggatgaagaggagaaactggaactgca
gaggcggctggaggctcagaatcaagaaagaagaaaatccaagtcaggag
caggaaaaggtaaactgactcgcagccttgctgtctgtgaggaatcttct
gccagaccaggaggtgaaagtcttcaggatcagactctctgaaaactgca
aatggaaaggaattcaaaagaatttagattaaaagttaaataaaaagtag
gcacagtagtgctgaattttcctcaaaggctctcttttgataaggctgaa
ccaaatataatcccaagtatcctctctccttccttgttggagatgtctta
cctctcagctccccaaaatgcacttgcctataagaaacacaattgctggt
tcatatgaaacttaggaaatagtgaataaggtgcatttaactttggagaa
atacttttatggctttggtggagatttctcaatactgcaaaagttgtcca
gaaatgaatctgagctgatggtgactttaagttaatattattaatatatc
actgcatatttttacccttatttttgctccttacagcaagattagtaggt
tataaaaatttaaatttaaacaaaattatttcatgacaaaatgggaaact
tcacatcatacttatttttgtttgcctttcaggcatcatattagctttta
taaaaaatggtcttgctgctgaaattgtacttattttatcagaggctggg
tgcagtcaagacaaaagtaaaatggtttacctgagcccaggggagggaaa
attgattaagatatcattatttttgtttggtttggttttgcttttttcct
cttactttaattgaaatactctgaattcccctcatggaaacagagagcat
tgagagcactttctttaaaaggaccaaaaataaattcctaatagattttg
tcctaagagagtgtttttttttctagcatcattttctttacatgccactc
atgtcataaggcatggacaggctatctttcagtggccattactatgtttc
gtacacatgctttattttacttgggctctgagaaatgtgtggctttcctt
cagcattttatttgtgcttctctttttaatggagattgaaaagggagaat
aatgtgaatatcacggcttatattattaaatgttgattgatggcttgtaa
tgtactgcacacaatatatgttaactctgcagaatgacagaccctgggag
aagtaatgccccagttgtcccccactcctaatgccaggcagagaaggaca
gcctttatagacttaatctgctttttgtcccatttgacaaggtaccagga
ggaaattttttaagggatcaactgtatcacagtgcccactctggacctaa
gtctagtgtatccatacaattggtgcagagaaataaggtgtaaatggtgc
tttgttcctgctggttccaagctcagaaaccaagactagctttgtaggag
agaatgagagcctgcaagcctctctttggattggctgaggagtggtggga
gcagggggttgatagaaaacatccagacacacatataagcaagtggccgt
gctacctttttagagaataaagaaacagacttttgagtttatatgcaatg
ccttcattaggtaccaccggcacttacaaaatgtgcggactgaatcccag
agaacactggcagatgtatacagtatatggattgtatcgcttccccaatg
tttgtaaattcacagtatttggaaaactgccttcattttccagtgtggga
aaaactcttgctacctgtattacttgatctcagacccatacctgatggtt
cagtctgtccttaagttaaaagaattttgcttttctaatgttatactatt
tacctgtcagtgtattactgcaacttgaatcactcttttactgttgttgg
atataaacttatcctgtaccaatgtatttattaacacttgtattttatta
ttgagcatatcaataaaaatattaaaaaataacagattgttttttaccaa
aaaaaaaaaaaaa
>NR_026816 1
caacccactctctgtgctatgacttcattactctttcccagcccagccct
gggcaagccccttacgaagtctcaggctacctggatgaccaccctttctt
atgatgctgcaaggagggcaggtgggcagagccccgtgcatcctgggctc
aggccagggacccaagagcttgggagaagctggttctcagactgaaggcc
agagcccagcaccttgtcaccatcccggggagcatcatggcacacaacaa
ccagagccaaggctacagctagagagttgactcctctatttgagattgac
aggcctcggaagtcaaaataagtggtttcctagaccgggtcgagagcaag
tctctattggtcccaactgagttttttcagctggtttttcaaccaaacag
cacctcatctcccagtgaggggaagggaaggctgggctgagagcagcaag
gctgctcatctcacctctccccacccagccatgccagccgcctcacctgg
tggggagaggtgggcctcacctgggtcccctggcagtgctctgtgaaggg
tcttgacattgcactgtaataataaaggtgtgtgtgaagtatcaaaaaaa
>NR_027917 1
atgaagatgattgagcagcacaatcaggaatacagggaagggaaacacag
cttcacaatggccatgaacgcctttggagaaatgaccagtgaagaattca
ggcaggtggtgaatggctttcaaaaccagaagcacaggaaggggaaagtg
ctccaggaacctctgcttcatgacatccgcaaatctgtggattggagaga
gaaaggctacgtgactcctgtgaaggatcagtgcagctggggctctgtaa
ggacagatgttaggaaaactgagaaactagtttcactgagtgtgcagacc
tggtggactgctctaggcttcaaggcaatgttggctgcatttttggagaa
ccattattttgcttccagtatgttgccgacaatggaggcctggactctga
ggaatccttttcatatgaagaaaagctctggagactggaaagtccaaggt
cacagaggtgcatctggtgagagccttcttgctagtggggaatctcagca
gagtcctgaggtggcacagtattctgggaagcatcaagtgcagtgtcatc
ttatcgaggaggctctgcagatgctaagtggtggggatgaggatcacgat
gaagacaaatggccccatgacatgaggaatcatctggctggagaggccca
ggtgtag
>NR_002777 3
cttgtcctttcagaagatcagagacaagtgatatctgtgccaatttggcc
ttttcagtgttataattatggtgtcttgggatcccaatatttctcctaat
gtttccctgatgtgatactttgagagcccaggatgccagtacaataattg
aaattcacaaatgtctggtatcttgtccctcgtgccccatatattatctg
tggtttcggagagctcacttgtctcttatcttcagaaatgacagcacatg
aaatgttgtttggagccactgtcacatcaactgtagaaaaattaacaggt
cagctaagggatataatgtaactttatttgtgatatgagagaaatcttga
taaagacttgagagaaaactgggaggaaccttgtttagaagttataagga
ggggtaagttatgtgtgtcttggaaggagaatcataaatcttaaaacatg
agcctaatagagaacataaaattctaaaagataaagataataataatgat
aagccgcagggtggcttatgataatgtgacttctccttaccccagtagcg
tcggacatctgtcagctctgaaatgataaaaatgcacaatattgaataca
aacaaaggagtcagcactgaaattcattttctctccagattagggaaaga
gtaggtatgccctatggtagggcagtaaattgctgaatgatgagatgaaa
cagccacctagccatttcccattaaatataatcccatcagcagcagacaa
tatctatcctcccctatcccctctatccatatttggaaactgcaccctct
tccctatttagcaccctaacaccacttgaattccataaccctgttgttga
tctagctctcctcacctctaaacacttctagcattcctttcagatcagga
gctcgaaacactctcctttgattttttggaaaagtttctggcttcttcaa
ggtcacgttctccgtcctaagaattaaaaaaaaaaaaaaaaacttccaaa
cctttgaccttgtgtccgtggaacacccctgacttcctatcatttcaacc
cattgaggcacttgaactctcttcttggggatcctgagaagggagagtgc
aaactcttgaccctggaggcaaacaaaatgttctcatgtttgccttccca
cttactttctgtgagaacgtgggaagatcttaacctctcagaagcacagt
ttcttccttctaaaatgaaataattaacctctccctgtctacattcttaa
actcataggacataaaaaaaaaaaaaa
>NR_033769 1
ggcctctggcgggcctccagccagttagaccatttgactaggacgtgtgc
agctcagccagccacagaactggaatttttcaggagcagggggagcatgg
agtttggactttgctgagcaactgaagtggagcgcagagcttgctcgctt
aggagagggcagcatggatggcaaacaagggggcatggatgggagcaagc
ccacggggccaagagactctcctgacaccaggcttctttcaaacccattg
atgggtgattctgtgtctgattggtctcctatgcctgaagctgcaatcta
cggacatcagctgtctctgaggaacctcatcagccacgggtggcttgtga
acatcatcatggcagatcatgtttccccactccatgaagcctgtctcaga
ggtcatccctctcgtgtaaagattttattaaagcatggagctcaggtgaa
tggcgtgacaacagactggcacactccactgtttaatgtttgtatcagca
gcagctgggattatgcttctgcagcatggagccagcgttcaacctgagag
tgatctggcatcccccgtccatgaagctgctaggagaggccacgtggagt
gtgtcgactctcttacagcttataggggcaaaaatgaccataacatcagc
cacgtgggcacttcactgtatttggcttgtgaaaaccagcagatagcctg
tgtcaagaagcttctggagtcaggagcagacctgaacccagggagaggtt
ccccacttcatgcagtggccttcatgaaggccctcatgaaggattcccca
cttcatgcagtggccaggacagccagtgaagagctggcctgcctgctcat
ggattttggagcagacacccaggccaagaatgctgaaggcaaatgtcatg
tggagctggtgcctccagagagccctttgatccagctcttcttggagaga
gaagggcccccttcttttgatgcagttatgcctagaaatcagaagggctt
tggaatccagcagcatcataagataaccaaagtcgtcctcccagaggatc
tgaaatggtttctcctacatctttgtatgtatcaatggaatggattcaca
aacaatgtgaaaacattattgagtgttgtagccactagaattttaaaatc
aagttaggtttatagagtttgactagttttttcgattagatttgtattag
ttataaatttgttcatagagtttgactaattttttcgattagatttgtat
ttgttaaactctgaagccagagtttaaacacactgcatacgtttgtatga
ttagttagaaggcatgaagacttttttccctgcttggagactgtctaaaa
taacagctattgttttgcatatccactgcaggccaagcactttcagcatc
atctaattcagccctcacagcaactgggtcaatctgtccaatttcccagg
gcaaggatagaggagtcagattcaaatacaggttttctgacgttaactta
tgtgatgatttgatcaaagcaggattttccagcatcactatccttgttcc
atctctgctatatgggaatgaaaataaagaaatgtatttcaaaaaaataa
aaagaaaagaaaaacagagacggtc
>NM_016326 3
atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc
ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg
cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac
gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag
tgtgaaaggccacgtgaagatgctgcggctggtgtttgcacttgtgacag
cagtatgctgtcttgccgacggggcccttatttaccggaagcttctgttc
aatcccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaagaagt
tttgtaattttatattactttttagtttgatactaagtattaaacatatt
tctgtattcttccacatattttctgcagttattttaactcagtataggag
ctagaggaagagatttccgaagtctgcaccccgcgcagagcactactgta
acttccaagggagcgctgggagcagcgggatcgggttttccggcacccgg
gcctgggtggcagggaagaatgtgccgggatccgcctcagggatctttga
atctctttactgcctggctggccggcagctccg
>NM_181641 2
atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc
ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg
cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac
gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag
tgtgaaaggccacgtgaagatgctgcggctggcactaactgtgacatcta
tgaccttttttatcatcgcacaagcccctgaaccatatattgttatcact
ggatttgaagtcaccgttatcttatttttcatacttttatatgtactcag
acttgatcgattaatgaagtggttattttggcctttgcttgtgtttgcac
ttgtgacagcagtatgctgtcttgccgacggggcccttatttaccggaag
cttctgttcaatcccagcggtccttaccagaaaaagcctgtgcatgaaaa
aaaagaagttttgtaattttatattactttttagtttgatactaagtatt
aaacatatttctgtattcttccacatattttctgcagttattttaactca
gtataggagctagaggaagagatttccgaagtctgcaccccgcgcagagc
actactgtaacttccaagggagcgctgggagcagcgggatcgggttttcc
ggcacccgggcctgggtggcagggaagaatgtgccgggatccgcctcagg
gatctttgaatctctttactgcctggctggccggcagctccg
>NM_001144931 1
gtttccgttcctctgcccgccatgccgttcctagagctgcacacgaattt
ccccgccaaccgagtgcccgcggggctggagaaacggctgtgcgccgtcg
ctgcctccatcttgggcaaacctgcagaccttgtgaacgtgacggtacgg
ccgggcctggccagggcgctgagcgggtccaccgagccctgcgcgcagct
gtccatctcctccatcggcgtagtgggcaccgccgaggacaaccgcagcc
acagtgcccacttctttgagtttctcaccaaggagctagccctgggccag
gaccggtgcgcaggggtagtaggcccggaatattattctaaaacacaatc
agagtactccattcctgctaacagtttaaagccaaacacctaggcaggcc
atttaggcttctgaatgactgggtcttgaccaggagagctgctgtctagg
ttttctcttcctgaccagttcctcaagagaaatgcaaaactagtgattaa
cagtaagagtcaggcagggcgcggtggctcacgcctgtaatcccagcact
ttgggaggccgag
>NR_029429 1
ggacaccaccccaaaatttcctagtcctctttgatacgggttcctccaat
ctgtagctgccctccatctactgccagagccaagtctgctccaatcacaa
caggttcaatcccagcctgtcctccaccttcagaaacgatggacaaacct
atggactatcctatgggagtggcagcctgagtgtgttcctgggctatgac
actgtgactgttcataacatcgttgtcaataaccaggagtttggcctgag
tgagaatgagcccagcgaccccttttactattcagactttgacgggatcc
tgggaatggcctacccaaacatggcagaggggaattcccctacagtaatg
caggggatgctgcagcagagccagcttactcagcccgtcttcagcttcta
cttcacctgccagccaacccgccagtattgtggagagctcatccttggag
gtgtggaccccaactttattctggtcagatcatctggacccctgtcagcc
cgtaactgtactggcagattgccatcgaggaatttgccatcggtaaccag
gccactggcttgtgctctgagggttgccaggccattgtggataccgagac
cttcctgc
>NR_026551 1
tgtggcctgagaggacggccaggactggccagaaaagagagggacgtggc
taaacgtgagggggcgtggccaagatggccgcgtgcgggatcctcgggta
ccgggagcgaacgaggaggttctggctcagtgcatccactctgggagagc
gtggacctggttcctgggggcgatcgccagtcacccatcaacattcggtg
gagggacagtgtttatgatcccggcttaaaaccactgaccatctcttatg
acccagccacctgcctccacgtctggaataatgggtactctttcctcgtg
gaatttgaagattctacagataaatcagctgcacttagtgcattggaacg
cagtcaaatttgaaaactttgaggatgcagcactggaagaaaatggtttg
gctgtgataggagtatttttaaagatttcggaaacttctggcagcccagt
gtctactggaaggcccaagccgcttgccagaaagctgcgccccgcccaaa
agcactgggttctgcagtccaggcccttcctcagctcccaggtccaggag
aactgcaaggtcacctacttccacaggaagcactgggtccgcatccggcc
cctccgcaccactcctcccagctgggactacacccgcatctgcatccaga
gagagatggtccccgcccgcatccgcgtcctgagagagatggtccccgag
gcctggaggtgctttcccaacaggctgccgctgctgagcaacatcaggcc
tgatttctccaaggctcccctggcctacgtgaagcggtggctttggaccg
cccgccacccccacagcctgtccgcagcctggtgaccgtgaaaatcgccc
cgccagagagcagaggaagcccgacgcccaggccatctgccttcaggtct
gtgatgagaaacggagtggcctgttccgttgtgcccaggtctaggccgct
gagcagagccctcactcccaggcagagttgtctgaatccttcct
>NM_181640 2
atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc
ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg
cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac
gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag
tgtgaaaggccacgtgaagatgctgcggctggatattatcaactcactgg
taacaacagtattcatgctcatcgtatctgtgttggcactgataccagaa
accacaacattgacagttggtggaggggtgtttgcacttgtgacagcagt
atgctgtcttgccgacggggcccttatttaccggaagcttctgttcaatc
ccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaagaagttttg
taattttatattactttttagtttgatactaagtattaaacatatttctg
tattcttccacatattttctgcagttattttaactcagtataggagctag
aggaagagatttccgaagtctgcaccccgcgcagagcactactgtaactt
ccaagggagcgctgggagcagcgggatcgggttttccggcacccgggcct
gggtggcagggaagaatgtgccgggatccgcctcagggatctttgaatct
ctttactgcctggctggccggcagctccg
>NM_016951 3
atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc
ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg
cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac
gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag
tgtgaaaggccacgtgaagatgctgcggctggcactaactgtgacatcta
tgaccttttttatcatcgcacaagcccctgaaccatatattgttatcact
ggatttgaagtcaccgttatcttatttttcatacttttatatgtactcag
acttgatcgattaatgaagtggttattttggcctttgcttgatattatca
actcactggtaacaacagtattcatgctcatcgtatctgtgttggcactg
ataccagaaaccacaacattgacagttggtggaggggtgtttgcacttgt
gacagcagtatgctgtcttgccgacggggcccttatttaccggaagcttc
tgttcaatcccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaa
gaagttttgtaattttatattactttttagtttgatactaagtattaaac
atatttctgtattcttccacatattttctgcagttattttaactcagtat
aggagctagaggaagagatttccgaagtctgcaccccgcgcagagcacta
ctgtaacttccaagggagcgctgggagcagcgggatcgggttttccggca
cccgggcctgggtggcagggaagaatgtgccgggatccgcctcagggatc
tttgaatctctttactgcctggctggccggcagctccg
>NR_002773 1
cagcaccacaccaggaccctccagaggctgtgagaaacatcctgcaccca
ggtcctctctatctgtttatcattgtctattttgtattctgcattcagaa
ccaagagcctgaagacgacccaggagctttagctatggctgtcttcatta
ttttgtccctgtttagtgttctggtgacaggcatgggtgaaggtggggct
gggagtgagaaaggaggtgagagggaatgtaagctgaaccagcttcccca
ttgcccctccgtatctcccagtgcccagccttggacacaccctggccaga
gccagctgtttgcagacctgagccgagaggagctgacggctgtgatgcgc
tttctgacccagcagctggggccagggctggtggatgcagcccaggccca
gccctcggacaactgtgtcttctcagtggagttgcagctgcctcccaagg
ctgcagccctggctcacttggacagggggagccccccacctgcccgggag
gcactggccatcgtcttctttggcaggcaaccccagcccaacgtgagtga
gctggtggtggggccactgcctcacccctcctacatgcgggacgtgactg
tggagcgtcatggaggccccctgccctatcaccgacgccccatgttgttc
caagagtacctggacatagaccagatgatcttcgacagagagctgcccca
ggcttctgggcttctccatcactgttgcttctacaagcgccggggacgga
acctggtgacaatgaccacggctccccgtggtctgcaatcaggggaccgg
gccacctagtttggcctctactacaacatctcgggcgctgggttcttcct
gcaccacgtgggcttggagctgctagtgaaccacaaggcccttgaccctg
cccgctggactatccagaaggtgttctatcaaggccgctactatgacagc
ctggcccagctggaggcccagtttgaggccggcctggtgaatgtggtgct
gatcccagacaatggcacaggtgggtcctggtccctgaagtcccctgtgc
ccccgggtccagctccccctctgcagttccatccccaaggcccccgcttc
agtgtccagggaagtcgagtggcctcctcactgtggactttctcctttgg
cctcggagcattcagtggcccaaggatctttgacgttcccttccaagggg
agagggtggcctatgaagtcagtgtccaggcggccttggccatctatgga
ggcaattctccttctgctctacgaagccggtacatagatagtggctttgg
cttgggccacttctccacgcccctgacccatggggtggactgcccctacc
tggccacctacgtggactggcacttcctttttgagtcccaggccgccaag
acaatacgcgatgccttttgtatatttgaacagaaccagggcctccccct
gcggcgacaccactcagatctctactcccactactttgggggccttgcgg
aaacggtgctggtcatcagatctgtgtctactatgctcaactatgactat
gtgtgggatatggtcttccaccctaatggggccatagaaatcagactcca
caccaccggctacatcagctcagcattcccctttggtgctgcccagaggt
atggaaacaaagtttcagagcacaccctgggcacggtccacacccacagc
gcccacttcaaggtggacctggatgtagcaggtaaggcatcctggcagag
gcaaaagtgctggaggggtgagctgaagtctccatgcctagctttaaaag
ttttcgttgggctgggagcagtagcttatgcctgtaagcccaacactttg
ggagactgaggggggtggatcacttgaggtcaggagttcaaaaccagcct
ggccaacatggcgaaatcctgtctgtactaaaaatacaaaaattagctgg
gcatgggtatgctgtaatcctagctactcgggaggctgaggcaggagaat
cacttgaatctgggagtcagaggttgcagtgagctgagattgagccactg
cactccatcctgcgtgactgaac
>NR_037806 1
attcccagtcacccactcactcagaaagccgggagtcatcggacaccttg
ctggtcagaggtcctgggggtggttttgaaccatcagagcttggactttt
ctgacttccccagcaaggatcttcccacttcctgctccctgtgttcccac
cctccagtgttggcacaggcccacccctggctccaccagagccagaagca
gaggtagaatcaggcgggccccgggctgcactccgagcagtgttcctggc
catctttgctactttcctagagaacccggctgttgccttaaatgtgtgag
agggacttggccaaggcaaaagctggggagatgccagtgacaacatacag
ttcatgactaggtttaggaattgggcactgagaaaattctcaatatttca
gagagtccttcccttatttgggactcttaacacggtatcctcgctagttg
gttttaagggaaacactctgctcctgggtgtgagcagaggctctggtctt
gccctgtggtttgactctccttagaaccaccgcccaccagaaacataaag
gattaaaatcacactaataacccctggatggtcaatctgataataggatc
agatttacgtctaccctaattcttaacattgcagctttctctccatctgc
agattattcccagtctcccagtaacacgtttctacccagatcctttttca
tttccttaagttttgatctccgtcttcctgatgaagcaggcagagctcag
aggatcttggcatcacccaccaaagttagctgaaagcagggcactcctgg
ataaagcagcttcactcaactctggggaatgctaccattttttttccaaa
gtagaaaggaagcacttctgagccagtgaccactgaaagatgaacactct
tcctgatcctctcctctagaattcatctcctcctgctagcagccgcgtcc
tggaggagcagcggatggggaatccattctgtttcttcctggtgtttagg
aagttgccccacacacagattgccccgatgtccaaccagaagaagtgaaa
ctgctgctgggtctggagaggtgaagacccgtggccagcttctgttgttg
ccatcggccattgctttttgttcgcttgcttttggttttgcaagaagagc
ggcctctgtctctgatctgcttcaaatcatcattccatcagtgacagaag
tggctgttccatcagtggtcgcagccagttcagctcctgcatccatcccc
aagtgttctgagtggaatttgaggcctccccaaccacctaccaaaaaagg
agggtgaaatgaaaggaagaagaaaaactcagcattctttcctctgacaa
agagtaaaacgacaaggaatatcggcctgaattctcttcccaagaagaaa
gaaagcacaccaacgcaggcatttgtcttctgtccatggtgctgaagttt
attcactttcaaaccactttcagtaacagcaaattctttagaaaaggaaa
atacagggaaagggataaacctcactgacttggaggaaatcaagaggagt
gagcacagcatcagaaagccccctggccccagactgcacccgctttcctg
gccctaccttgaaatccatcaggtctgcgttggacacggcattgtacatg
ggattagctctg

Any help and input would be deeply appreciated.

Thank you for taking the time to go through my problem!

Answer 1

Rather than splitting the sequence into three parts, the way I see this working is to find all occurrences of $pattern in the complete sequence and determine in which third the pattern starts.

The built-in variable $-[0] contains the offset of the start of the most recent successful match.

The code below does what I think you want. It works by accumulating each sequence (which ends either when a new sequence ID is found or the end of file is reached) and passing it to the process_seq subroutine.

The subroutine takes the length of the sequence and caclulates the offset of the end of each third of the string. The idiomatic sprintf '%.0f', $value is used to round fractional values to the nearest character position.

The @counts array is adjusted for each occurrence of $regex in the sequence. The element of @counts to be incremented is established by comparing the starting position of the match in $-[0] with the end offset of each of the three segments of the sequence.

Once each sequence has been processed the values in @counts are accumulated into @totals to give overall figures for all sequences.

The output of the program when using your sample data is shown. The grand total is (9, 1, 6).

use strict;
use warnings;

my $gpat = '[G]{3,5}';
my $npat = '[A-Z]{1,25}';
my $pattern = $gpat.$npat.$gpat.$npat.$gpat.$npat.$gpat; 
my $regex = qr/$pattern/i;

open my $fh, '<', 'sequences.txt' or die $!;

my ($id, $seq);
my @totals = (0, 0, 0);

while (<$fh>) {

  chomp;

  if (/^>(\w+)/) {
    process_seq($seq) if $id;
    $id = $1;
    $seq = '';
    print "$id\n";
  }
  elsif ($id) {
    $seq .= $_;
    process_seq($seq) if eof;
  }
}

print "Total: @totals\n";



sub process_seq {

  my $sequence = shift;
  my $length = length $sequence;

  my @offsets = map {sprintf '%.0f', $length * $_ / 3} 1..3;

  my @counts = (0, 0, 0);

  while ($sequence =~ /$regex/g) {
    my $place = $-[0];
    for my $i (0..2) {
      next if $place >= $offsets[$i];
      $counts[$i]++;
      last;
    }
  }

  print "@counts\n\n";
  $totals[$_] += $counts[$_] for 0..2;
}

output

NR_037701
0 0 1

NM_198399
1 0 0

NR_026816
1 0 1

NR_027917
0 0 0

NR_002777
0 0 0

NR_033769
1 0 0

NM_016326
1 0 1

NM_181641
1 0 1

NM_001144931
0 0 0

NR_029429
0 1 0

NR_026551
1 0 0

NM_181640
1 0 1

NM_016951
1 0 1

NR_002773
1 0 0

NR_037806
0 0 0

Total: 9 1 6

Answer 2

I lifted Borodin's process_seq function but used Bio:SeqIO to read in the file sequence by sequence, an advantage over manually reading line by line and the logic to determine various processing. I believe those advantages are:

• Code that has been developed and tested by many others
• Whenever possible, if output is done via the Bio::SeqIO module, the result file can then be read using Bio::SeqIO read (next_seq) method.
• Other reasons I can't think of now :-)

I imagine the BioPerl package of Bio Genetic code modules must be overwhelming to a biologist beginning programming. He might not be willing to try to dig out the information he needs to begin building a program. BioPerl wiki is a good starting place, especially the Howto section, and then there's a how to for beginners and others. You'll find code examples which are mostly(?) helpful. Bio::Seq has some good code examples in the beginning and is where most of the general sequence functions are. Also, for input/output, the Bio::SeqIO module is used and it has examples at the beginning of it's manual.

#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

my $gpat = '[G]{3,5}'; 
my $npat = '[A-Z]{1,25}'; 
my $pattern = $gpat.$npat.$gpat.$npat.$gpat.$npat.$gpat;  
my $regex = qr/$pattern/i; 

my $in = Bio::SeqIO->new ( -file   => "fasta_dat.txt",
                           -format => 'fasta');
my @totals;
while ( my $seq = $in->next_seq() ) {
    process($seq);
}

print "Totals:   ";
print "@totals\n";

sub process {
    my $seq = shift;
    my @offset = map {sprintf '%.0f', $seq->length * $_ / 3} 1..3;
    my $sequence = $seq->seq;

    my @count = (0,0,0);
    while ($sequence =~ /$regex/g) {
        my $place = $-[0];
        for my $i (0 .. 2) {
            next if $place >= $offset[$i];
            $count[$i]++;
            last;
        }
    }
    print $seq->id, "\n@count\n";
    $totals[$_] += $count[$_] for 0 .. $#count; 
}