I have a file which contains several 100s of fasta sequences in the form as such:
>hsa_circ_0000001|chr1:1080738-1080845-|None|None ATGGGGTTGGGTCAGCCGTGCGGTCAGGTCAGGTCGGCCATGAGGTCAGGTGGGGTCGGCCATGAAGGTG +GTGGGGGTCATGAGGTCACAAGGGGGTCGGCCATGTG >hsa_circ_0000002|chr1:1158623-1159348-|NM_016176|SDF4 GGTGGATGTGAACACTGACCGGAAGATCAGTGCCAAGGAGATGCAGCGCTGGATCATGGAGAAGACGGCC +GAGCACTTCCAGGAGGCCATGGAGGAGAGCAAGACACACTTCCGCGCCGTGGACCCTGACGGGGACGGT +CACGTGTCTTGGGACGAGTATAAGGTGAAGTTTTTGGCGAGTAAAGGCCATAGCGAGAAGGAGGTTGCC +GACGCCATCAGGCTCAACGAGGAACTCAAAGTGGATGAGGAAA
I wrote a script that counts the sequence length (bases) in each sequence and creates a file containing them all, but the problem is that it also adds the new line character into the count making it count+1. Is there a way to -1 from the count in order to obtain the true count of the sequence length? My script is as follows:
my $filename = 'counts.txt'; open (my $fh, '>', $filename) or die "Could not open '$filename' $!"; my $count = ""; while (my $line = <>){ if ($line =~ /^>hsa/){ $line = <>; $count .= length$line; $count .= " "; } } print $fh $count; close $fh;

In reply to How to amend character count. by Peter Keystrokes

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