Your problem description didn't mention how your code fails. So, my first step was to add a
line "exit;" right at the start of your code and then try to run the code. I put that exit statement in
just to see compile errors. Your code does not come anywhere close to
compiling. Perl gives up after the first 34 compile errors!
I would strongly recommend investigating BioPerl. Due to the regex matching capabilities
of Perl, Perl excels at DNA bio stuff.
You should be aware that a FORTRAN or C style loop, eg. for ($start=0; $start <= $index_max; $start++) is
rare in Perl. While this is legal syntax, the very most common error in programming is the "off by one error".
Perl can iterate over an array without using index values.
Again, I recommend that you investigate bioperl. Without any experience or proof, I HIGHLY suspect that parsing
a record like shown below is a basic function of that universe of programs and modules.
I recoded part of what I think you are trying to do below.
I did not code the option to eliminate the "sig_peptide" line from @CDS.
See Flipin good, or a total flop? for more details of how to do that.
Without more data like shown below, I am unable to help further.
use strict;
use warnings;
$|=1;
my @CDS;
my @ORIGIN;
while (my $line =<DATA>)
{
next unless ($line =~ /\S/); #skip blank data lines
push (@CDS,$line) if ( $line =~ /^\s+CDS/ ... $line =~/^\s*[a-z]+/
+);
push (@ORIGIN, $line) if ($line =~ /^\s*ORIGIN/...$line !~/\s*\d/);
+
}
print "CDS section:\n";
print @CDS;
print "\nORIGIN section:\n";
print @ORIGIN;
=PRINTS: ########## a copy from my command line output ####
CDS section:
CDS 10..1011
/gene="hemoglobin"
/codon_start=1
/product="hemoglobin"
/protein_id="AAA29796.1"
/translation="MHSSIVLATVLFVAIASASKTRELCMKSLEHAKVG
+TSKEAKQDG
IDLYKHMFEHYPAMKKYFKHRENYTPADVQKDPFFIKQGQNILLACHVL
+CATYDDRET
FDAYVGELMARHERDHVKVPNDVWNHFWEHFIEFLGSKTTLDEPTKHAW
+QEIGKEFSH
EISHHGRHSVRDHCMNSLEYIAIGDKEHQKQNGIDLYKHMFEHYPHMRK
+AFKGRENFT
KEDVQKDAFFVNKDTRFCWPFVCCDSSYDDEPTFDYFVDALMDRHIKDD
+IHLPQEQWH
EFWKLFAEYLNEKSHQHLTEAEKHAWSTIGEDFAHEADKHAKAEKDHHE
+GEHKEEHH"
sig_peptide 10..63
ORIGIN section:
ORIGIN
1 ggaaccatta tgcactcttc aatagttttg gccaccgtgc tctttgtagc gattg
+cttca
61 gcatcaaaaa cgcgagagct atgcatgaaa tcgctcgagc atgccaaggt tggca
+ccagc
=cut
## Data is abbreviated from https://www.ncbi.nlm.nih.gov/nuccore/M8505
+0.1
## example URL courtesty of [glycine]
__DATA__
COMMENT Original source text: Pseudoterranova decipiens larval cDN
+A to
mRNA.
FEATURES Location/Qualifiers
source 1..1353
/organism="Pseudoterranova decipiens"
/mol_type="mRNA"
/db_xref="taxon:6271"
/dev_stage="larval"
gene 1..1353
/gene="hemoglobin"
5'UTR 1..9
/gene="hemoglobin"
CDS 10..1011
/gene="hemoglobin"
/codon_start=1
/product="hemoglobin"
/protein_id="AAA29796.1"
/translation="MHSSIVLATVLFVAIASASKTRELCMKSLEHAKVG
+TSKEAKQDG
IDLYKHMFEHYPAMKKYFKHRENYTPADVQKDPFFIKQGQNILLACHVL
+CATYDDRET
FDAYVGELMARHERDHVKVPNDVWNHFWEHFIEFLGSKTTLDEPTKHAW
+QEIGKEFSH
EISHHGRHSVRDHCMNSLEYIAIGDKEHQKQNGIDLYKHMFEHYPHMRK
+AFKGRENFT
KEDVQKDAFFVNKDTRFCWPFVCCDSSYDDEPTFDYFVDALMDRHIKDD
+IHLPQEQWH
EFWKLFAEYLNEKSHQHLTEAEKHAWSTIGEDFAHEADKHAKAEKDHHE
+GEHKEEHH"
sig_peptide 10..63
/gene="hemoglobin"
mat_peptide 64..1008
/gene="hemoglobin"
/product="hemoglobin"
misc_feature 696..737
/gene="hemoglobin"
/phenotype="'altered epitope (frameshift)'"
3'UTR 1013..1353
/gene="hemoglobin"
ORIGIN
1 ggaaccatta tgcactcttc aatagttttg gccaccgtgc tctttgtagc gattg
+cttca
61 gcatcaaaaa cgcgagagct atgcatgaaa tcgctcgagc atgccaaggt tggca
+ccagc
