Using index to extract substring from an array in perl

Question

I would like to use perl to extract 30 character substrings from an array, using another array that consists of indices where I would like the substring from each line to start. For instance, Line 1 extract 30 characters starting at position 21, line 2 starting at 5, line 3 ... etc. Is this possible? I know its easy to do with a fixed index but I have never tried using indices stored in a separate array. Thanks so much.

For example, Array 1 would consist of strings for instance in my case:

ATGTCAAATCCAGAAAGCTTGAAAAAACAGGTTGAACCTCCTGGTTACAATGAGTTATTTATGGTGGAAGATGTTTGTAATGTGGACCTAGAGCAGGGACT
TGATTTGTGTAAGCCTGAAAAGGTAAACAAACAATCTCAACGATCTCGACAATCCCGACAATCCCTCTTTACCAACACCATTAAGCCTCAAAAAGACAAGA
TGAATATTAAAACAAATAAAATAAAAGAGTTTTTAAATGACCTTTTTACTGAATTTTCTAAATTCCACAATAGCTATTATCCTAATGGAAGAATTTCTACT
CAGGACAAATCTCGATGGGTCTTGCTTATTATTTGGTCTATTATCACTATTTTAACAATAGACAAGAAATTTAAAATAAAAGAGTCATATTTAGAATGGAT
AGGTGAAAATCAGTCCCACAGTGAAATTTGGGGGCCTATTGTTATTTATGTTGGCTTATTCATACTCTTATTGTCTGCTTTTAACTGTACGTTTCCTTCAC

And Array two consists of indices that I want to start each 30 char substring I extract from such as

Leaving an output of:

AAAAAACAGGTTGAACCTCCTGGTTACAAT
AATCTCAACGATCTCGACAATCCCGACAAT
ATAAAATAAAAGAGTTTTTAAATGACCTTT
AATCTCGATGGGTCTTGCTTATTATTTGGT
CAGTGAAATTTGGGGGCCTATTGTTATTTA

I'm not quite sure I understand you. Could you perhaps show code that you tried but didn't work as expected? Actual example data (instead of a description of this data) plus the expected output would help as well. — amon
– amon, Commented Jul 12, 2013 at 20:45

amon · Accepted Answer · 2013-07-12 21:29:41Z

2

Lets assume we have a string, and an offset:

my $string = "ATGTCAAATCCAGAAAGCTTGAAAAAACAGGTTGAACCTCCTGGTTACAATGAGTTATTTATGGTGGAAGATGTTTGTAATGTGGACCTAGAGCAGGGACT";
my $offset = 21;
my $length = 30;

We can then get the required substring like

substr $string, $offset, $length;

But if we have an array @strings and a corresponding array @offsets, then for the i-th element we have:

substr $strings[$i], $offsets[$i], $length;

When we loop over all indices of the arrays (0 .. $#strings), we can get each substring.

answered Jul 12, 2013 at 21:29

amon

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