Re^4: How to expand a string

Thanks, all the replies are helping me get there but it's still a bit of a nightmare to code. Here's some example inputs etc.

R = A or G
S = C or G
K = G or T
All the other letters stay constant.

my $seq1 = "CAG GTR CAG CTG AAG SAG TCA GG";
my $seq2 = "GAK GTG CAG CTT CAG CAG TCR GG";

The gaps between sets of 3 letters aren't important - it just signifies DNA codons.

So, both seq 1 and seq 2 have 4 possible resulting sequences. I need to store the 4 seqs associated with seq 1 separately e.g. in a different array to those of seq 2.

If you have any ideas about the best way to do this I'd be very grateful! Speed isn't a big consideration, as long as it works!

Thanks for your help.

Comment on Re^4: How to expand a string

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Re^5: How to expand a string by BrowserUk (Patriarch) on Nov 29, 2007 at 16:52 UTC
#! perl -slw use strict; my @seqs = ( "CAG GTR CAG CTG AAG SAG TCA GG", "GAK GTG CAG CTT CAG CAG TCR GG", ); for my $seq ( @seqs ) { print $seq; $seq =~ tr[ ][_]; $seq =~ s[R][{A,G}]g; $seq =~ s[S][{C,G}]g; $seq =~ s[K][{G,T}]g; tr[_][ ] and print "\t$_" while glob $seq; } __END__ CAG GTR CAG CTG AAG SAG TCA GG CAG GTA CAG CTG AAG CAG TCA GG CAG GTA CAG CTG AAG GAG TCA GG CAG GTG CAG CTG AAG CAG TCA GG CAG GTG CAG CTG AAG GAG TCA GG GAK GTG CAG CTT CAG CAG TCR GG GAG GTG CAG CTT CAG CAG TCA GG GAG GTG CAG CTT CAG CAG TCG GG GAT GTG CAG CTT CAG CAG TCA GG GAT GTG CAG CTT CAG CAG TCG GG [download] Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice. "Too many [] have been sedated by an oppressive environment of political correctness and risk aversion."	[reply] [d/l]
Re^5: How to expand a string by GrandFather (Saint) on Nov 29, 2007 at 20:10 UTC
A somewhat general solution could look like: `use strict; use warnings; use Data::Dump::Streamer; my %replace = ( R => '{A,G}', S => '{C,G}', K => '{G,T}', ' ' => '_', ); my %seqs = ( seq1 => {org => "CAG GTR CAG CTG AAG SAG TCA GG"}, seq2 => {org => "GAK GTG CAG CTT CAG CAG TCR GG"} ); for my $seqKey (keys %seqs) { $seqs{$seqKey}{glob} = $seqs{$seqKey}{org}; $seqs{$seqKey}{glob} =~ s/$_/$replace{$_}/g for keys %replace; push @{$seqs{$seqKey}{expanded}}, map {y/_/ /; $_} glob $seqs{$seq +Key}{glob}; } Dump (\%seqs);` [download] Prints: $RO1 = 'seq1'; make_ro($RO1); $HASH1 = { expanded => [ 'CAG GTA CAG CTG AAG CAG TCA GG', 'CAG GTA CAG CTG AAG GAG TCA GG', 'CAG GTG CAG CTG AAG CAG TCA GG', 'CAG GTG CAG CTG AAG GAG TCA GG' ], glob => 'CAG_GT{A,G}_CAG_CTG_AAG_{C,G}AG_TCA_GG', org => 'CAG GTR CAG CTG AAG SAG TCA GG' }; $RO2 = 'seq2'; make_ro($RO2); $HASH2 = { expanded => [ 'GAG GTG CAG CTT CAG CAG TCA GG', 'GAG GTG CAG CTT CAG CAG TCG GG', 'GAT GTG CAG CTT CAG CAG TCA GG', 'GAT GTG CAG CTT CAG CAG TCG GG' ], glob => 'GA{G,T}_GTG_CAG_CTT_CAG_CAG_TC{A,G}_GG', org => 'GAK GTG CAG CTT CAG CAG TCR GG' }; [download] Note that you well need Perl 5.6.0 or later for the glob to work correctly. Perl is environmentally friendly - it saves trees	[reply] [d/l] [select]


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