extract only uppercases from string

losher has asked for the wisdom of the Perl Monks concerning the following question:

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Re: extract only uppercases from string by BrowserUk (Patriarch) on Aug 23, 2012 at 11:11 UTC
First remove non-ACGTacgt, then split on acgt: `$s = 'G_I1E2_GTGGAG^303CTGgacgCCCTGC_I2E3_TACA';; $s =~ tr[ACGTacgt][]cd;; print for split '[acgt]+', $s;; GGTGGAGCTG CCCTGCTACA` [download] With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday' 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. The start of some sanity?	[reply] [d/l]
Re: extract only uppercases from string by grondilu (Friar) on Aug 23, 2012 at 10:41 UTC
I'm not sure it's easy to do it in just one regex. But you can just use two steps: `my $seq = "G_I1E2_GTGGAG^303CTGgacgCCCTGC_I2E3_TACA"; $seq =~ s/[^ACTGactg]//g; my @result = $seq =~ /[ACTG]+/g; say for @result;` [download] You can do it in one line if your version of perl is recent enough to support the r regex modifier: `perl -wE 'say for "G_I1E2_GTGGAG^303CTGgacgCCCTGC_I2E3_TACA" =~ s/[^AC +TGactg]//gr =~ /[ACTG]+/g;'` [download]	[reply] [d/l] [select]
Re^2: extract only uppercases from string by losher (Initiate) on Aug 23, 2012 at 10:53 UTC
Little modification of your idea works for me! Thanks a lot!	[reply]
Re: extract only uppercases from string by johngg (Canon) on Aug 23, 2012 at 11:11 UTC
`$ perl -E ' > $str = q{G_I1E2_GTGGAG^303CTGgacgCCCTGC_I2E3_TACA}; > say for > map { tr{[ACGT]}{}cd; $_ } > split m{[a-z]+}, $str;' GGTGGAGCTG CCCTGCTACA $` [download] Cheers, JohnGG	[reply] [d/l]
Re: extract only uppercases from string by fisher (Priest) on Aug 23, 2012 at 10:18 UTC
Well, what did you try?	[reply]
Re^2: extract only uppercases from string by losher (Initiate) on Aug 23, 2012 at 10:39 UTC
ie. for the left string I have tried trick like: if ($string =~ m/([ACTG]+).*[actg]/) { print $1 } and several other variations but all I get is an uppercase string till the first character other than ACTG.	[reply]
Re^3: extract only uppercases from string by Anonymous Monk on Aug 23, 2012 at 10:56 UTC
`#!/usr/bin/perl -- use strict; use warnings; use Data::Dump; $_ = 'G_I1E2_GTGGAG^303CTGgacgCCCTGC_I2E3_TACA'; my @matches = ""; while( m{ ([ACTG]+)# $1 is upper \| ([actg]+) # $2 is lower }gxsm ){ if( $1 ){ $matches[-1] .= $1; } if( $2 ){ push @matches, ""; } } dd \@matches; __END__ ["GGTGGAGCTG", "CCCTGCTACA"]` [download]	[reply] [d/l]
Re: extract only uppercases from string by aitap (Curate) on Aug 23, 2012 at 10:31 UTC
Use character classes, grouping and global matching (m//g). Also, have a look at split and there is no ACTG in your string. _{Edit: fixed link} Sorry if my advice was wrong.	[reply]
Re: extract only uppercases from string by cheekuperl (Monk) on Aug 23, 2012 at 10:36 UTC
Replace all except A,C,T,G in the string with nothing. Check perlre for substituition.	[reply]
Re: extract only uppercases from string by Kenosis (Priest) on Aug 23, 2012 at 18:19 UTC
Here's another option: `use Modern::Perl; my $str = 'G_I1E2_GTGGAG^303CTGgacgCCCTGC_I2E3_TACA'; say for map s/[^ACGT]//gr, split 'gacg', $str;` [download] Output: `GGTGGAGCTG CCCTGCTACA` [download] The following will produce the same printed output, but it's actually a single string with an embedded \n separating the two segments: `say $str =~ s/gacg/\n/r =~ /[ACGT\n]/g;` [download]	[reply] [d/l] [select]


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