Re: What one-liners do people actually use?

here is a liner I use to find reverse complementary / palindromic D|RNA sequences (thought this would be up your alley because of your sig.) :

perl -nle 'tr/A-Z/a-z/;$m=length();reverse(substr($_,($m/2)+($m%2))) e
+q substr($_,0,$m/2) ? print : next'  /file/of/sequences/one_per_line
[download]

works on any list of "words" tho ... /usr/share/dict/words, etc.

update: ... this node_id has 2X \d{3} palindromes and my username is a palindrome ...

Comment on Re: What one-liners do people actually use? Download Code

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Re^2: What one-liners do people actually use?
by l3v3l (Monk) on Dec 12, 2005 at 18:26 UTC

(line|entry) #, org.string, st. position of pal., length of pal., palindrome found

perl -nle 'tr/a-z/A-Z/;$l=length();for $m(3..$l){for $c(0..($l-3)){las
+t if $m+$c>$l;$f=substr($_,$c,$m);($r=reverse($f))=~s/s+//g;print "$.
+\t$_\t$c\t$m\t$f" if ($f eq $r);}}' example | more
[download]

1    TTTATCGGTCGTTATATAGATGTTTGCA    0    3    TTT
1    TTTATCGGTCGTTATATAGATGTTTGCA    2    3    TAT
1    TTTATCGGTCGTTATATAGATGTTTGCA    12    3    TAT
1    TTTATCGGTCGTTATATAGATGTTTGCA    13    3    ATA
1    TTTATCGGTCGTTATATAGATGTTTGCA    14    3    TAT
1    TTTATCGGTCGTTATATAGATGTTTGCA    15    3    ATA
1    TTTATCGGTCGTTATATAGATGTTTGCA    17    3    AGA
1    TTTATCGGTCGTTATATAGATGTTTGCA    20    3    TGT
1    TTTATCGGTCGTTATATAGATGTTTGCA    22    3    TTT
1    TTTATCGGTCGTTATATAGATGTTTGCA    12    5    TATAT
1    TTTATCGGTCGTTATATAGATGTTTGCA    13    5    ATATA
1    TTTATCGGTCGTTATATAGATGTTTGCA    16    5    TAGAT
1    TTTATCGGTCGTTATATAGATGTTTGCA    21    5    GTTTG
[download]

# echo "TTTATCGGTCGTTATATAGATGTTTGCA" | perl -ne ...
[download]

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