comment on

and here is another I put together to show me :

(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]

so for your sig : "TTTATCGGTCGTTATATAGATGTTTGCA" I get the following output:

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]

again works with any list passed as $ARGV[0] or with individual strings ala:

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

etc. and it does not match whitespace(s) as part of a reverse complementary match

In reply to Re^2: What one-liners do people actually use? by l3v3l
in thread What one-liners do people actually use? by TomDLux

Are you posting in the right place? Check out Where do I post X? to know for sure.
Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
<code> <a> <b> <big> <blockquote> <br /> <dd> <dl> <dt> <em> <font> <h1> <h2> <h3> <h4> <h5> <h6> <hr /> <i> <li> <nbsp> <ol> <p> <small> <strike> <strong> <sub> <sup> <table> <td> <th> <tr> <tt> <u> <ul>
Snippets of code should be wrapped in <code> tags not <pre> tags. In fact, <pre> tags should generally be avoided. If they must be used, extreme care should be taken to ensure that their contents do not have long lines (<70 chars), in order to prevent horizontal scrolling (and possible janitor intervention).
Want more info? How to link or How to display code and escape characters are good places to start.


Do you know where your variables are?
	PerlMonks