Beefy Boxes and Bandwidth Generously Provided by pair Networks
The stupid question is the question not asked
 
PerlMonks  

comment on

( #3333=superdoc: print w/replies, xml ) Need Help??
This may help. Not polished or thoroughly tested, but should get you to a starting point.

enjoy!
dageek

#!/usr/bin/perl -w use strict; ## set minimum length for polytail to search for my $polytail_min_len = 10; my $polytail_curr_len = $polytail_min_len; my $workline; my $polya_str_base; ## read data record for (<DATA>) { ## remove exteranious characters s/[\r\n]//g; # add new data to end of working data string $workline = $workline . $_; while (length($workline) > $polytail_curr_len) { $polya_str_base = substr($workline,0,$polytail_curr_len); ## remove desired characters from string $polya_str_base =~ s/[AN]//g; ## no characters left = all characters were in desired character set if (length($polya_str_base) == 0) { ## add a character from data set to string to test (ok - bump subscrip +t) $polytail_curr_len++; } else { ## a polytail of at least minimum length was found if ($polytail_curr_len > $polytail_min_len) { print substr($workline,0,$polytail_curr_len-1) . "\n"; ## trim characters of found polytail from working string $workline = substr($workline,$polytail_curr_len); ## reset length of string to test $polytail_curr_len = $polytail_min_len; } ## trim lead character from working field $workline = substr($workline,1); } } } __DATA__ 123456789abcdefghijklmnopqrstuvwxyz ACGGAAAAAAAAAAATCGGATCTGAATGTCTAGAGGGGTTCTCTCCCTTGGTGTGAGTCTAGCCCTGAAA +GTTGCANANAN NANANAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAA NTCCCACTCTANCGCGAAGCCAAATTTGTCGAGAGTACTCTGGGGGGAAGAGATCAGAATTGTGCAGACT +AATCCGTAACTGC CAAGTACTATTGGCCCTGTTCCAACCATCTAACCTCCTTATGATAACCATGCCACTAAATGGGTTCCTGG +ATCTGCACCT CATTCGCTCGCCTTATGGCCTCGGCTCTCTGCGTATCCACCCTCCTCGTCACCGCCATGCCCTTCGACCT +TCAGCGGGGG

In reply to Re: BioInformatics - polyA tail search by johndageek
in thread BioInformatics - polyA tail search by MiamiGenome

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post; it's "PerlMonks-approved HTML":



  • 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.
Log In?
Username:
Password:

What's my password?
Create A New User
Domain Nodelet?
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others pondering the Monastery: (4)
As of 2023-02-05 07:12 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?
    I prefer not to run the latest version of Perl because:







    Results (31 votes). Check out past polls.

    Notices?