Beefy Boxes and Bandwidth Generously Provided by pair Networks
"be consistent"
 
PerlMonks  

comment on

( [id://3333]=superdoc: print w/replies, xml ) Need Help??

Hi,

I'm processing the text below, trying to extract all mentions of chromosomal bands (they're the ones with the numbers and p's and q's). Using this code:

$c='[\d\-\.pqxy]'; #regexp (@chroms)=($text=~/\s$c*?\s/sig); #extract all for ($i=0; $i<@chroms; $i++) { splice(@chroms, $i, 1) if (!($chroms[$i]=~/[pqxy]/i)); } #eliminate pure numbers print "$_\n" foreach (@chroms);

The print statement yields:

Xq27-q28 q11q12 22q121 1q422q43 19q 17p11 1q25 13q123 11p112 1q25 1q2331 8p22 8p22 7q1123 7p22 19q12q1311 52 15 19q12q1311

Two questions: why doesn't the splice statement get rid of the "52" and "15" elements? Why do none of the dots or hyphens appear for the captured elements?

Whole-genome scan studies recently identified a locus on Xq27-q28 Xq11-q12 22q12.1 1q42.2-q43 19q 17p11 1q25 13q12.3 11p11.2 10q25 10q23.31 8p22 8p22 7q11.23 7p22 chromosome segments 19q12-q13.11 linked to prostate tumor aggressiveness by use of the Gleason score as a quantitative trait. We have now completed finer-scale linkage mapping across this region that confirmed and narrowed the candidate region to 2 cM, with a peak between markers D19S875 and D19S433. We also performed allelic imbalance (AI) studies across this region in primary prostate tumors from 52 patients unselected for family history or disease status. A high level of AI was observed, with the highest rates at markers D19S875 (56%) and D19S433 (60%). Furthermore, these two markers defined a smallest common region of AI of 0.8 Mb, with 15 (29%) prostate tumors displaying interstitial AI involving one or both markers. In addition, we noted a positive association between AI at marker D19S875 and extension of tumor beyond the margin (P = 0.02) as well as a higher Gleason score (P = 0.06). These data provide strong evidence that we have mapped a prostate tumor aggressiveness locus to chromosome segments 19q12-q13.11 that may play a role in both familial and non-familial forms of prostate cancer.


In reply to regexp and substitute operator problem by dannoura

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?Last hourOther CB clients
Other Users?
Others sharing their wisdom with the Monastery: (5)
As of 2024-03-28 13:17 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    No recent polls found