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);

[download]

The print statement yields:

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

[download]

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

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