One approach would be to reset the input record separator.

#!/usr/bin/perl

use warnings;
use strict;

$/ = "\n> ";

while (<DATA>) {
    chomp;
    print;
}

__DATA__
.06669701$-.1672469$.02157899$.0346167$.65879324$.91614802$.45012441$r
+s11080516
-.05563282$-.00141932$.00036263$.00035752$.00541792$.00345471$.9269254
+3$rs11080
> 530
-.00042649$-.00475721$.00167316$.00182299$.99057815$.90393977$.6990673
+3$rs11080
> 537
.10901125$.0361255$.02148475$.00853908$.74113541$.45908988$.68361003$r
+s11080542
-.03866776$-.05004879$.00185491$.00145606$.38131545$.36141448$.1755140
+3$rs11080
> 557
-.004521$.01312692$.00033174$.00070174$.77873394$.88615378$.63499741$r
+s1108056
.0339248$.02398934$.00276444$.00303152$.80478053$.55026576$.67512938$r
+s11080561

[download]

outputs:

.06669701$-.1672469$.02157899$.0346167$.65879324$.91614802$.45012441$r
+s11080516
-.05563282$-.00141932$.00036263$.00035752$.00541792$.00345471$.9269254
+3$rs11080530
-.00042649$-.00475721$.00167316$.00182299$.99057815$.90393977$.6990673
+3$rs11080537
.10901125$.0361255$.02148475$.00853908$.74113541$.45908988$.68361003$r
+s11080542
-.03866776$-.05004879$.00185491$.00145606$.38131545$.36141448$.1755140
+3$rs11080557
-.004521$.01312692$.00033174$.00070174$.77873394$.88615378$.63499741$r
+s1108056
.0339248$.02398934$.00276444$.00303152$.80478053$.55026576$.67512938$r
+s11080561

[download]

EDIT:
The simple example I gave just outputs the data, but, instead, you could push each line onto an array or append it to a string for further processing.

In reply to Re: append data to previous line by fishmonger
in thread append data to previous line by Anonymous Monk

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


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.