Dear Monks,
I have a file of the following format:
> gi|11SB_CUCMA Train|1 21
MARSSLFTFLCLAVFINGCLSQIEQQSPWEFQGS
EVWQQHRYQSPRACRLENLRAQDPVRLLLPGFSNAPKLIFV
AQGFGIRGIAIPGCAETYQT
SSSSSSSSSSSSSSSSSSSSS....................
...........................
.................
..........
> gi|1A43_HUMAN Train|1 24
MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPG
RGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWSQTDRANLGTLRGYYNQSEDGSHTIQ
+R
MYGCDVGPDGRFLRGYQQDAYDGKDYIALNEDLRSWTAADMAAQITQRKWETAHEAE
SSSSSSSSSSSSSSSSSSSSSSSS..............................................
+...........................................
.............
..........................................

[download]

which I need to bring into the format of:
> gi|11SB_CUCMA Train|1 21
MARSSLFTFLCLAVFINGCLSQIEQQSPWEFQGSEVWQQHRYQSPRACRLENLRAQDPVRLLLPGFSNAP
+KLIFVAQGFGIRGIAIPGCAETYQT
SSSSSSSSSSSSSSSSSSSSS.................................................
+.........................
> gi|1A43_HUMAN Train|1 24
MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRME
+PRAPWIEQEGPEYWSQTDRANLGTLRGYYNQSEDGSHTIQRMYGCDVGPDGRFLRGYQQDAYDGKDYIA
+LNEDLRSWTAADMAAQITQRKWETAHEAE
SSSSSSSSSSSSSSSSSSSSSSSS..............................................
+.....................................................................
+.............................

[download]

which, in essence, means that one should keep 3 lines for each "entry", the line that starts with ">", then the lines that do not contain any "." and finally the lines that contain "."
I have tried this, but without result...
$/="> ";
while(<>)
{
    $seq='';
    $top='';

    if($_=~/^gi\|(.*?) \.*?|.*/m)
    {
        $id=$1;
        #print $id."\n";
    }

    if($_!~/^gi/mg )
    {
        print $_;
        $seq.=$_;
    }

    print $seq."\n";
}
$/="\n";

[download]

Can you point me to some direction please?

In reply to Help in joining these lines 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.