Hello all!
I have this code to create oneline-fasta files for some protein sequences.
Oneline means getting all lines that do not start with ">" into a single line. Here are the files and the code I have.
SAMPLE ENTRIES
>gi|321257144|ref|XP_003193485.1| flap endonuclease [Cryptococcus gatt
+ii WM276]
MGIKGLTGLLSENAPKCMKDHEMKTLFGRKVAIDASMSIYQFLIAVRQQDGQMLMNESGDVTSHLMGFFY
RTIRMVDHGIKPCYIFDGKPPELKGSVLAKRFARREEAKEGEEEAKETGTAEDVDKLARRQVRVTREHNE
ECKKLLSLMGIPVVTAPGEAEAQCAELARAGKVYAAGSEDMDTLTFHSPILLRHLTFSEAKKMPISEIHL
DVALRDLEMSMDQFIELCILLGCDYLEPCKGIGPKTALKLMREHGTLGKVVEHIRGKMAEKAEEIKAAAD
EEAEAEAEAEKYDSDPENEEGGETMINSDGEEVPAPSKPKSPKKKAPAKKKKIASSGMQIPEFWPWEEAK
QLFLKPDVVNGDDLVLEWKQPDTEGLVEFLCRDKGFNEDRVRAGAAKLSKMLAAKQQGRLDGFFTVKPKE
PAAKDAGKGKGKDTKGEKRKAEEKGAAKKKTKK
>gi|321473340|gb|EFX84308.1| hypothetical protein DAPPUDRAFT_47502 [Da
+phnia pulex]
MGIKGLTQVIGDTAPTAIKENEIKNYFGRKVAIDASMSIYQFLIAVRSEGAMLTSADGETTSHLMGIFYR
TIRMVDNGIKPVYVFDGKPPDMKGGELTKRAEKREEASKQLVLATDAGDAVEMEKMNKRLVKVNKGHTDE
CKQLLTLMGIPYVEAPCEAEAQCAALVKAGKVYATATEDMDSLTFGSNVLLRYLTYSEAKKMPIKEFHLD
KILDGLSYTMDEFIDLCIMLGCDYCDTIKGIGAKRAKELIDKHRCIEKVIENLDTKKYTVPENWPYQEAR
RLFKTPDVADAETLDLKWTQPDEEGLVKFMCGDKNFNEERIRSGAKKLCKAKTGQTQGRLDSFFKVLPSS
KPSTPSTPASKRKVGCIIYLFLYF

[download]

The code as it is now:
if(@ARGV!=1) { die "correct usage:\n\t perl oneline.pl <fasta_file> "}
+;

open(FASTA,$ARGV[0]) || die "can't open fasta file";
$line="";
while($line !~ /^>/){
    $line=<FASTA>;
}
$line  =~ s/[\r]//g; # remove carriage return
print $line;
$prev="";
while (1){
    $line=<FASTA>;
    $line=~ s/[\r]//g; # remove carriage return
    while ($line !~ /^>/){
        chomp $line;
        $prev=$prev.$line;
        $prev =~ s/[\r]//g; # remove carriage return
        $line=<FASTA>;
        if(!(defined $line)) { print $prev."\n"; close(FASTA); exit(1)
+;}
    }
    print $prev."\n";
    $line  =~ s/[\r]//g; # remove carriage return
    print $line;
    $prev="";
}

[download]

Can you help me make it faster and smaller if possible?

In reply to Can you make this code shorter and/or quicker as well? 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.