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
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="";
}
Can you help me make it faster and smaller if possible?