translating awk script into perl - regex

Question

I'm trying to translate this code into perl.
gawk '/^>c/ {OUT=substr($0,2) ".fa";print " ">OUT}; OUT{print >OUT}' your_input
Can someone help me?

Answer 1

Perl has a utility to do this for you called a2p. If your script is call script.awk then you would run:
$ a2p script.awk
Which produces:
#!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$#"}'
if $running_under_some_shell;
# this emulates #! processing on NIH machines.
# (remove #! line above if indigestible)
eval '$'.$1.'$2;' while $ARGV[0] =~ /^([A-Za-z_0-9]+=)(.*)/ && shift;
# process any FOO=bar switches
$, = ' '; # set output field separator
$\ = "\n"; # set output record separator
while (<>) {
chomp; # strip record separator
if (/^>c/) {
$OUT = substr($_, (2)-1) . '.fa';
&Pick('>', $OUT) &&
(print $fh ' ');
}
;
if ($OUT) {
&Pick('>', $OUT) &&
(print $fh $_);
}
}
sub Pick {
local($mode,$name,$pipe) = #_;
$fh = $name;
open($name,$mode.$name.$pipe) unless $openammeamme}++;
}
To save this to a file, use redirection:
$ a2p script.awk > script.pl
Perl also provides a tool for converting sed scripts: s2p.

Answer 2

#!/usr/bin/perl
my ($outf,$OUT) ;
while(<>){
if(/^>(c.*)/){ $OUT = "$1.fa";
close($outf) if $outf;
open($outf,">",$OUT);
print OUT " \n"}
if($outf){ print $outf $_ }
}
if input is:
>caaa
sdf
sdff
>cbbb
ew
ew
Creats 2 files:
==> caaa.fa <==
>caaa
sdf
sdff
==> cbbb.fa <==
>cbbb
ew
ew

Answer 3

This perl one liner should be equivalent of that awk command:
perl -ane 'if($F[0] =~ /^>c/){$OUT=substr($F[0],1).".fa"; if(OUT==null) {open(OUT,">$OUT");} print OUT " \n"} if ($OUT){print OUT $_} END{close(OUT)}' file
Indented command line:
perl -ane 'if ($F[0] =~ /^>c/) {
$OUT = substr($F[0], 1).".fa";
if (OUT==null) { open(OUT, ">$OUT") }
print OUT " \n"
}
if ($OUT) {
print OUT $_
}
END{close(OUT)
}' file