lenti240 [~/perltest]>more file.pl
#!/opt/local/bin/perl -w
#  file.pl

$filename = "tests.pep";

#open file and associate it with a "filehandle"
open (PROTEINFILE, $filename);

#while there are unread lines in PROTEINFILE
#read one line and, if the first character is a ">", print it

# regular expressions (regexps) are enclosed in / /s.
# ^ in a regexp means first character
# ^> means first character is a ">"

while (<PROTEINFILE>)
  { if (/^>/)
     { print $_; }
  }
exit;
lenti241 [~/perltest]>perl file.pl
>A28086  Length: 104
>gi|79882|pir||B29504 hypothetical 18K protein (mer operon) -
Staphylococcus aureus plasmid pI258
>ORF15 S. aureus pathogenicity island
lenti242 [~/perltest]>