lenti216 [~/perltest]>more file5.pl
#!/opt/local/bin/perl -w
#  file.pl

$filename = shift;    

unless (defined($filename) )  {
print "What sequence to analyze? ";
$filename = <STDIN>;
chomp ($filename);
                              }

# open file for reading from and associate it with a "filehandle"
# if open fails (returns "false"), inform user and end

unless (open (PROTEINFILE, $filename)) {
   print "Cannot open file: $filename \n\n";
   exit;
                                       }
$outputfile = "good.pep";               

open (OUTFILE, ">>$outputfile"); #open file for appending to

#initialize (set to an initial value) scalar string variable $seq
$seq = "";

#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 ">"

# s/ / / means replace (substitute) one regular expression for another
# \s means white space (tab, blank space, new line, etc.)
# s/\s// means replace a white space character by nothing (delete it)
# s/\s//g means do the substitution as many times as possible (globally)
# without the g, the substitution is only done once each string

# =~ is the binding operator, used to assign regexp to variables

while (<PROTEINFILE>)

    { if (/^>/)  {
         print $seq,"\n"; # print on the screen
         print OUTFILE $seq,"\n";  # also print to a file
         $seq = ""; 
         print $_;
         print OUTFILE $_; 
                 }
  else { 
       chomp $_; $_ =~ s/\s//g;  
       $seq = $seq . $_; 
       }  # . is the string concatenation operator
    }

# process last sequence

print $seq,"\n";
print OUTFILE $seq,"\n";

# close output file
# close (OUTFILE);

exit;  
lenti217 [~/perltest]>perl file5.pl tests.pep

>A28086  Length: 104  
VKQIESKSAFQEVLDSAGDKLVVVDFSATWCGPCKMIKPFFHALSEKFNNVVFIEVDVDDCKDIAAECEVKCMPTFQFFKKGQKVGEFSGANKEKLEATINELL
>gi|79882|pir||B29504 hypothetical 18K protein (mer operon) -
Staphylococcus aureus plasmid pI258
MKKRISFTAIMTVLLIGLTACGAESDTANESKVQDIQGNPVSLPNEKPTLIYFMATWCPSCIYNEEIFKEMHQLNPNDVQLITVSLDPNTDTKESLAKFKQDYGGDWPHVLKNGKEIADTYGVKQLEEIVLVNSENEVFYRSVRPSFDDLKEALTQIGVEL
>ORF15 S. aureus pathogenicity island
MEDVTNEEVFEMIDSRTGVLNANDWKSQLRRSATTQALKKTTTNAEIILCNDESLKGLVQYDAFEKVTKLKRLPYWRSKGDTNYYWADIDTTHVISHIDKLYNVQFSRDLIDTVIEKEAYQNRFHPIKSMIESKSWDGIKRIETLFIDYLGAEDNHYNREVTKKWMMGAVARIYQPGIKYDSMIILYGGQGVGKSTAVSKLGGHWYNQSIKTFKGDEVYKKLQGSWICEIEELSAFQKSTIEDIKGFISAIVDIYRASYGKRTERHPRQCVFVGTTNNYEFLKDQTGNRRFFPITTDKNKATKSPFDDLTPDVVQQMFAEAKVYFDEDPTDKALLLDKEASEMALKVQEAHSEKDALVGEIEEFLERPIPSDYWYRTLEEKRVSAHDVIDQDYIKLYGDGKLIELPNTKPGAYVWRDKVCSMEIWKVMMKRDDQPQQHHLRKIDKALRNTNYCDTVKKQTRYGEGIGKQYGFSVDLASYYKNLKV
lenti218 [~/perltest]>more good.pep

>A28086  Length: 104  
VKQIESKSAFQEVLDSAGDKLVVVDFSATWCGPCKMIKPFFHALSEKFNNVVFIEVDVDDCKDIAAECEVKCMPTFQFFK
KGQKVGEFSGANKEKLEATINELL
>gi|79882|pir||B29504 hypothetical 18K protein (mer operon) -
Staphylococcus aur
eus plasmid pI258
MKKRISFTAIMTVLLIGLTACGAESDTANESKVQDIQGNPVSLPNEKPTLIYFMATWCPSCIYNEEIFKEMHQLNPNDVQ
LITVSLDPNTDTKESLAKFKQDYGGDWPHVLKNGKEIADTYGVKQLEEIVLVNSENEVFYRSVRPSFDDLKEALTQIGVE
L
>ORF15 S. aureus pathogenicity island
MEDVTNEEVFEMIDSRTGVLNANDWKSQLRRSATTQALKKTTTNAEIILCNDESLKGLVQYDAFEKVTKLKRLPYWRSKG
DTNYYWADIDTTHVISHIDKLYNVQFSRDLIDTVIEKEAYQNRFHPIKSMIESKSWDGIKRIETLFIDYLGAEDNHYNRE
VTKKWMMGAVARIYQPGIKYDSMIILYGGQGVGKSTAVSKLGGHWYNQSIKTFKGDEVYKKLQGSWICEIEELSAFQKST
IEDIKGFISAIVDIYRASYGKRTERHPRQCVFVGTTNNYEFLKDQTGNRRFFPITTDKNKATKSPFDDLTPDVVQQMFAE
AKVYFDEDPTDKALLLDKEASEMALKVQEAHSEKDALVGEIEEFLERPIPSDYWYRTLEEKRVSAHDVIDQDYIKLYGDG
KLIELPNTKPGAYVWRDKVCSMEIWKVMMKRDDQPQQHHLRKIDKALRNTNYCDTVKKQTRYGEGIGKQYGFSVDLASYY
KNLKV
lenti219 [~/perltest]>