lenti242 [~/perltest]>more bioperl1.pl
#!/opt/local/bin/perl
#  fastabioperl.pl

use Bio::Tools::SeqStats;

$filename = "tests.pep";
open (PROTEINFILE,$filename);

#initialize variable to hold sequence
$seq ="";

#while there are sequence lines to be read
while (<PROTEINFILE>) {
        if (/^>/)  { # if on a > line
                if (length($seq) > 0) { # if there is a prior sequence to
proces
s
                        $seqobj = Bio::Seq->new('-seq'=>$seq);
                        print $seq,"\n";
                        $seq_stats  =  Bio::Tools::SeqStats->new($seqobj);
                        $weight = $seq_stats->get_mol_wt();
                        @weight_array = @$weight;
                        $monomer_ref = $seq_stats->count_monomers();
                        %monomer_hash = %$monomer_ref;
print "largest MW = @weight_array[0]; smallest MW = @weight_array[1] \n";
                        foreach $aa (keys (%monomer_hash)) {
                                print "$aa: $monomer_hash{$aa} \n";
                                }
                        $seq = "";
                        } # end of prior sequence
                print $_;
                }  # end of > line

        else {
                chomp $_; s/\s//g;
                $seq = $seq . $_;
                }
        }
        #end of sequence lines to be read

#process last sequence
$seqobj = Bio::Seq->new('-seq'=>$seq);
print $seq,"\n";

$seq_stats  =  Bio::Tools::SeqStats->new($seqobj);
$weight = $seq_stats->get_mol_wt();
@weight_array = @$weight;
$monomer_ref = $seq_stats->count_monomers();
%monomer_hash = %$monomer_ref;

print "largest MW = @weight_array[0]; smallest MW = @weight_array[1]
\n";

foreach $aa (keys (%monomer_hash)) {
        print "$aa: $monomer_hash{$aa} \n";
        }
exit;
lenti243 [~/perltest]>perl bioperl1.pl
>A28086  Length: 104
VKQIESKSAFQEVLDSAGDKLVVVDFSATWCGPCKMIKPFFHALSEKFNNVVFIEVDVDDCKDIAAECEVKCMPTFQFFK
KGQKVGEFSGANKEKLEATINELL
largest MW = 11629; smallest MW = 11629
A: 8
C: 5
D: 7
E: 10
F: 10
G: 5
H: 1
I: 5
K: 13
L: 6
M: 2
N: 4
P: 3
Q: 4
R:
S: 6
T: 3
V: 11
W: 1
Y:
>gi|79882|pir||B29504 hypothetical 18K protein (mer operon) -
Staphylococcus aur
eus plasmid pI258
MKKRISFTAIMTVLLIGLTACGAESDTANESKVQDIQGNPVSLPNEKPTLIYFMATWCPSCIYNEEIFKEMHQLNPNDVQ
LITVSLDPNTDTKESLAKFKQDYGGDWPHVLKNGKEIADTYGVKQLEEIVLVNSENEVFYRSVRPSFDDLKEALTQIGVE
L
largest MW = 18118; smallest MW = 18118
A: 8
C: 3
D: 10
E: 14
F: 6
G: 8
H: 2
I: 11
K: 12
L: 15
M: 4
N: 10
P: 8
Q: 7
R: 3
S: 10
T: 11
V: 12
W: 2
Y: 5
>ORF15 S. aureus pathogenicity island
MEDVTNEEVFEMIDSRTGVLNANDWKSQLRRSATTQALKKTTTNAEIILCNDESLKGLVQYDAFEKVTKLKRLPYWRSKG
DTNYYWADIDTTHVISHIDKLYNVQFSRDLIDTVIEKEAYQNRFHPIKSMIESKSWDGIKRIETLFIDYLGAEDNHYNRE
VTKKWMMGAVARIYQPGIKYDSMIILYGGQGVGKSTAVSKLGGHWYNQSIKTFKGDEVYKKLQGSWICEIEELSAFQKST
IEDIKGFISAIVDIYRASYGKRTERHPRQCVFVGTTNNYEFLKDQTGNRRFFPITTDKNKATKSPFDDLTPDVVQQMFAE
AKVYFDEDPTDKALLLDKEASEMALKVQEAHSEKDALVGEIEEFLERPIPSDYWYRTLEEKRVSAHDVIDQDYIKLYGDG
KLIELPNTKPGAYVWRDKVCSMEIWKVMMKRDDQPQQHHLRKIDKALRNTNYCDTVKKQTRYGEGIGKQYGFSVDLASYY
KNLKV
largest MW = 56365; smallest MW = 56365

A: 26
C: 5
D: 39
E: 35
F: 17
G: 27
H: 10
I: 34
K: 48
L: 32
M: 11
N: 19
P: 13
Q: 21
R: 24
S: 27
T: 31
V: 29
W: 10
Y: 27
lenti244 [~/perltest]>