# Searching for motifs

# Ask the user for the filename of the file containing 
# the protein sequence data, and collect it from the keyboard
print "Please type the filename of the protein sequence data:\n";
$proteinfilename = <STDIN>;
# Remove the newline from the protein filename 
chomp $proteinfilename;

# open the file, or exit
unless( open(PROTEINFILE, $proteinfilename)) {
    print "Cannot open file \"proteinfilename\"\n\n";
    exit;
}


# Read the protein sequence data from the file, and store it
# into the array variable @protein
@protein = <PROTEINFILE>;

# Close the file - we've read all the data into @protein now.
close PROTEINFILE;
# Put the protein sequence data into a single string, as it's easier
# to search for a motif in a string than in an array of lines
$protein = join ('', @protein);

# Remove whitespace 
$protein =~ s/\s//g;

# In a loop, ask the user for a motif, search for the motif,
# and report if it was found.
# Exit if no motif is entered.
do{
    print "Enter a motif to search for:";
    $motif = <STDIN>;

    # Remove the newline at the end of $motif
    chomp $motif;
    # Look for the motif
    if ($protein =~ /$motif/){
        print "I found it! \n\n";
    }else{
        print "I could\'t find it. \n\n"
    }
# exit on a empty user input
} until ($motif =~ /^\s*$/);

# exit then program
exit;

运行

wsx@wsx-ubuntu:~/桌面/Perl$ perl example_chapter5.pl 
Please type the filename of the protein sequence data:
NM_021964fragment.pep
Enter a motif to search for:SVLQ
I found it! 

Enter a motif to search for:jkl
I could't find it. 

Enter a motif to search for:
I could't find it. 

NM_021964fragment.pep

MNIDDKLEGLFLKCGGIDEMQSSRTMVVMGGVSGQSTVSGELQD
SVLQDRSMPHQEILAADEVLQESEMRQQDMISHDELMVHEETVKNDEEQMETHERLPQ
GLQYALNVPISVKQEITFTDVSEQLMRDKKQIR