Need help with backticks script!!!

Using system_cmd.pl as a starting point,
rename the script as blast_grep.pl
Add comments to explain the code you write.
You will lose points for inadequate comments.

Make the following modifications to the script:
a. Remove the code that creates a file with numbered lines
b. Using backtics, run the command `grep JAY291 $file.blastn` and capture the results of the grep in an array
c. For each element in the resulting array, print a substring of the array element that includes only the GI number (use substr).
(Note that in general, substr is not a good way to extract GI numbers as they may vary in length…we’ll learn a better way soon.)
d. To make the script more flexible, add code to accept a second command line argument that
replaces the hard-coded JAY291 in the grep command. Example runs with output might
look like this:

[service1][~/ ecol553_week7]> perl blast_grep.pl yeastgenes.fa Patent
Starting BLAST run...Finished BLAST run.
254748699
257307076
257307082

[service1][~/week7]> perl blast_grep.pl yeastgenes.fa EC1118
Starting BLAST run...Finished BLAST run.
259149040
259145041
259148440
259145824


WHAT I HAVE SO FAR:

#!/usr/bin/perl
use warnings;
use strict;

# Demonstration of Perl's system function
# Run a BLAST job

my $file = $ARGV[0];
if (!defined $file) {
die "Usage: $0 FASTAfile\n";
}

print "Starting BLAST run...";
#show_gis = show the GI numbers
my $cmd = "/uaopt/ncbi/blast-2.2.25+/bin/blastn -db /genome/eeb553/yeast_sub -query $file -out $file.blastn -num_descriptions 1 -num_alignments 0 -evalue 1e-100 -show_gis";
system($cmd);
print "Finished BLAST run.\n";
`grep JAY291 $file.blastn` > my @grep_results

foreach $grep_results {

THIS IS THE ORIGINAL:
#!/usr/bin/perl
use warnings;
use strict;

# Demonstration of Perl's system function
# Run a BLAST job

my $file = $ARGV[0];
if (!defined $file) {
die "Usage: $0 FASTAfile\n";
}

print "Starting BLAST run...";
my $cmd = "/uaopt/ncbi/blast-2.2.25+/bin/blastn -db /genome/eeb553/yeast_sub -query $file -out $file.blastn -num_descriptions 1 -num_alignments 0 -evalue 1e-100 -show_gis";
system($cmd);
print "Finished BLAST run.\nNumbering output lines.\n";
$cmd = "perl file_output.pl $file.blastn";
system($cmd);
print "Finished numbering output lines.\n";


Please help me!

Hi,

follow the instructions.


You did not remove that code, as far as I can say.


Your try:


You can't redirect output in Perl the same way as you would do in a shell script. The backticks command returns the result of the system command.

Try something like this:



Here is an example of a Perl one-liner where I look for all instances of the "use" word in the Perl files of my current directory:



This is part of the output:



Then, you need to go through each element of your @grep_result array. Something like this:


I'll leave it there, as this is obviously homework assignment, you should probably try to figure out the rest by yourself.