Re: perl script question

[John W. Krahn]

On 2019-10-09 7:21 p.m., 刘东 wrote:

hellow:
I have written a script, but it does not work, can you tell me what wrong with 
me?


#! /usr/bin/perl

use strict;
use warnings;
use Getopt::Long;

my ($dir, $files, $file_name, $file_format, $file_dir, $file_main);

GetOptions ('dr=s'  =>\$dir);

open INF,"<",'sine.fa' or die "can't read open sine";

foreach $files (glob("$dir/*.fa")) {
open FASEQ, "<", $files or die "can not read open $!";
   ($file_dir, $file_main) = split (/\/\//,$files);
   ($file_name,$file_format) =split(/\./,$file_main);
open OUTFILE, '>', $file_name.".txt";
`./usearch -ublast FASEQ -db INF -evalue 1e-5 -userout OUTFILE -strand both 
-userfields query+qlo+qhi+ql+qs+qstrand+target+tlo+thi+tl`;
}

close FASEQ;
close OUTFILE;
close INF;

Perhaps it may work better like this:

#!/usr/bin/perl

use strict;
use warnings;
use Getopt::Long;

GetOptions( 'dr=s' => \my $dir );

opendir my $DH, $dir or "Cannot open '$dir' because: $!";

while ( my $file = readdir $DH ) {

    my $file_name = $file =~ s/\.fa\z/.txt/r or next;

    0 == system './usearch',
        '-ublast', "$dir/$file",
        '-db', 'sine.fa',
        '-evalue', '1e-5',
        '-userout', $file_name,
        '-strand', 'both',
        '-userfields', 'query+qlo+qhi+ql+qs+qstrand+target+tlo+thi+tl'
            or die "system ./usearch failed: $?";
    }


John

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