fix sequence/fasta_trim_aligned_fasta.pl

sequence/fasta_trim_aligned_fasta.pl

@@ -9,6 +9,7 @@
 local $| = 1;
 
 my @GAPS = ( '-', '.' );
+my $tmpfile_prefix = "fasta_trim_aligned_fasta_tmpfile_";
 
 my $usage = <<USAGE;
 
@@ -57,7 +58,9 @@
 }
 if ( @files == 0 ) {
     push @files, 'STDIN';
-    ( $tmp_file_fh, $tmp_file ) = tempfile();
+    ( $tmp_file_fh, $tmp_file )
+        = tempfile( $tmpfile_prefix . "XXXXXX", DIR => ".", SUFFIX => '.fa' );
+
     $use_stdin = 1;
 }
 
@@ -67,13 +70,13 @@
 my $gaploc  = {};    # store the gap location
 my $do_once = 1;
 my ( $header, $seq, $len, $i, $base ) = (undef) x 5;
-my ($sum, $n) = (0) x 2;
+my ( $sum, $n ) = (0) x 2;
 for my $file (@files) {
     my $next_seq = FastaReader($file);
     while ( my $fa = &$next_seq() ) {
         ( $header, $seq ) = @$fa;
         $sum++;
-        print STDERR "\r$sum";
+        print STDERR "\rsum: $sum";
         if ($do_once) {
             $len = length $seq;
             $$gaploc{$_} = 1 for 0 .. ( $len - 1 );
@@ -87,14 +90,19 @@
             }
         }
 
-        die "no gap to trim.\n" if scalar keys %$gaploc == 0;
+        if ( scalar keys %$gaploc == 0 ) {
+            close $tmp_file_fh if $use_stdin;
+            remove_tmpfile()   if $use_stdin;
+            die "no gap to trim\n";
+        }
 
         print $tmp_file_fh ">$header\n$seq\n" if $use_stdin;
     }
 }
 
 close $tmp_file_fh if $use_stdin;
 
+print STDERR scalar keys %$gaploc, " gaps to trim\n";
 print STDERR "\nextract sequences...\n";
 
 @files = ($tmp_file) if $use_stdin;
@@ -114,7 +122,11 @@
 
 print STDERR "\n";
 
-if ($use_stdin) {
-    print STDERR "remove $tmp_file\n";
-    unlink $tmp_file or die "fail to remove $tmp_file\n";
+remove_tmpfile() if $use_stdin;
+
+sub remove_tmpfile {
+    print STDERR "\nremove temporary files\n";
+    for ( glob "$tmpfile_prefix*" ) {
+        unlink $_ or die "fail to remove $_\n";
+    }
 }