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post_phylosift.pl

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post_phylosift.pl [2017/11/13 11:29] – created hyjeongpost_phylosift.pl [2021/03/17 13:09] (current) – external edit 127.0.0.1
Line 15: Line 15:
      
   @org_dir = grep { not /^\./ } readdir OUTDIR;   @org_dir = grep { not /^\./ } readdir OUTDIR;
-  print STDERR "Organisms detected: @org_dir";+  print STDERR "Organisms detected: @org_dir"\n;
   closedir OUTDIR;   closedir OUTDIR;
-  $final = "$ARGV[1].aln";+  $final = "$ARGV[1].fsa";
   unlink $final if -f $final;   unlink $final if -f $final;
   open ALIGN, ">>$final";   open ALIGN, ">>$final";
Line 27: Line 27:
   #    print "Seq ID: $seq_id\n";   #    print "Seq ID: $seq_id\n";
       $fasta = "$ARGV[0]/$org/alignDir/$ARGV[1].codon.updated.1.fasta";       $fasta = "$ARGV[0]/$org/alignDir/$ARGV[1].codon.updated.1.fasta";
-      open RESULT, $fasta or die "Can't open file $fasta for reading!";+      $fasta = "$ARGV[0]/$org/alignDir/$ARGV[1].long.1.fasta" if $ARGV[1] =~ /16s_reps_bac/; 
 +      open RESULT, $fasta or print STDERR "Can't open file $fasta for reading!\n";
       while (<RESULT>) {       while (<RESULT>) {
           chomp;           chomp;
post_phylosift.pl.1510540141.txt.gz · Last modified: (external edit)