https://bioinformaticsonline.com/snippets/view/27294/check-all-seqs-in-a-folder? https://bioinformaticsonline.com/snippets/view/27294/check-all-seqs-in-a-folder Wed, 11 May 2016 10:16:47 -0500 https://bioinformaticsonline.com/snippets/view/27294/check-all-seqs-in-a-folder #!/usr/local/bin/perl -w # Can be easily modified to run any command on every sequence in a folder # Directory of sequences $myDir = "/home/anjana/seqs"; # Output directory (relative to $myDir or full path) $outputDir = "OutDir"; # Path to pattern file $patFile = "/home/anjana/patterns/polyA.pat"; # Go to sequence directory and open it (i.e, read contents) chdir($myDir) || die "Cannot change to $myDir: $!"; # Go to $myDir opendir(DIR, ".") || die "Cannot open .: $!"; # Open $myDir foreach $seqFile (sort readdir(DIR)) { if ($seqFile =~ /\.fa$/) # if file ends in .fa { print "Processing $seqFile\n"; $outFile = $seqFile; # Create $outFile name $outFile =~ s/\.fa/\.polyA\.out/; # s/old/new/; #User can process these files as per their need print "$patFile \t$seqFile \t $outputDir/$outFile\n"; } }]]> Anjana