--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/align_parsing.pl	Thu Dec 19 10:24:45 2019 -0500
@@ -0,0 +1,111 @@
+#!/usr/bin/env perl
+
+# Parses align file, calculates read depth (RD) and genome representation (GR)
+# of individual contigs; outputs contig sequences in fasta format with this
+# information in the fasta header: 
+# >CLXConitgY (length-average_RD-GR)
+#
+# RD profiles along the contig sequences can also be calculated and saved 
+# in a separate file.
+#
+# (renamed from align_parsing_2.pl, 2010-05-10)
+
+
+use Getopt::Std;
+use warnings;
+
+getopt('iop');
+if ($opt_i) {
+  $align_file = $opt_i;    # 
+} else {
+  die "Missing parameter: -i align_file\n";
+}
+if ($opt_o) {
+  $out_file = $opt_o;    # 
+} else {
+  $out_file = $align_file.".info";
+  print "Output file not set, using \"$out_file\"\n";
+}
+if ($opt_p) {
+  $profile_file = $opt_p;    # RD profiles will be recorded
+} else {
+  $profile_file = 0;     # will be used below to switch profile output off 
+  print "Parameter -p not set, RD profiles will not be saved\n";
+}
+
+open (ALIGN,$align_file) or die "Could not read from $align_file\n";
+open (OUT,">$out_file") or die "Could not write to $out_file\n";
+if ($profile_file) {
+  open (PROF,">$profile_file") or die "Could not write to $profile_file\n";
+}
+
+while ($radek = <ALIGN>) {
+  if ($radek =~/^DETAILED DISPLAY OF CONTIGS/) {    # start of alignment section
+      # print $radek;
+    $radek = <ALIGN>;
+    while ($radek =~/\*\*\* (CL\d+) {0,1}Contig (\d+) \*\*\*/) {   # parsing individual contigs
+      #  print $radek;
+      $contig_id = $1."Contig".$2;
+      @pokryti = ();       # array ve ktere bude pro kazdou pozici v sekvenci pokryti
+      $seq = "";           # consensus sekvence contigu
+#      print "$contig_id\n";
+#      print $radek;
+      $radek = <ALIGN>;
+      while ($radek =~/\:    \.    \:/) {  # -> nasleduje dalsi blok 
+        @blok = ();                        # radky z aktualniho bloku alignmentu
+        do {
+          $radek = <ALIGN>;
+          push(@blok,$radek); 
+        } while (not $radek =~/^consensus/);
+        $cons_line = $radek;
+        $radek = <ALIGN>;
+        $radek = <ALIGN>;     # toto posledni nacteni radku slouzi v podmince tohoto i nadrazeneho cyklu while
+        if (not $radek) { $radek = " "; };      # aby to nehlasilo chyby na konci souboru kde ty radky muzou chybet
+      
+        pop(@blok); pop(@blok);            # odstrani posledni dva radky (mezera a consensus)
+      
+        for ($f=10;$f<=length($cons_line);$f++) {
+          $suma_pozice = 0;
+          if (substr($cons_line,$f,1) =~/([A,T,G,C,N])/) {
+            $seq .= $1;
+            foreach $cteni (@blok) {
+              if (substr($cteni,$f,1) =~/[A,T,G,C,N]/) {
+                $suma_pozice++;
+              }
+            }
+            push(@pokryti,$suma_pozice);
+          }
+        }
+      
+      }
+    
+      $delka_cons = @pokryti;
+      $soucet = 0;
+      $prumer = 0;
+      foreach $suma_pozice (@pokryti) { 
+        $soucet += $suma_pozice;
+      }
+      $prumer = sprintf("%0.1f",$soucet/$delka_cons);
+
+      print OUT ">$contig_id ($delka_cons-$prumer-$soucet)\n";
+      while ($seq_line = substr($seq,0,60,"")) {
+        print OUT "$seq_line\n";
+      }
+      if ($profile_file) {
+        print PROF ">$contig_id ($delka_cons-$prumer-$soucet)\n";
+        foreach $suma_pozice (@pokryti) {
+          print PROF "$suma_pozice ";
+        }
+        print PROF "\n";
+      }
+      
+    }
+  }
+}
+
+close ALIGN;
+close OUT;
+if ($profile_file) {
+  close PROF;
+}
+