#!/usr/bin/perl -w
#
# PURPOSE:  removes a list of chromats from an assembly.  After running this,
#   you must reassemble to create an ace file without the given phd files.
#   
# Note:  This removes phd files from the phd_dir directory.  Thus previously
#        created ace files may no longer be useable after running this since
#        they may reference some of these phd files.  Fortunately, this
#        script just copies these phd files to ../deleted_phd_files so
#        you can move them back to ../edit_dir for the purpose of using
#        an old ace file.
#
# HOW TO USE IT:  make a file of filenames with a list of the chromats
#        you want removed from the assembly
#        Run it as:
#        removeReads (name of fof's)
#

$szUsage = "Usage: removeReads listOfReads.fof";

die "$szUsage" if ( $#ARGV != 0 );

$szListOfReads = $ARGV[0];

die "Can't read $szListOfReads" if (! -r $szListOfReads );

die "Must be in edit_dir so that ../chromat_dir and ../phd_dir can be found" 
  if ( (! -r "../chromat_dir") || (! -r "../phd_dir" ) );

die "Must have write access to both ../chromat_dir and ../phd_dir" 
       if ( (! -w "../chromat_dir" ) || ( ! -w "../phd_dir" ) );

if ( !-e "../deleted_chromats" ) {
  mkdir( "../deleted_chromats", 0777 ) || die "couldn't create ../deleted_chromats to put the deleted chromats into";
}

die "Must have write access to ../deleted_chromats" if (! -w "../deleted_chromats" );

if ( !-e "../deleted_phd_files" ) {
  mkdir( "../deleted_phd_files", 0777 ) || die "couldn't create ../deleted_phd_files to put the deleted phd files into";
}

die "Must have write access to ../delete_phd_files" if (! -w "../deleted_phd_files" );


open( filListOfReads, $szListOfReads ) || die "couldn't open $szListOfReads";

while( <filListOfReads> ) {
  chomp;
  if ( rename( "../chromat_dir/$_", "../deleted_chromats/$_" )  ) {
    print "removed $_\n";
  }
  else {
    print "couldn't move chromat $_ from ../chromat_dir to ../deleted_chromats\n";
  }
  $szPhdFiles = "../phd_dir/" . $_ . ".phd.";
  print "glob pattern: $szPhdFiles\n";
  foreach $szOnePhdFile (<${szPhdFiles}*> ) {
    print "one phd file: $szOnePhdFile\n";
    ( $szNewName = $szOnePhdFile ) =~ s/^\.\.\/phd_dir/..\/deleted_phd_files/;
    print "new name = $szNewName\n";
    if ( rename( $szOnePhdFile, $szNewName ) ) {
      print "removed phd file $szOnePhdFile\n";
    }
    else {
      print "problem removing phd file $szOnePhdFile\n";
    }
  }
}