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Sarah Richardson  committed dbf044a

begin cutter cleanup

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  • Parent commits 0df8cd2

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Files changed (1)

File bin/BS_ChromosomeCutter.pl

 my $chrseq = $chr->sequence;
 my $chrlen = length $chrseq;
 
-my $BS_FEATS = $BS->fetch_custom_features();
+my $BS_FEATS = $BS->custom_features();
 
 $p{OUTPUT} = $p{OUTPUT} || 'html';
 
 if (! $p{EDITOR} || ! $p{MEMO})
 {
-  die "\n ERROR: Both an editor's id and a memo must be supplied.\n\n";
+  die "BSERROR: Both an editor's id and a memo must be supplied.\n\n";
 }
 
 if (! $p{ACTION})
 {
-  print "\n ERROR: No action was specified.\n\n";
+  print "BSERROR: No action was specified.\n\n";
   pod2usage(-verbose=>99, -sections=>'ARGUMENTS');
 }
 if (! exists $ACTIONS{$p{ACTION}})
 }
 if ($p{ACTION} =~ m{feat}msix && ! $p{TYPE})
 {
-  print "\n ERROR: A feature type based action was requested, ";
+  print "BSERROR: A feature type based action was requested, ";
   print "but no feature type was specified.\n";
   die;
 }
 if ($p{ACTION} eq 'listdel' && ! $p{FEATURES})
 {
-  print "\n ERROR: A list based action was requested, ";
+  print "BSERROR: A list based action was requested, ";
   print "but no features were specified.\n";
   die;
 }
 if ($p{INSERT} && ! exists $BS_FEATS->{$p{INSERT}})
 {
-  die "\n ERROR: Unrecognized custom feature requested for insertion.\n";
+  die "BSERROR: Unrecognized custom feature requested for insertion.\n";
 }
 
 $p{STARTPOS} = $p{STARTPOS} || 1;
 
 Required arguments:
 
-  -C,   --CHROMOSOME : The chromosome to be modified
-  -E,   --EDITOR : The person responsible for the edits
-  -M,   --MEMO : Justification for the edits
-  -A,   --ACTION : The action to take.
-                seqdel : delete the defined segment
-                seqdelprp : propose the defined segment for deletion
-                featdel : delete features of type -T from the defined segment
-                          requires -T
-                featdelprp : propose features of type -T for deletion
-                          requires -T
-                listdel : delete the features listed in -F
-                          requires -F
+  --CHROMOSOME : The chromosome to be modified
+  --EDITOR : The person responsible for the edits
+  --MEMO : Justification for the edits
+  --ACTION : The action to take.
+        seqdel : delete the defined segment
+        seqdelprp : propose the defined segment for deletion
+        featdel : delete features of type -T from the defined segment
+                  requires -T
+        featdelprp : propose features of type -T for deletion
+                  requires -T
+        listdel : delete the features listed in -F
+                  requires -F
 
 Optional arguments:
 
-  -STA, --STARTPOS : The first base eligible for editing (default 1)
-  -STO, --STOPPOS : The last base eligible for editing (default chr length)
-  -SC,  --SCALE : [genome, chrom (def)] Which version number to increment
-  -T,   --TYPE : The type of feature to be targeted
-  -DES, --DESTROY : Whether or not other features should be disrupted by
-            insertions; default 0 for no
-  -F,   --FEATURES : A comma separated list of feature names to be deleted
-  -I,   --INSERT : The feature to be inserted in each deletion;
-                   must be an entry in config/features.txt
-  -OU,  --OUTPUT : html or txt
+  --STARTPOS : The first base eligible for editing (default 1)
+  --STOPPOS : The last base eligible for editing (default chr length)
+  --ITERATE : [genome, chromosome (def)] Which version number to increment?
+  --TYPE : The type of feature to be targeted
+  --DESTROY : Whether or not other features should be disrupted by
+      insertions; default 0 for no
+  --FEATURES : A comma separated list of feature names to be deleted
+  --INSERT : The feature to be inserted in each deletion;
+             must be an entry in config/features.txt
+  --OUTPUT : html or txt
   -h,   --help : Display this message
 
 =cut