[ENSCORESW-1096]. Andy Y. confirms this is no longer used.

misc-scripts/utilities/index_fasta.pl

-#!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2018] EMBL-European Bioinformatics Institute
-# 
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-# 
-#      http://www.apache.org/licenses/LICENSE-2.0
-# 
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-use strict;
-use warnings;
-use File::Basename;
-
-use Bio::EnsEMBL::Utils::IO::FileFaidx;
-
-my $current_time = time();
-
-my $file = $ARGV[0];
-my $faidx = Bio::EnsEMBL::Utils::IO::FileFaidx->new($file, 'write_index');
-
-my $index = $faidx->index_path($file);
-if(-f $index) {
-  print "Removing the existing index at $index\n";
-  unlink $index;
-}
-
-print "Generating the index\n";
-$faidx->lookup();
-my $finished_time = time();
-my $elapsed = $finished_time - $current_time;
-my $time = gmtime($finished_time);
-print "Finished @ $time. Took $elapsed second(s)\n";