not used as far as I can tell

scripts/aligner

-#!/usr/local/ensembl/bin/perl -w
-
-# Output a transcript (or raw contig) and its supporting evidence
-# (or similarity features) in Fasta format, to stdout.
-# Can also output more than one such alignment. With raw contigs,
-# output may be limited to all hits with a given logic name.
-#
-# usage: aligner [--user <username>] [--pass <password>] [--dbname <dbname>] \
-#        [--host <host>] --transcript <id> [<id>...]
-#
-#        aligner [--user <username>] [--pass <password>] [--dbname <dbname>] \
-#        [--host <host>] --contig [--logic_name <logicname>] <id> [<id>...]
-#
-# Stable IDs and/or internal dbIDs may be used for transcripts.
-# It isn't possible to mix contigs and transcripts in the
-# same command.
-#
-# For example:
-#
-# transcript stable ID, default database details, supporting evidence:
-#     aligner --transcript ENST00000279043 > ENST00000279043.fa
-#
-# transcript internal ID, default database details:
-#     aligner --transcript --evidence 12213 > 12213.fa
-#
-# raw contig, nondefault database details, all hits:
-#     aligner --contig --host ecs1h --dbname homo_sapiens_core_4_28 \
-#     --user ensro AL356104.6.1.96693 > AL356104.6.1.96693.fa
-#
-# raw contig, default database details, human_mrna hits only:
-#     aligner --logic_name human_mrna --contig AP001464.1.1.115915 > out.fa
-
-use constant DEFAULT_USER   => 'anonymous';
-use constant DEFAULT_DBNAME => 'current';
-use constant DEFAULT_HOST   => 'kaka.sanger.ac.uk';
-
-use strict;
-use Getopt::Long;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::EvidenceAlignment;
-
-sub usage_die {
-  die "usage: aligner [--user <username>] [--pass <password>] [--dbname <dbname>] \\\n         [--host <host>] --transcript [--evidence] <id> [<id>...]\n       aligner [--user <username>] [--pass <password>] [--dbname <dbname>] \\\n         [--host <host>] --contig [--logic_name <logicname>] <id> [<id>...]\n";
-}
-
-
-# main program
-
-my ($using_transcripts, $using_contigs, $user, $pass, $dbname, $host,
-    $logic_name, $evidence);
-
-GetOptions("transcript"   => \$using_transcripts,
-           "contig"       => \$using_contigs,
-	   "user=s"       => \$user,
-	   "pass=s"       => \$pass,
-	   "dbname=s"     => \$dbname,
-	   "host=s"       => \$host,
-           "logic_name=s" => \$logic_name,
-	   "evidence"     => \$evidence
-          ) or usage_die();
-
-usage_die()
-  if ( ( $using_transcripts and  $using_contigs)
-    || (!$using_transcripts and !$using_contigs)
-    || ( $using_transcripts and $logic_name) );
-
-$user = DEFAULT_USER if (!$user);
-$dbname = DEFAULT_DBNAME if (!$dbname);
-$host = DEFAULT_HOST if (!$host);
-
-my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-user   => $user,
-                                            -pass   => $pass,
-                                            -dbname => $dbname,
-					    -host   => $host
-					   );
-
-my $ea = Bio::EnsEMBL::EvidenceAlignment->new(-DBADAPTOR => $db);
-if ($evidence) {
-  $ea->use_supporting_evidence(1);
-}
-
-foreach my $id (@ARGV) {
-  if ($using_transcripts) {
-    $ea->transcriptid($id);
-  } else {
-    $ea->contigname($id);
-  }
-  my @evidence_seq_arr;
-  eval {
-    if ($logic_name) {
-      @evidence_seq_arr = $ea->fetch_alignment($logic_name);
-    } else {
-      @evidence_seq_arr = $ea->fetch_alignment;
-    }
-  };
-  if ($@) {
-    die "error: can't fetch alignment for $id: $@\n";
-  }
-  foreach my $evidence_obj (@evidence_seq_arr) {
-    print ">", $evidence_obj->accession_number , "\n"
-      or die "write error for $id";
-    print $evidence_obj->seq , "\n\n"
-      or die "write error for $id";
-  }
-}