rename output gene multfastas and pass all sequences through

.gitignore

@@ -22,4 +22,8 @@ example_2.faa.tmp.filtered.fa
 pan_genome.fa
 query_1.fa.tmp.filtered.fa
 query_2.fa.tmp.filtered.fa
-query_3.fa.tmp.filtered.fa
+query_3.fa.tmp.filtered.fa
+accessory.header.embl
+blast_identity_frequency.Rtab
+core_accessory.header.embl
+reannotated_groups_file

lib/Bio/PanGenome/External/Muscle.pm

@@ -40,7 +40,7 @@ sub _build__memory_required_in_mb {
 sub _command_to_run {
     my ( $self, $fasta_file, $output_file ) = @_;
     return
-      join( " ", ( $self->exec, '-in', $fasta_file, '-out', $output_file, '-quiet', '-maxhours', 7, ) );
+      join( " ", ( $self->exec, '-in', $fasta_file, '-out', $output_file, '-quiet', '-maxhours', 7, '> /dev/null 2>&1') );
 }
 
 sub run {

lib/Bio/PanGenome/External/Revtrans.pm

@@ -35,14 +35,16 @@ sub _command_to_run {
             $self->nucleotide_filename,
             $self->protein_filename,
             '-mtx', 11,
+            '-readthroughstop',
+            '-allinternal', 
+            '-match', 'name',
             '>', $self->output_filename
         )
     );
 }
 
 sub run {
   my ($self) = @_;
-  my @commands_to_run;
   my $cmd = $self->_command_to_run;
   system($cmd);
   1;

lib/Bio/PanGenome/Output/GroupsMultifastaNucleotide.pm

@@ -67,9 +67,8 @@ sub _group_file_name
 { 
   my ($self,$group_name,$num_group_genes) = @_;
   my $annotated_group_name = $self->annotate_groups->_groups_to_consensus_gene_names->{$group_name};
-  my $num_group_genes_leading_zeros = sprintf("%05d", $num_group_genes);
   $annotated_group_name =~ s!\W!_!gi;
-  my $filename = join('-', ($num_group_genes_leading_zeros,$annotated_group_name)).'.fa';
+  my $filename = $annotated_group_name.'.fa';
   my $group_file_name = join('/',($self->output_directory, $filename ));
   return $group_file_name;
 }

lib/Bio/PanGenome/Output/GroupsMultifastaProtein.pm

@@ -6,7 +6,7 @@ package Bio::PanGenome::Output::GroupsMultifastaProtein;
 
 Take a multifasta nucleotide file and output it as proteins.
    use Bio::PanGenome::Output::GroupsMultifastaProtein;
-   
+
    my $obj = Bio::PanGenome::Output::GroupsMultifastaProtein->new(
        nucleotide_fasta_file => 'example.fa'
      );
@@ -29,29 +29,34 @@ sub _build_output_filename
 {
   my ($self) = @_;
   my ( $filename, $directories, $suffix ) = fileparse($self->nucleotide_fasta_file, qr/\.[^.]*/);
-  
+
   return join('',($directories, $filename.$self->_suffix));
 }
 
-sub _fastatranslate_filename
+# Read all the sequences for a gene into memory to sort them - very small files so shouldnt be a problem
+sub _fastatranslate
 {
   my ($self) = @_;
-  return $self->output_filename.".intermediate";
-}
+  my $input_fasta_file_obj    = Bio::SeqIO->new(-file => $self->nucleotide_fasta_file, -format => 'Fasta' );
+  my $output_protein_file_obj = Bio::SeqIO->new(-file =>">".$self->output_filename,    -format => 'Fasta', -alphabet => 'protein' );
 
-sub _fastatranslate_cmd
-{
-  my ($self) = @_;
-  return 'fastatranslate --geneticcode 11  -f '. $self->nucleotide_fasta_file.' > '.$self->_fastatranslate_filename;
+  my %protein_sequence_objs;
+  while (my $seq = $input_fasta_file_obj->next_seq){
+    $protein_sequence_objs{$seq->display_id} = $seq->translate(-codontable_id => 11 );
+  }
+
+  for my $sequence_name ( sort keys %protein_sequence_objs)
+  {
+    $output_protein_file_obj->write_seq($protein_sequence_objs{$sequence_name});
+  }
+
+  return 1;
 }
 
 sub convert_nucleotide_to_protein
 {
   my ($self) = @_;
-  system($self->_fastatranslate_cmd());
-  my $cmd = 'fasta_grep -f '.$self->_fastatranslate_filename.' | sed \'s/*//\' > '.$self->output_filename;
-  system($cmd);
-  unlink($self->_fastatranslate_filename);
+  $self->_fastatranslate();
   1;
 }
 

t/Bio/PanGenome/CommandLine/CreatePanGenome.t

@@ -30,7 +30,7 @@ cleanup_files();
 
 %scripts_and_expected_files = (
   ' -j Local --dont_create_rplots --output_multifasta_files t/data/query_1.gff t/data/query_2.gff t/data/query_6.gff  ' =>
-    [ 'pan_genome_sequences/00002-speH.fa.aln', 't/data/00002-speH.fa.aln' ],
+    [ 'pan_genome_sequences/speH.fa.aln', 't/data/speH.fa.aln' ],
 );
 mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files );
 

t/Bio/PanGenome/CommandLine/ProteinMuscleAlignmentFromNucleotides.t

@@ -20,6 +20,8 @@ my %scripts_and_expected_files = (
       [ 't/data/nuc_multifasta.fa.aln', 't/data/expected_nuc_multifasta.fa.aln' ],
 );
 
+
+
 unlink('t/data/nuc_multifasta.fa.aln');
 mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files );
 unlink('t/data/nuc_multifasta.fa.aln');

t/Bio/PanGenome/Output/GroupsMultifastasNucleotide.t

@@ -36,12 +36,12 @@ ok(
 );
 ok( $obj->create_files(), 'Create multiple fasta files' );
 
-is(read_file('pan_genome_sequences/00003-hly.fa'),     read_file('t/data/pan_genome_sequences/00003-hly.fa' ), 'Check multifasta content is correct for 3-hly.fa ');
-is(read_file('pan_genome_sequences/00002-speH.fa'),    read_file('t/data/pan_genome_sequences/00002-speH.fa' ), 'Check multifasta content is correct for 2-speH.fa ');
-is(read_file('pan_genome_sequences/00002-argF.fa'),    read_file('t/data/pan_genome_sequences/00002-argF.fa' ), 'Check multifasta content is correct for 2-argF.fa ');
-is(read_file('pan_genome_sequences/00001-group_7.fa'), read_file('t/data/pan_genome_sequences/00001-group_7.fa' ), 'Check multifasta content is correct for 1-group_7.fa ');
-is(read_file('pan_genome_sequences/00001-group_6.fa'), read_file('t/data/pan_genome_sequences/00001-group_6.fa' ), 'Check multifasta content is correct for 1-group_6.fa ');
-is(read_file('pan_genome_sequences/00001-yfnB.fa'),    read_file('t/data/pan_genome_sequences/00001-yfnB.fa' ), 'Check multifasta content is correct for 1-yfnB.fa ');
+is(read_file('pan_genome_sequences/hly.fa'),     read_file('t/data/pan_genome_sequences/hly.fa' ), 'Check multifasta content is correct for 3-hly.fa ');
+is(read_file('pan_genome_sequences/speH.fa'),    read_file('t/data/pan_genome_sequences/speH.fa' ), 'Check multifasta content is correct for 2-speH.fa ');
+is(read_file('pan_genome_sequences/argF.fa'),    read_file('t/data/pan_genome_sequences/argF.fa' ), 'Check multifasta content is correct for 2-argF.fa ');
+is(read_file('pan_genome_sequences/group_7.fa'), read_file('t/data/pan_genome_sequences/group_7.fa' ), 'Check multifasta content is correct for 1-group_7.fa ');
+is(read_file('pan_genome_sequences/group_6.fa'), read_file('t/data/pan_genome_sequences/group_6.fa' ), 'Check multifasta content is correct for 1-group_6.fa ');
+is(read_file('pan_genome_sequences/yfnB.fa'),    read_file('t/data/pan_genome_sequences/yfnB.fa' ), 'Check multifasta content is correct for 1-yfnB.fa ');
 remove_tree('pan_genome_sequences');
 
 done_testing();

t/data/expected_nuc_multifasta.fa.aln

@@ -2,50 +2,159 @@
 ATGTCAGTACCACTTATTCTGACCTTACTGGCGGGCGCTGCCACCTTTAT
 TGGCGCGTTTCTTGGCGTTCTTGGCCAAAAACCGTCTAACCGCGTGCTGG
 CTTTTTCGCTGGGCTTCGCCGCAGGGATCATGCTGCTCATCTCGCTGATG
-GAGATGCTGCCCGCCGCGTTAGATACCGAGGGGATGTCGCCTGTACTGGG
-CTACGGGATGTTTATTATCGGCCTGTTGGGCTACTTCGGGCTGGATCGTC
-TGCTTCCTCACGCTCATCCGCAGGATCTGGTGCAAAAAAGGCAGCAGCCG
-CTTCCCGGCTCGATAAAACGCACTGCGATTTTATTGACGCTCGGCATTAG
-CCTGCACAACTTTCCGGAAGGAATCGCCACCTTTGTCACTGCCAGCAGCA
-ATCTTGAACTGGGTTTCGGCATCGCACTGGCGGTGGCGTTGCACAATATT
-CCTGAAGGGCTGGCGGTTGCCGGCCCGGTTTATGCCGCGACGGGCTCAAA
-ACGTACCGCGATTTTTTGGGCCGGTATCTCCGGCATGGCGGAAATTCTC-
---GGCGTGCTGGCGTGGCTGATTTTGGGCAGCCTGGTTTCACCGATCGTT
-ATGGCGGCTATCATGGCAGCAGTCGCCGGCATTATGGTGGCGCTCTCCGT
+GAGATGCTGCCCGCCGCG---------------TTAGATACCGAGGGGAT
+GTCGCCTGTACTGGGCTAC------GGGATGTTTATTATCGGCCTGTTGG
+GCTACTTCGGGCTGGATCGTCTGCTTCCTCACGCTCATCCGCAGGATCTG
+GTGCAAAAAAGGCAGCAGCCGCTTCCCGGCTCGATAAAACGCACTGCGAT
+TTTATTGACGCTCGGCATTAGCCTGCACAACTTTCCGGAAGGAATCGCCA
+CCTTTGTCACTGCCAGCAGCAATCTTGAACTGGGTTTCGGCATCGCA---
+--------------------------------------------------
+-CTGGCGGTGGCGTTGCACAATATTCCTGAAGGG------CTGGCGGTTG
+CCGGCCCGGTTTATGCCGCGACGGGCTCAAAACGTACCGCGATTTTTTGG
+GCC---------------GGTATCTCCGGCATGGCGGAAATTCTCGGCGT
+GCTGGCG---TGGCTGATTTTGGGCAGCCTGGTTTCACCGATC-------
+--------------------------------GTTATGGCGGCTATCATG
+GCAGCA---------------GTCGCCGGCATTATGGTGGCGCTCTCCGT
 CGATGAACTGATGCCGTTGGCAAAAGAGATCGATCCTAACAATAACCCCA
 GCTATGGTGTGCTTTGCGGTATGTCCATCATGGGGCTCAGTCTCGTCATT
 TTGCAGACGATAGGTATCGGT
->DDDD#77_01105 
+>HHHH 
 ATGTCAGTACCACTTATTCTGACCTTACTGGCGGGCGCTGCCACCTTTAT
 TGGCGCGTTTCTTGGCGTTCTTGGCCAAAAACCGTCTAACCGCGTGCTGG
 CTTTTTCGCTGGGCTTCGCCGCAGGGATCATGCTGCTCATCTCGCTGATG
-GAGATGCTGCCCGCCGCGTTAGATACCGAGGGGATGTCGCCTGTACTGGG
-CTACGGGATGTTTATTATCGGCCTGTTGGGCTACTTCGGGCTGGATCGTC
-TGCTTCCTCACGCTCATCCGCAGGATCTGGTGCAAAAAAGGCAGCAGCCG
-CTTCCCGGCTCGATAAAACGCACTGCGATTTTATTGACGCTCGGCATTAG
-CCTGCACAACTTTCCGGAAGGAATCGCCACCTTTGTCACTGCCAGCAGCA
-ATCTTGAACTGGGTTTCGGCATCGCACTGGCGGTGGCGTTGCACAATATT
-CCTGAAGGGCTGGCGGTTGCCGGCCCGGTTTATGCCGCGACGGGCTCAAA
-ACGTACCGCGATTTTTTGGGCCGGTATCTCCGGCATGGCGGAAATTCTTG
-GCGGCGTGCTGGCGTGGCTGATTTTGGGCAGCCTGGTTTCACCGATCGTT
+GAGATGCTGCCCGCCGCG---------------TTAGATACCGAGGGGAT
+GTCGCCTGTACTGGGCTAC------GGGATGTTTATTATCGGCCTGTTGG
+GCTACTTCGGGCTGGATCGTCTGCTTCCTCACGCT---------------
+------------------TCCGCAGGATCTGGTGCAAAAAAGGCAGCAGC
+CGCTTCCCGGCTCGATAAAACGCACTGCGATTTTATTGACGCTCGGCATT
+AGCCTGCACAACTTTCCGGAAGGAATCGCCACCTTTGTCACTGCCAG---
+------------------------------------CAGCAATCTTGAAC
+TGGGTTTCGGCATCGCACTGGCGGTGGCGTTGCACAATATTCCTGAAGGG
+CTGGCGGTTGCCGGCCCGGTTTATGCCGCGACGGGCTCAAAACGTACCGC
+GATTTTTTGGGCCGGTATCTC------CGGCATGGCGGAAATTCTTGGCG
+GCGTGCT---GGCGTGGCTGATTTTGGGCAGCCTGGTTTCACCGATCGTT
 ATGGCGGCTATCATGGCAGCAGTCGCCGGCATTATGGTGGCGCTCTCCGT
 CGATGAACTGATGCCGTTGGCAAAAGAGATCGATCCTAACAATAACCCCA
+G------------------------------------------CTATGGT
+GTGCTTTGCGGTATGTCCATCATGGGGCTCAG------------------
+---TCTCGTCATTTTGCA---
+>FFFF 
+ATGTCAGTACCACTTATTCTGACCTTACTGGCGGGCGCTGCCACCTTTAT
+TGGCGCGTTTCTTGGCGTTCTTGGCCAAAAACCGTCTAACCGCGTGCTGG
+CTTTTTCGCTGGGCTTCGCCGCAGGGATCATGCTGCTCATCTCGCTGATG
+GAGATGCTGCCCGCCGCG---------------TTAGATACCGAGGGGAT
+GTCGCCTGTACTGGGCTAC------GGGATGTTTATTATCGGCCTGTTGG
+GCTACTTCGGGCTGGATCGTCTGCTTCCTCACGCTCATCCGCAGGATCTG
+GTGCAAAAAAGGCAGCAGCCGCTTCCCGGCTCGATAAAACGCACTGCGAT
+TTTATTGACGCTCGGCATTAGCCTGCACAACTTTCCGGAAGGAATCGCCA
+CCTTTGTCACTGCCAGCAGCAATCTTGAACTGGGTTTCGGCATCGCA---
+--------------------------------------------------
+-CTGGCGGTGGCGTTGCACAATATTCCTGAAGGG------CTGGCGGTTG
+CCGGCCCGGTTTATGCCGCGACGGGCTCAAAACGTACCGCGATTTTTTGG
+GCC---------------GGTATCTCCGGCATGGCGGAAATTCTTGGCGG
+CGTGCTGGCGTGGCTGATTTTGGGCAGCCTG---GCACCGATC-------
+--------------------------------GTTATGGCGGCTATCATG
+GCAGCA---------------GTCGCCGGCATTATGGTGGCGCTCTCCGT
+CGATGAACTGATGCCGTTGGCAAAAGAGATCGATCCTAACAATAACCCCA
 GCTATGGTGTGCTTTGCGGTATGTCCATCATGGGGCTCAGTCTCGTCATT
 TTGCAGACGATAGGTATCGGT
->FFFF 
+>DDDD#77_01105 
 ATGTCAGTACCACTTATTCTGACCTTACTGGCGGGCGCTGCCACCTTTAT
 TGGCGCGTTTCTTGGCGTTCTTGGCCAAAAACCGTCTAACCGCGTGCTGG
 CTTTTTCGCTGGGCTTCGCCGCAGGGATCATGCTGCTCATCTCGCTGATG
-GAGATGCTGCCCGCCGCGTTAGATACCGAGGGGATGTCGCCTGTACTGGG
-CTACGGGATGTTTATTATCGGCCTGTTGGGCTACTTCGGGCTGGATCGTC
-TGCTTCCTCACGCTCATCCGCAGGATCTGGTGCAAAAAAGGCAGCAGCCG
-CTTCCCGGCTCGATAAAACGCACTGCGATTTTATTGACGCTCGGCATTAG
-CCTGCACAACTTTCCGGAAGGAATCGCCACCTTTGTCACTGCCAGCAGCA
-ATCTTGAACTGGGTTTCGGCATCGCACTGGCGGTGGCGTTGCACAATATT
-CCTGAAGGGCTGGCGGTTGCCGGCCCGGTTTATGCCGCGACGGGCTCAAA
-ACGTACCGCGATTTTTTGGGCCGGTATCTCCGGCATGGCGGAAATTCTTG
-GCGGCGTGCTGGCGTGGCTGATTTTGGGCAGCCTG---GCACCGATCGTT
-ATGGCGGCTATCATGGCAGCAGTCGCCGGCATTATGGTGGCGCTCTCCGT
+GAGATGCTGCCCGCCGCG---------------TTAGATACCGAGGGGAT
+GTCGCCTGTACTGGGCTAC------GGGATGTTTATTATCGGCCTGTTGG
+GCTACTTCGGGCTGGATCGTCTGCTTCCTCACGCTCATCCGCAGGATCTG
+GTGCAAAAAAGGCAGCAGCCGCTTCCCGGCTCGATAAAACGCACTGCGAT
+TTTATTGACGCTCGGCATTAGCCTGCACAACTTTCCGGAAGGAATCGCCA
+CCTTTGTCACTGCCAGCAGCAATCTTGAACTGGGTTTCGGCATCGCA---
+--------------------------------------------------
+-CTGGCGGTGGCGTTGCACAATATTCCTGAAGGG------CTGGCGGTTG
+CCGGCCCGGTTTATGCCGCGACGGGCTCAAAACGTACCGCGATTTTTTGG
+GCC---------------GGTATCTCCGGCATGGCGGAAATTCTTGGCGG
+CGTGCTGGCGTGGCTGATTTTGGGCAGCCTGGTTTCACCGATC-------
+--------------------------------GTTATGGCGGCTATCATG
+GCAGCA---------------GTCGCCGGCATTATGGTGGCGCTCTCCGT
 CGATGAACTGATGCCGTTGGCAAAAGAGATCGATCCTAACAATAACCCCA
 GCTATGGTGTGCTTTGCGGTATGTCCATCATGGGGCTCAGTCTCGTCATT
 TTGCAGACGATAGGTATCGGT
+>GGGG 
+ATGTCAGTACCACTTATTCTGACCTTACTGGCGGGCGCTGCCACCTTTAT
+TGGCGCGTTTCTTGGCGTTCTTGGCCAAAAACCGTCTAACCGCGTGCTGG
+CTTTTTCGCTGGGCTTCGCCGCAGGGATCATGCTGCTCATCTCGCTGATG
+GAGATGCTGCCCGCCGCG---------------TTAGATACCGAGGGGAT
+GTCGCCTGTACTGGGCTAC------GGGATGTTTATTATCGGCCTGTTGG
+GCTACTTCGGGCTGGATCGTCTGCTTCCTCACGCTCATCCGCAGGATCTG
+GTGCAAAAAAGGCAGCAGCCGCTTCCCGGCTCGATAAAACGCACTGCGAT
+TTTATTGACGCTCGGCATTAGCCTGCACAACTTTCCGGAAGGAATCGCCA
+CCTTTGTCACTGCCAGCAGCAATCTTGAACTGGGTTTCGGCATCGCACTG
+GGGTGGCGTTGCACAATATTCCTGAAGGGCTGGCGGTTGCCGGCCCGGTT
+TATGCCGCGACGGGCTCAAAACGTACCGCGATTT------TTTGGGCCGG
+TATCTCCGGCATGGCGGAAATTCTTGGCGGCGTGCTGGCGTGGCTGATTT
+TGGGCAGCCTGGTTTCACCGATCGTTATGGCGGCTATCATGGCAGCAGTC
+GCCGGCA---TTATGGTGGCGCTCT---CCGATGAACTGATGC-------
+--------------------------------CGTTGGCAAAAGAGATCG
+ATCCTA------------------ACAATAACCCCAGCTATGGTGTGCTT
+T------------------------------------------GCGGTAT
+GTCCATCATGGGGCTCAGTCTCGTCA------------------------
+---TTTTGCAGACGATAG---
+>CCCC#76_00877 
+ATGTCAGTACCACTTATTCTGACCTTACTGGCGGGCGCTGCCACCTTTAT
+TGGCGCGTTTCTTGGCGTTCTTGGCCAAAAACCGTCTAACCGCGTGCTGG
+CTTTTTCGCTGGGCTTCGCCGCAGGGATCATGCTGCTCATCTCGCTGATG
+GAGATGCTGCCCGCCGCG---------------TTAGATACCGAGGGGAT
+GTCGCCTGTACTGGGCTAC------GGGAGTTTATTATCGGCCTGTTGGG
+CTACTTCGGGCTGGATCGTCTGCTTCCTCACGCTCATCCGCAGGATCTGG
+TGCAAAAAAGGCAGCAGCCGCTTCCCG------GCTCGATAAAACGCACT
+GCGATTTTATTGACGCTCGGCATTAGCCTGCACAACTTTCCGG---AAGG
+AATCACCTTTGTCACTGCCAGCAGCAATCTTGAACTGGGTTTCGGCATCG
+CACTGGCGGTGGCGTTGCACAATATTCCTGAAGGGCTGGCGGTTGCCGGC
+CCGGTTTATGCCGCGACGGGCTCAAAACGTACCG------CGATTTTTTG
+GGCCGGTATCTCCGGCATGGCGGAAATTCTTGGCGGCGTGCTGGCGTGGC
+TGATTTTGGGCAGCCTGGTTTCACCGATCGTTATGGCGGCTATCATGGCA
+GCAGTCG---CCGGCATTATGGTGGCGCTCTCCGTCGATGAAC-------
+--------------------------------TGATGCCGTTGGCAAAAG
+AGATCG------------------ATCCTAACAATAACCCCAGCTATGGT
+G------------------------------------------TGCTTTG
+CGGTATGTCCATCATGGGGCTCAGTC------------------------
+---TCGTCATTTTGCAGA---
+>AAAA#74_01075 
+TGTCAGTACCACTTATTCTGACCTTACTGGCGGGCGCTGCCA---CCTTT
+ATTGGCGCGTTTCTTGGCGTTCTTGGCCAAAAACCGTCTAACCGCGTGCT
+GGCTTTTTCGCTGGGCTTCGCCGCAGGGATCATGCTGCTCATCTCGCTGA
+TGGAGATGCTGCCCGCCG---------------------CGTTAGATACC
+GAGGGGATGTCGCCTGTAC------TGGGCTACGGGATGTTTATTATCGG
+CCTGTTGGGCTACTTCGGGCTGGATCGTCTGCTTCCTCACGCTCATCCGC
+AGGATCTGGTGCAAAAAAGGCAGCAGC------CGCTTCCCGGCTCGATA
+AAACGCACTGCGATTTTATTGACGCTCGGCATTAGCCTGCACAACTTTCC
+GGAAGGAATCGCCACCTTTGTCACTGCCAGCAGCAATCTTGAACTGGGTT
+TCGGCATCGCACTGGCGGTGGCGTTGCACAATATTCCTGAAGGGCTGGCG
+GTTGCCGGCCCGGTTTATGCCGCGACGGGCTCAA------AACGTACCGC
+GATTTTTTGGGCCGGTATCTCCGGCATGGCGGAAATTCTTGGCGGCGTGC
+TGGCGTGGCTGATTTTGGGCAGCCTGGTTTCACCGATCGTTATGGCGGCT
+ATCATGG---CAGCAGTCGCCGGCATTATGGTGGCGCTCTCCG-------
+--------------------------------TCGATGAACTGATGCCGT
+TGGCAA------------------AAGAGATCGATCCTAACAATAACCCC
+A------------------------------------------GCTATGG
+TGTGCTTTGCGGTATGTCCATCATGG------------------------
+---GGCTCAGTCTCGTCA---
+>BBBB#75_01314 
+ATGTCAGTACCACTTATTCTGACCTTACTGGCGGGCGCTGCCACCTTTAT
+TGGCGCGTTTCTTGGCGTTCTTGGCCAAAAACCGTCTAACCGCGTGCTGG
+CTTTTTCGCTGGGCTTCGCCGCAGGGATCATGCTGCTCATCTCGCTGATG
+GATGCTGCCCGCCGCGTTAGATACCGAGGGGATGTCGCCTGTACTGGGCT
+ACGGGATGTTTATTATCGGCCTGTTGGGCTACTTCGGGCTGGATCGTCTG
+CTTCCTCA------------------------------------------
+------------CGCTCATCCGCAGGATCTGGTGCAAAAAAGGCAGCAGC
+CGCTTCCCGGCTCGATAAAACGCACTGCGATTTTATTGACGCTCGGCATT
+AGCCTGCACAACTTTCCGGAAGGAATCGCCACCTTTGTCACTGCCAG---
+------------------------------------CAGCAATCTTGAAC
+TGGGTTTCGGCATCGCACTGGCGGTGGCGTTGCACAATATTCCTGAAGGG
+CTGGCGGTTGCCGGCCCGGTTTATGCCGCGACGGGCTCAAAACGTACCGC
+GATTTTTTGGGCCGGTATCTC------CGGCATGGCGGAAATTCTTGGCG
+GCGTGCT---GGCGTGGCTGATTTTGGGCAGCCTGGTTTCACCGATCGTT
+ATGGCGGCTATCATGGCAGCAGTCGCCGGCATTATGGTGGCGCTCTCCGT
+CGATGAACTGATGCCGTTGGCAAAAGAGATCGATCCTAACAATAACCCCA
+G------------------------------------------CTATGGT
+GTGCTTTGCGGTATGTCCATCATGGGGCTCAG------------------
+---TCTCGTCATTTTGCA---

t/data/expected_nuc_multifasta.faa

@@ -1,8 +1,48 @@
->AAAA#74_01075 [translate(3)]
-SVPLILTLLAGAATFIGAFLGVLGQKPSNRVLAFSLGFAAGIMLLISLMEMLPAALDTEGMSPVLGYGMFIIGLLGYFGLDRLLPHAHPQDLVQKRQQPLPGSIKRTAILLTLGISLHNFPEGIATFVTASSNLELGFGIALAVALHNIPEGLAVAGPVYAATGSKRTAIFWAGISGMAEILGGVLAWLILGSLVSPIVMAAIMAAVAGIMVALSVDELMPLAKEIDPNNNPSYGVLCGMSIMGLSLVILQTIGIG
->DDDD#77_01105 [translate(1)]
-MSVPLILTLLAGAATFIGAFLGVLGQKPSNRVLAFSLGFAAGIMLLISLMEMLPAALDTEGMSPVLGYGMFIIGLLGYFGLDRLLPHAHPQDLVQKRQQPLPGSIKRTAILLTLGISLHNFPEGIATFVTASSNLELGFGIALAVALHNIPEGLAVAGPVYAATGSKRTAIFWAGISGMAEILGGVLAWLILGSLVSPIVMAAIMAAVAGIMVALSVDELMPLAKEIDPNNNPSYGVLCGMSIMGLSLVILQTIGIG
->EEEE [translate(1)]
-MSVPLILTLLAGAATFIGAFLGVLGQKPSNRVLAFSLGFAAGIMLLISLMEMLPAALDTEGMSPVLGYGMFIIGLLGYFGLDRLLPHAHPQDLVQKRQQPLPGSIKRTAILLTLGISLHNFPEGIATFVTASSNLELGFGIALAVALHNIPEGLAVAGPVYAATGSKRTAIFWAGISGMAEILGVLAWLILGSLVSPIVMAAIMAAVAGIMVALSVDELMPLAKEIDPNNNPSYGVLCGMSIMGLSLVILQTIGIG
->FFFF [translate(1)]
-MSVPLILTLLAGAATFIGAFLGVLGQKPSNRVLAFSLGFAAGIMLLISLMEMLPAALDTEGMSPVLGYGMFIIGLLGYFGLDRLLPHAHPQDLVQKRQQPLPGSIKRTAILLTLGISLHNFPEGIATFVTASSNLELGFGIALAVALHNIPEGLAVAGPVYAATGSKRTAIFWAGISGMAEILGGVLAWLILGSLAPIVMAAIMAAVAGIMVALSVDELMPLAKEIDPNNNPSYGVLCGMSIMGLSLVILQTIGIG
+>AAAA#74_01075
+CQYHLF*PYWRALPPLLARFLAFLAKNRLTACWLFRWASPQGSCCSSR*WRCCPPR*IPR
+GCRLYWATGCLLSACWATSGWIVCFLTLIRRIWCKKGSSRFPAR*NALRFY*RSALACTT
+FRKESPPLSLPAAILNWVSASHWRWRCTIFLKGWRLPARFMPRRAQNVPRFFGPVSPAWR
+KFLAACWRG*FWAAWFHRSLWRLSWQQSPALWWRSPSMN*CRWQKRSILTITPAMVCFAV
+CPSWGSVSSFCRR*VSV
+>BBBB#75_01314
+MSVPLILTLLAGAATFIGAFLGVLGQKPSNRVLAFSLGFAAGIMLLISLMDAARRVRYRG
+DVACTGLRDVYYRPVGLLRAGSSASSRSSAGSGAKKAAAASRLDKTHCDFIDARH*PAQL
+SGRNRHLCHCQQQS*TGFRHRTGGGVAQYS*RAGGCRPGLCRDGLKTYRDFLGRYLRHGG
+NSWRRAGVADFGQPGFTDRYGGYHGSSRRHYGGALRR*TDAVGKRDRS*Q*PQLWCALRY
+VHHGAQSRHFADDRYRL
+>CCCC#76_00877
+MSVPLILTLLAGAATFIGAFLGVLGQKPSNRVLAFSLGFAAGIMLLISLMEMLPAALDTE
+GMSPVLGYGSLLSACWATSGWIVCFLTLIRRIWCKKGSSRFPAR*NALRFY*RSALACTT
+FRKESPLSLPAAILNWVSASHWRWRCTIFLKGWRLPARFMPRRAQNVPRFFGPVSPAWRK
+FLAACWRG*FWAAWFHRSLWRLSWQQSPALWWRSPSMN*CRWQKRSILTITPAMVCFAVC
+PSWGSVSSFCRR*VSV
+>DDDD#77_01105
+MSVPLILTLLAGAATFIGAFLGVLGQKPSNRVLAFSLGFAAGIMLLISLMEMLPAALDTE
+GMSPVLGYGMFIIGLLGYFGLDRLLPHAHPQDLVQKRQQPLPGSIKRTAILLTLGISLHN
+FPEGIATFVTASSNLELGFGIALAVALHNIPEGLAVAGPVYAATGSKRTAIFWAGISGMA
+EILGGVLAWLILGSLVSPIVMAAIMAAVAGIMVALSVDELMPLAKEIDPNNNPSYGVLCG
+MSIMGLSLVILQTIGIG*
+>EEEE
+MSVPLILTLLAGAATFIGAFLGVLGQKPSNRVLAFSLGFAAGIMLLISLMEMLPAALDTE
+GMSPVLGYGMFIIGLLGYFGLDRLLPHAHPQDLVQKRQQPLPGSIKRTAILLTLGISLHN
+FPEGIATFVTASSNLELGFGIALAVALHNIPEGLAVAGPVYAATGSKRTAIFWAGISGMA
+EILGVLAWLILGSLVSPIVMAAIMAAVAGIMVALSVDELMPLAKEIDPNNNPSYGVLCGM
+SIMGLSLVILQTIGIG*
+>FFFF
+MSVPLILTLLAGAATFIGAFLGVLGQKPSNRVLAFSLGFAAGIMLLISLMEMLPAALDTE
+GMSPVLGYGMFIIGLLGYFGLDRLLPHAHPQDLVQKRQQPLPGSIKRTAILLTLGISLHN
+FPEGIATFVTASSNLELGFGIALAVALHNIPEGLAVAGPVYAATGSKRTAIFWAGISGMA
+EILGGVLAWLILGSLAPIVMAAIMAAVAGIMVALSVDELMPLAKEIDPNNNPSYGVLCGM
+SIMGLSLVILQTIGIG*
+>GGGG
+MSVPLILTLLAGAATFIGAFLGVLGQKPSNRVLAFSLGFAAGIMLLISLMEMLPAALDTE
+GMSPVLGYGMFIIGLLGYFGLDRLLPHAHPQDLVQKRQQPLPGSIKRTAILLTLGISLHN
+FPEGIATFVTASSNLELGFGIALGWRCTIFLKGWRLPARFMPRRAQNVPRFFGPVSPAWR
+KFLAACWRG*FWAAWFHRSLWRLSWQQSPALWWRSPMN*CRWQKRSILTITPAMVCFAVC
+PSWGSVSSFCRR*VSV
+>HHHH
+MSVPLILTLLAGAATFIGAFLGVLGQKPSNRVLAFSLGFAAGIMLLISLMEMLPAALDTE
+GMSPVLGYGMFIIGLLGYFGLDRLLPHASAGSGAKKAAAASRLDKTHCDFIDARH*PAQL
+SGRNRHLCHCQQQS*TGFRHRTGGGVAQYS*RAGGCRPGLCRDGLKTYRDFLGRYLRHGG
+NSWRRAGVADFGQPGFTDRYGGYHGSSRRHYGGALRR*TDAVGKRDRS*Q*PQLWCALRY
+VHHGAQSRHFADDRYRL