change to using /pseudogene qualifier

etc/feature_keys

@@ -10,59 +10,59 @@
 3'UTR           allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial standard_name trans_splicing
 5'UTR           allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial standard_name trans_splicing
 CAAT_signal     allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial
-CDS             EC_number allele artificial_location citation codon_start db_xref exception experiment function gene gene_synonym inference locus_tag map note number old_locus_tag operon partial product protein_id pseudo ribosomal_slippage standard_name trans_splicing transl_except transl_table translation
-C_region        allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudo standard_name
+CDS             EC_number allele artificial_location citation codon_start db_xref exception experiment function gene gene_synonym inference locus_tag map note number old_locus_tag operon partial product protein_id pseudogene ribosomal_slippage standard_name trans_splicing transl_except transl_table translation
+C_region        allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudogene standard_name
 D-loop          allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial
-D_segment       allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudo standard_name
+D_segment       allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudogene standard_name
 GC_signal       allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial
-J_segment       allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudo standard_name
+J_segment       allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudogene standard_name
 LTR             allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial standard_name
-N_region        allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudo standard_name
+N_region        allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudogene standard_name
 RBS             allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial standard_name
 STS             allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial standard_name
-S_region        allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudo standard_name
+S_region        allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudogene standard_name
 TATA_signal     allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial
-V_region        allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudo standard_name
-V_segment       allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudo standard_name
+V_region        allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudogene standard_name
+V_segment       allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudogene standard_name
 assembly_gap    @gap_type @estimated_length linkage_evidence
 attenuator      allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag operon partial phenotype
 enhancer        allele bound_moiety citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial standard_name
-exon            EC_number allele citation db_xref experiment function gene gene_synonym inference locus_tag map note number old_locus_tag partial product pseudo standard_name
+exon            EC_number allele citation db_xref experiment function gene gene_synonym inference locus_tag map note number old_locus_tag partial product pseudogene standard_name
 gap             @estimated_length experiment inference map note
-gene            allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial phenotype product pseudo standard_name trans_splicing
+gene            allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial phenotype product pseudogene standard_name trans_splicing
 iDNA            allele citation db_xref experiment function gene gene_synonym inference locus_tag map note number old_locus_tag partial standard_name
-intron          allele citation db_xref experiment function gene gene_synonym inference locus_tag map note number old_locus_tag partial pseudo standard_name
-mRNA            allele artificial_location citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial product pseudo standard_name trans_splicing
-mat_peptide     EC_number allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudo standard_name
-misc_RNA        allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial product pseudo standard_name trans_splicing
+intron          allele citation db_xref experiment function gene gene_synonym inference locus_tag map note number old_locus_tag partial pseudogene standard_name
+mRNA            allele artificial_location citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial product pseudogene standard_name trans_splicing
+mat_peptide     EC_number allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudogene standard_name
+misc_RNA        allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial product pseudogene standard_name trans_splicing
 misc_binding    @bound_moiety allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial
 misc_difference allele citation clone compare db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial phenotype replace standard_name
-misc_feature    allele citation db_xref experiment function gene gene_synonym inference locus_tag map note number old_locus_tag partial phenotype product pseudo standard_name
+misc_feature    allele citation db_xref experiment function gene gene_synonym inference locus_tag map note number old_locus_tag partial phenotype product pseudogene standard_name
 misc_recomb     allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial standard_name
 misc_signal     allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial phenotype standard_name
 misc_structure  allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial standard_name
 mobile_element  @mobile_element_type allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial rpt_family rpt_type standard_name
 modified_base   @mod_base allele citation db_xref experiment frequency gene gene_synonym inference locus_tag map note old_locus_tag
-ncRNA           @ncRNA_class allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial product pseudo standard_name trans_splicing
+ncRNA           @ncRNA_class allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial product pseudogene standard_name trans_splicing
 old_sequence    allele citation compare db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial replace
-operon          @operon allele citation db_xref experiment function inference map note phenotype pseudo standard_name
+operon          @operon allele citation db_xref experiment function inference map note phenotype pseudogene standard_name
 oriT            allele bound_moiety citation db_xref direction experiment gene gene_synonym inference locus_tag map note old_locus_tag rpt_family rpt_type rpt_unit_range rpt_unit_seq standard_name
 polyA_signal    allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial
 polyA_site      allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag
 precursor_RNA   allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial product standard_name trans_splicing
 prim_transcript allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial standard_name
 primer_bind     PCR_conditions allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag partial standard_name
-promoter        allele bound_moiety citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial phenotype pseudo standard_name
+promoter        allele bound_moiety citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial phenotype pseudogene standard_name
 protein_bind    @bound_moiety allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial standard_name
-rRNA            allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial product pseudo standard_name
+rRNA            allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial product pseudogene standard_name
 rep_origin      allele citation db_xref direction experiment gene gene_synonym inference locus_tag map note old_locus_tag partial standard_name
 repeat_region   allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial rpt_family rpt_type rpt_unit_range rpt_unit_seq satellite standard_name
-sig_peptide     allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudo standard_name
+sig_peptide     allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudogene standard_name
 source          @mol_type @organism PCR_primers bio_material cell_line cell_type chromosome citation clone clone_lib collected_by collection_date country cultivar culture_collection db_xref dev_stage ecotype environmental_sample focus frequency germline haplogroup haplotype host identified_by isolate isolation_source lab_host lat_lon macronuclear map mating_type note organelle plasmid pop_variant proviral rearranged segment serotype serovar sex specimen_voucher strain sub_clone sub_species sub_strain tissue_lib tissue_type transgenic variety
 stem_loop       allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial standard_name
-tRNA            allele anticodon citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial product pseudo standard_name trans_splicing
+tRNA            allele anticodon citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag operon partial product pseudogene standard_name trans_splicing
 terminator      allele citation db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag operon partial standard_name
-tmRNA           allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag product pseudo standard_name tag_peptide
-transit_peptide allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudo standard_name
+tmRNA           allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag product pseudogene standard_name tag_peptide
+transit_peptide allele citation db_xref experiment function gene gene_synonym inference locus_tag map note old_locus_tag partial product pseudogene standard_name
 unsure          allele citation compare db_xref experiment gene gene_synonym inference locus_tag map note old_locus_tag replace
 variation       allele citation compare db_xref experiment frequency gene gene_synonym inference locus_tag map note old_locus_tag partial phenotype product replace standard_name

etc/options

@@ -531,6 +531,7 @@ extra_qualifiers = \
     previous_systematic_id "text" \
     primary_name "text" \
     prosite_match "text" \
+    pseudo none \
     psu_db_xref "text" \
     psu_domain "text" \
     reserved_name "text" \
@@ -648,6 +649,7 @@ invisible_qualifiers = \
     percent_id     \
     pfam_match     \
     prosite_match  \
+    pseudo         \
     psu_domain     \
     reserved_gene_name \
     query_id       \

etc/qualifier_types

@@ -90,7 +90,7 @@ pop_variant              no        "text"
 product                  no        "text"
 protein_id               yes       "text"
 proviral                 yes        none
-pseudo                   yes        none
+pseudogene               yes       "list"   "processed" "unprocessed" "unitary" "allelic" "unknown"
 rearranged               yes        none
 replace                  yes       "text"
 ribosomal_slippage       yes        text