- &script_list_biotools( $ENV{ 'INST_DIR'} . "/biotools/usage/" ) if $script eq "list_biotools";
-
- &script_print_usage( $ENV{ 'INST_DIR'} . "/biotools/usage/$script" ) if -t STDIN and not @ARGV;
-
- $options = &get_options( $script );
-
- $in = &read_stream( $options->{ "stream_in" } );
- $out = &write_stream( $options->{ "stream_out" } );
-
- if ( $script eq "read_fasta" ) { &script_read_fasta( $in, $out, $options ) }
- elsif ( $script eq "read_align" ) { &script_read_align( $in, $out, $options ) }
- elsif ( $script eq "read_tab" ) { &script_read_tab( $in, $out, $options ) }
- elsif ( $script eq "read_psl" ) { &script_read_psl( $in, $out, $options ) }
- elsif ( $script eq "read_bed" ) { &script_read_bed( $in, $out, $options ) }
- elsif ( $script eq "read_blast_tab" ) { &script_read_blast_tab( $in, $out, $options ) }
- elsif ( $script eq "read_embl" ) { &script_read_embl( $in, $out, $options ) }
- elsif ( $script eq "read_stockholm" ) { &script_read_stockholm( $in, $out, $options ) }
- elsif ( $script eq "read_phastcons" ) { &script_read_phastcons( $in, $out, $options ) }
- elsif ( $script eq "read_soft" ) { &script_read_soft( $in, $out, $options ) }
- elsif ( $script eq "read_gff" ) { &script_read_gff( $in, $out, $options ) }
- elsif ( $script eq "read_2bit" ) { &script_read_2bit( $in, $out, $options ) }
- elsif ( $script eq "read_solexa" ) { &script_read_solexa( $in, $out, $options ) }
- elsif ( $script eq "read_solid" ) { &script_read_solid( $in, $out, $options ) }
- elsif ( $script eq "read_mysql" ) { &script_read_mysql( $in, $out, $options ) }
- elsif ( $script eq "count_seq" ) { &script_count_seq( $in, $out, $options ) }
- elsif ( $script eq "length_seq" ) { &script_length_seq( $in, $out, $options ) }
- elsif ( $script eq "uppercase_seq" ) { &script_uppercase_seq( $in, $out, $options ) }
- elsif ( $script eq "shuffle_seq" ) { &script_shuffle_seq( $in, $out, $options ) }
- elsif ( $script eq "analyze_seq" ) { &script_analyze_seq( $in, $out, $options ) }
- elsif ( $script eq "analyze_tags" ) { &script_analyze_tags( $in, $out, $options ) }
- elsif ( $script eq "complexity_seq" ) { &script_complexity_seq( $in, $out, $options ) }
- elsif ( $script eq "oligo_freq" ) { &script_oligo_freq( $in, $out, $options ) }
- elsif ( $script eq "create_weight_matrix" ) { &script_create_weight_matrix( $in, $out, $options ) }
- elsif ( $script eq "calc_bit_scores" ) { &script_calc_bit_scores( $in, $out, $options ) }
- elsif ( $script eq "reverse_seq" ) { &script_reverse_seq( $in, $out, $options ) }
- elsif ( $script eq "complement_seq" ) { &script_complement_seq( $in, $out, $options ) }
- elsif ( $script eq "remove_indels" ) { &script_remove_indels( $in, $out, $options ) }
- elsif ( $script eq "transliterate_seq" ) { &script_transliterate_seq( $in, $out, $options ) }
- elsif ( $script eq "transliterate_vals" ) { &script_transliterate_vals( $in, $out, $options ) }
- elsif ( $script eq "translate_seq" ) { &script_translate_seq( $in, $out, $options ) }
- elsif ( $script eq "extract_seq" ) { &script_extract_seq( $in, $out, $options ) }
- elsif ( $script eq "get_genome_seq" ) { &script_get_genome_seq( $in, $out, $options ) }
- elsif ( $script eq "get_genome_align" ) { &script_get_genome_align( $in, $out, $options ) }
- elsif ( $script eq "get_genome_phastcons" ) { &script_get_genome_phastcons( $in, $out, $options ) }
- elsif ( $script eq "fold_seq" ) { &script_fold_seq( $in, $out, $options ) }
- elsif ( $script eq "split_seq" ) { &script_split_seq( $in, $out, $options ) }
- elsif ( $script eq "split_bed" ) { &script_split_bed( $in, $out, $options ) }
- elsif ( $script eq "align_seq" ) { &script_align_seq( $in, $out, $options ) }
- elsif ( $script eq "tile_seq" ) { &script_tile_seq( $in, $out, $options ) }
- elsif ( $script eq "invert_align" ) { &script_invert_align( $in, $out, $options ) }
- elsif ( $script eq "patscan_seq" ) { &script_patscan_seq( $in, $out, $options ) }
- elsif ( $script eq "create_blast_db" ) { &script_create_blast_db( $in, $out, $options ) }
- elsif ( $script eq "blast_seq" ) { &script_blast_seq( $in, $out, $options ) }
- elsif ( $script eq "blat_seq" ) { &script_blat_seq( $in, $out, $options ) }
- elsif ( $script eq "match_seq" ) { &script_match_seq( $in, $out, $options ) }
- elsif ( $script eq "create_vmatch_index" ) { &script_create_vmatch_index( $in, $out, $options ) }
- elsif ( $script eq "vmatch_seq" ) { &script_vmatch_seq( $in, $out, $options ) }
- elsif ( $script eq "write_fasta" ) { &script_write_fasta( $in, $out, $options, $options ) }
- elsif ( $script eq "write_align" ) { &script_write_align( $in, $out, $options ) }
- elsif ( $script eq "write_blast" ) { &script_write_blast( $in, $out, $options ) }
- elsif ( $script eq "write_tab" ) { &script_write_tab( $in, $out, $options ) }
- elsif ( $script eq "write_bed" ) { &script_write_bed( $in, $out, $options ) }
- elsif ( $script eq "write_psl" ) { &script_write_psl( $in, $out, $options ) }
- elsif ( $script eq "write_2bit" ) { &script_write_2bit( $in, $out, $options, $options ) }
- elsif ( $script eq "write_solid" ) { &script_write_solid( $in, $out, $options, $options ) }
- elsif ( $script eq "head_records" ) { &script_head_records( $in, $out, $options ) }
- elsif ( $script eq "remove_keys" ) { &script_remove_keys( $in, $out, $options ) }
- elsif ( $script eq "rename_keys" ) { &script_rename_keys( $in, $out, $options ) }
- elsif ( $script eq "uniq_vals" ) { &script_uniq_vals( $in, $out, $options ) }
- elsif ( $script eq "merge_vals" ) { &script_merge_vals( $in, $out, $options ) }
- elsif ( $script eq "grab" ) { &script_grab( $in, $out, $options ) }
- elsif ( $script eq "compute" ) { &script_compute( $in, $out, $options ) }
- elsif ( $script eq "flip_tab" ) { &script_flip_tab( $in, $out, $options ) }
- elsif ( $script eq "add_ident" ) { &script_add_ident( $in, $out, $options ) }
- elsif ( $script eq "count_records" ) { &script_count_records( $in, $out, $options ) }
- elsif ( $script eq "random_records" ) { &script_random_records( $in, $out, $options ) }
- elsif ( $script eq "sort_records" ) { &script_sort_records( $in, $out, $options ) }
- elsif ( $script eq "count_vals" ) { &script_count_vals( $in, $out, $options ) }
- elsif ( $script eq "plot_histogram" ) { &script_plot_histogram( $in, $out, $options ) }
- elsif ( $script eq "plot_lendist" ) { &script_plot_lendist( $in, $out, $options ) }
- elsif ( $script eq "plot_chrdist" ) { &script_plot_chrdist( $in, $out, $options ) }
- elsif ( $script eq "plot_karyogram" ) { &script_plot_karyogram( $in, $out, $options ) }
- elsif ( $script eq "plot_matches" ) { &script_plot_matches( $in, $out, $options ) }
- elsif ( $script eq "plot_seqlogo" ) { &script_plot_seqlogo( $in, $out, $options ) }
- elsif ( $script eq "plot_phastcons_profiles" ) { &script_plot_phastcons_profiles( $in, $out, $options ) }
- elsif ( $script eq "analyze_bed" ) { &script_analyze_bed( $in, $out, $options ) }
- elsif ( $script eq "analyze_vals" ) { &script_analyze_vals( $in, $out, $options ) }
- elsif ( $script eq "length_vals" ) { &script_length_vals( $in, $out, $options ) }
- elsif ( $script eq "sum_vals" ) { &script_sum_vals( $in, $out, $options ) }
- elsif ( $script eq "mean_vals" ) { &script_mean_vals( $in, $out, $options ) }
- elsif ( $script eq "median_vals" ) { &script_median_vals( $in, $out, $options ) }
- elsif ( $script eq "max_vals" ) { &script_max_vals( $in, $out, $options ) }
- elsif ( $script eq "min_vals" ) { &script_min_vals( $in, $out, $options ) }
- elsif ( $script eq "upload_to_ucsc" ) { &script_upload_to_ucsc( $in, $out, $options ) }
+ $options = get_options( $script );
+
+ $options->{ "SCRIPT" } = $script;
+
+ if ( $script ne "list_biopieces" and $script ne "list_genomes" ) {
+ $script = "print_usage" if ( -t STDIN and keys %{ $options } <= 1 or $options->{ 'help' } );
+ }
+
+ $in = read_stream( $options->{ "stream_in" } );
+ $out = write_stream( $options->{ "stream_out" } );
+
+ if ( $script eq "print_usage" ) { script_print_usage( $in, $out, $options ) }
+ elsif ( $script eq "list_biopieces" ) { script_list_biopieces( $in, $out, $options ) }
+ elsif ( $script eq "list_genomes" ) { script_list_genomes( $in, $out, $options ) }
+ elsif ( $script eq "read_fasta" ) { script_read_fasta( $in, $out, $options ) }
+ elsif ( $script eq "read_tab" ) { script_read_tab( $in, $out, $options ) }
+ elsif ( $script eq "read_psl" ) { script_read_psl( $in, $out, $options ) }
+ elsif ( $script eq "read_bed" ) { script_read_bed( $in, $out, $options ) }
+ elsif ( $script eq "read_fixedstep" ) { script_read_fixedstep( $in, $out, $options ) }
+ elsif ( $script eq "read_blast_tab" ) { script_read_blast_tab( $in, $out, $options ) }
+ elsif ( $script eq "read_embl" ) { script_read_embl( $in, $out, $options ) }
+ elsif ( $script eq "read_stockholm" ) { script_read_stockholm( $in, $out, $options ) }
+ elsif ( $script eq "read_phastcons" ) { script_read_phastcons( $in, $out, $options ) }
+ elsif ( $script eq "read_soft" ) { script_read_soft( $in, $out, $options ) }
+ elsif ( $script eq "read_gff" ) { script_read_gff( $in, $out, $options ) }
+ elsif ( $script eq "read_2bit" ) { script_read_2bit( $in, $out, $options ) }
+ elsif ( $script eq "read_solexa" ) { script_read_solexa( $in, $out, $options ) }
+ elsif ( $script eq "read_solid" ) { script_read_solid( $in, $out, $options ) }
+ elsif ( $script eq "read_mysql" ) { script_read_mysql( $in, $out, $options ) }
+ elsif ( $script eq "format_genome" ) { script_format_genome( $in, $out, $options ) }
+ elsif ( $script eq "length_seq" ) { script_length_seq( $in, $out, $options ) }
+ elsif ( $script eq "uppercase_seq" ) { script_uppercase_seq( $in, $out, $options ) }
+ elsif ( $script eq "shuffle_seq" ) { script_shuffle_seq( $in, $out, $options ) }
+ elsif ( $script eq "analyze_seq" ) { script_analyze_seq( $in, $out, $options ) }
+ elsif ( $script eq "analyze_tags" ) { script_analyze_tags( $in, $out, $options ) }
+ elsif ( $script eq "complexity_seq" ) { script_complexity_seq( $in, $out, $options ) }
+ elsif ( $script eq "oligo_freq" ) { script_oligo_freq( $in, $out, $options ) }
+ elsif ( $script eq "create_weight_matrix" ) { script_create_weight_matrix( $in, $out, $options ) }
+ elsif ( $script eq "calc_bit_scores" ) { script_calc_bit_scores( $in, $out, $options ) }
+ elsif ( $script eq "reverse_seq" ) { script_reverse_seq( $in, $out, $options ) }
+ elsif ( $script eq "complement_seq" ) { script_complement_seq( $in, $out, $options ) }
+ elsif ( $script eq "remove_indels" ) { script_remove_indels( $in, $out, $options ) }
+ elsif ( $script eq "transliterate_seq" ) { script_transliterate_seq( $in, $out, $options ) }
+ elsif ( $script eq "transliterate_vals" ) { script_transliterate_vals( $in, $out, $options ) }
+ elsif ( $script eq "translate_seq" ) { script_translate_seq( $in, $out, $options ) }
+ elsif ( $script eq "extract_seq" ) { script_extract_seq( $in, $out, $options ) }
+ elsif ( $script eq "get_genome_seq" ) { script_get_genome_seq( $in, $out, $options ) }
+ elsif ( $script eq "get_genome_align" ) { script_get_genome_align( $in, $out, $options ) }
+ elsif ( $script eq "get_genome_phastcons" ) { script_get_genome_phastcons( $in, $out, $options ) }
+ elsif ( $script eq "fold_seq" ) { script_fold_seq( $in, $out, $options ) }
+ elsif ( $script eq "split_seq" ) { script_split_seq( $in, $out, $options ) }
+ elsif ( $script eq "split_bed" ) { script_split_bed( $in, $out, $options ) }
+ elsif ( $script eq "align_seq" ) { script_align_seq( $in, $out, $options ) }
+ elsif ( $script eq "tile_seq" ) { script_tile_seq( $in, $out, $options ) }
+ elsif ( $script eq "invert_align" ) { script_invert_align( $in, $out, $options ) }
+ elsif ( $script eq "patscan_seq" ) { script_patscan_seq( $in, $out, $options ) }
+ elsif ( $script eq "create_blast_db" ) { script_create_blast_db( $in, $out, $options ) }
+ elsif ( $script eq "blast_seq" ) { script_blast_seq( $in, $out, $options ) }
+ elsif ( $script eq "blat_seq" ) { script_blat_seq( $in, $out, $options ) }
+ elsif ( $script eq "soap_seq" ) { script_soap_seq( $in, $out, $options ) }
+ elsif ( $script eq "match_seq" ) { script_match_seq( $in, $out, $options ) }
+ elsif ( $script eq "create_vmatch_index" ) { script_create_vmatch_index( $in, $out, $options ) }
+ elsif ( $script eq "vmatch_seq" ) { script_vmatch_seq( $in, $out, $options ) }
+ elsif ( $script eq "write_fasta" ) { script_write_fasta( $in, $out, $options ) }
+ elsif ( $script eq "write_align" ) { script_write_align( $in, $out, $options ) }
+ elsif ( $script eq "write_blast" ) { script_write_blast( $in, $out, $options ) }
+ elsif ( $script eq "write_tab" ) { script_write_tab( $in, $out, $options ) }
+ elsif ( $script eq "write_bed" ) { script_write_bed( $in, $out, $options ) }
+ elsif ( $script eq "write_psl" ) { script_write_psl( $in, $out, $options ) }
+ elsif ( $script eq "write_fixedstep" ) { script_write_fixedstep( $in, $out, $options ) }
+ elsif ( $script eq "write_2bit" ) { script_write_2bit( $in, $out, $options ) }
+ elsif ( $script eq "write_solid" ) { script_write_solid( $in, $out, $options ) }
+ elsif ( $script eq "head_records" ) { script_head_records( $in, $out, $options ) }
+ elsif ( $script eq "remove_keys" ) { script_remove_keys( $in, $out, $options ) }
+ elsif ( $script eq "remove_adaptor" ) { script_remove_adaptor( $in, $out, $options ) }
+ elsif ( $script eq "rename_keys" ) { script_rename_keys( $in, $out, $options ) }
+ elsif ( $script eq "uniq_vals" ) { script_uniq_vals( $in, $out, $options ) }
+ elsif ( $script eq "merge_vals" ) { script_merge_vals( $in, $out, $options ) }
+ elsif ( $script eq "merge_records" ) { script_merge_records( $in, $out, $options ) }
+ elsif ( $script eq "grab" ) { script_grab( $in, $out, $options ) }
+ elsif ( $script eq "compute" ) { script_compute( $in, $out, $options ) }
+ elsif ( $script eq "flip_tab" ) { script_flip_tab( $in, $out, $options ) }
+ elsif ( $script eq "add_ident" ) { script_add_ident( $in, $out, $options ) }
+ elsif ( $script eq "count_records" ) { script_count_records( $in, $out, $options ) }
+ elsif ( $script eq "random_records" ) { script_random_records( $in, $out, $options ) }
+ elsif ( $script eq "sort_records" ) { script_sort_records( $in, $out, $options ) }
+ elsif ( $script eq "count_vals" ) { script_count_vals( $in, $out, $options ) }
+ elsif ( $script eq "plot_histogram" ) { script_plot_histogram( $in, $out, $options ) }
+ elsif ( $script eq "plot_lendist" ) { script_plot_lendist( $in, $out, $options ) }
+ elsif ( $script eq "plot_chrdist" ) { script_plot_chrdist( $in, $out, $options ) }
+ elsif ( $script eq "plot_karyogram" ) { script_plot_karyogram( $in, $out, $options ) }
+ elsif ( $script eq "plot_matches" ) { script_plot_matches( $in, $out, $options ) }
+ elsif ( $script eq "plot_seqlogo" ) { script_plot_seqlogo( $in, $out, $options ) }
+ elsif ( $script eq "plot_phastcons_profiles" ) { script_plot_phastcons_profiles( $in, $out, $options ) }
+ elsif ( $script eq "analyze_bed" ) { script_analyze_bed( $in, $out, $options ) }
+ elsif ( $script eq "analyze_vals" ) { script_analyze_vals( $in, $out, $options ) }
+ elsif ( $script eq "length_vals" ) { script_length_vals( $in, $out, $options ) }
+ elsif ( $script eq "sum_vals" ) { script_sum_vals( $in, $out, $options ) }
+ elsif ( $script eq "mean_vals" ) { script_mean_vals( $in, $out, $options ) }
+ elsif ( $script eq "median_vals" ) { script_median_vals( $in, $out, $options ) }
+ elsif ( $script eq "max_vals" ) { script_max_vals( $in, $out, $options ) }
+ elsif ( $script eq "min_vals" ) { script_min_vals( $in, $out, $options ) }
+ elsif ( $script eq "upload_to_ucsc" ) { script_upload_to_ucsc( $in, $out, $options ) }