- parallelize() (in module pdm_utils.functions.parallelize), [1]
- parenthesize() (pdm_utils.classes.filter.Filter method), [1]
- parse_accession() (in module pdm_utils.functions.phagesdb), [1]
- parse_amino_acid() (pdm_utils.classes.trna.Trna method), [1]
- parse_anticodon() (pdm_utils.classes.trna.Trna method), [1]
- parse_args() (in module pdm_utils.pipelines.compare_db)
- parse_cds_seqfeature() (in module pdm_utils.functions.flat_files), [1]
- parse_cluster() (in module pdm_utils.functions.phagesdb), [1]
- parse_cmd_list() (in module pdm_utils.functions.parsing), [1]
- parse_cmd_string() (in module pdm_utils.functions.parsing), [1]
- parse_column() (in module pdm_utils.functions.parsing), [1]
- parse_config() (in module pdm_utils.functions.configfile)
- parse_coordinates() (in module pdm_utils.functions.flat_files), [1]
- parse_description() (pdm_utils.classes.genome.Genome method), [1]
- parse_determinate_trnas() (pdm_utils.classes.aragornhandler.AragornHandler method), [1]
- parse_export() (in module pdm_utils.pipelines.export_db), [1]
- parse_fasta_data() (in module pdm_utils.functions.phagesdb), [1]
- parse_fasta_filename() (in module pdm_utils.functions.phagesdb), [1]
- parse_feature_data() (in module pdm_utils.functions.mysqldb), [1]
- parse_feature_table() (in module pdm_utils.functions.fileio)
- parse_filter() (in module pdm_utils.functions.parsing), [1]
- parse_flag_file() (in module pdm_utils.functions.basic), [1]
- parse_gene_table_data() (in module pdm_utils.functions.mysqldb), [1]
- parse_genome_data() (in module pdm_utils.functions.flat_files), [1]
- parse_genomes_dict() (in module pdm_utils.functions.phagesdb), [1]
- parse_host() (pdm_utils.classes.source.Source method), [1]
- parse_host_genus() (in module pdm_utils.functions.phagesdb), [1]
- parse_import_ticket_data() (in module pdm_utils.functions.tickets), [1]
- parse_in_spaces() (in module pdm_utils.functions.parsing), [1]
- parse_indeterminate_trnas() (pdm_utils.classes.aragornhandler.AragornHandler method), [1]
- parse_lab_host() (pdm_utils.classes.source.Source method), [1]
- parse_mcl_output() (in module pdm_utils.functions.phameration), [1]
- parse_mmseqs_output() (in module pdm_utils.functions.phameration), [1]
- parse_names_from_record_field() (in module pdm_utils.functions.basic), [1]
- parse_organism() (pdm_utils.classes.genome.Genome method), [1]
- parse_out_ends() (in module pdm_utils.functions.parsing), [1]
- parse_out_spaces() (in module pdm_utils.functions.parsing), [1]
- parse_peptide_tag() (pdm_utils.classes.tmrna.Tmrna method), [1]
- parse_phage_name() (in module pdm_utils.functions.phagesdb), [1]
- parse_phage_table_data() (in module pdm_utils.functions.mysqldb), [1]
- parse_pham_finder() (in module pdm_utils.pipelines.pham_finder)
- parse_revise() (in module pdm_utils.pipelines.revise)
- parse_source() (pdm_utils.classes.genome.Genome method), [1]
- parse_source_seqfeature() (in module pdm_utils.functions.flat_files), [1]
- parse_subcluster() (in module pdm_utils.functions.phagesdb), [1]
- parse_tbl_data_type() (in module pdm_utils.classes.fileio)
- parse_tmrna_seqfeature() (in module pdm_utils.functions.flat_files), [1]
- parse_tmrna_table_data() (in module pdm_utils.functions.mysqldb), [1]
- parse_tmrnas() (pdm_utils.classes.aragornhandler.AragornHandler method), [1]
- parse_trna_seqfeature() (in module pdm_utils.functions.flat_files), [1]
- parse_trna_table_data() (in module pdm_utils.functions.mysqldb), [1]
- parse_trnas() (pdm_utils.classes.aragornhandler.AragornHandler method), [1]
- parse_value_input() (in module pdm_utils.functions.pipelines_basic)
- partition_list() (in module pdm_utils.functions.basic), [1]
- password (pdm_utils.classes.alchemyhandler.AlchemyHandler property), [1]
-
pdm_utils
-
pdm_utils.classes
-
pdm_utils.classes.alchemyhandler
-
pdm_utils.classes.aragornhandler
-
pdm_utils.classes.bundle
-
pdm_utils.classes.cds
-
pdm_utils.classes.cdspair
-
pdm_utils.classes.dbcomparesummary
-
pdm_utils.classes.evaluation
-
pdm_utils.classes.fileio
-
pdm_utils.classes.filter
-
pdm_utils.classes.genome
-
pdm_utils.classes.genomepair
-
pdm_utils.classes.genometriad
-
pdm_utils.classes.randomfieldupdatehandler
-
pdm_utils.classes.source
-
pdm_utils.classes.ticket
-
pdm_utils.classes.tmrna
|
-
pdm_utils.classes.trna
-
pdm_utils.classes.trnascansehandler
-
pdm_utils.constants
-
pdm_utils.constants.constants
-
pdm_utils.constants.db_schema_0
-
pdm_utils.constants.eval_descriptions
-
pdm_utils.constants.schema_conversions
-
pdm_utils.functions
-
pdm_utils.functions.annotation
-
pdm_utils.functions.basic
-
pdm_utils.functions.cartography
-
pdm_utils.functions.configfile
-
pdm_utils.functions.eval_modes
-
pdm_utils.functions.fileio
-
pdm_utils.functions.flat_files
-
pdm_utils.functions.mysqldb
-
pdm_utils.functions.mysqldb_basic
-
pdm_utils.functions.ncbi
-
pdm_utils.functions.parallelize
-
pdm_utils.functions.parsing
-
pdm_utils.functions.phagesdb
-
pdm_utils.functions.phameration
-
pdm_utils.functions.pipelines_basic
-
pdm_utils.functions.querying
-
pdm_utils.functions.server
-
pdm_utils.functions.tickets
-
pdm_utils.pipelines
-
pdm_utils.pipelines.compare_db
-
pdm_utils.pipelines.convert_db
-
pdm_utils.pipelines.export_db
-
pdm_utils.pipelines.find_domains
-
pdm_utils.pipelines.freeze_db
-
pdm_utils.pipelines.get_data
-
pdm_utils.pipelines.get_db
-
pdm_utils.pipelines.get_gb_records
-
pdm_utils.pipelines.import_genome
-
pdm_utils.pipelines.pham_finder
-
pdm_utils.pipelines.phamerate
-
pdm_utils.pipelines.push_db
-
pdm_utils.pipelines.revise
-
pdm_utils.pipelines.update_field
-
pdm_utils.run
- pipe_commands() (in module pdm_utils.functions.mysqldb_basic)
- prepare_bundle() (in module pdm_utils.pipelines.import_genome), [1]
- prepare_download() (in module pdm_utils.pipelines.get_db), [1]
- prepare_filepath() (in module pdm_utils.functions.basic), [1]
- prepare_tickets() (in module pdm_utils.pipelines.import_genome), [1]
- prepare_unmatched_to_gbk_output() (in module pdm_utils.pipelines.compare_db)
- prepare_unmatched_to_pdb_output() (in module pdm_utils.pipelines.compare_db)
- preserve_phams() (in module pdm_utils.functions.phameration), [1]
- print_genbank_tallies() (in module pdm_utils.pipelines.get_data), [1]
- print_match_results() (in module pdm_utils.pipelines.get_data), [1]
- print_results() (pdm_utils.classes.filter.Filter method), [1]
- print_summary() (in module pdm_utils.pipelines.convert_db), [1]
- process_align() (in module pdm_utils.pipelines.find_domains), [1]
- process_failed_retrieval() (in module pdm_utils.pipelines.get_data), [1]
- process_files_and_tickets() (in module pdm_utils.pipelines.import_genome), [1]
- process_gbk_data() (in module pdm_utils.pipelines.compare_db)
- process_mysql_data() (in module pdm_utils.pipelines.compare_db)
- process_phagesdb_data() (in module pdm_utils.pipelines.compare_db)
- process_rps_output() (in module pdm_utils.pipelines.find_domains), [1]
|