Code Summary

DIGS

modules/DIGS/Pipeline.pm:# Subroutine:  new
modules/DIGS/Pipeline.pm:# Subroutine:  run_digs_function
modules/DIGS/Pipeline.pm:# Subroutine:  create_screening_db
modules/DIGS/Pipeline.pm:# Subroutine:  initialise 
modules/DIGS/Pipeline.pm:# Subroutine:  run_screen
modules/DIGS/Pipeline.pm:# Subroutine:  do pipeline screen 
modules/DIGS/Pipeline.pm:# Subroutine:  search
modules/DIGS/Pipeline.pm:# Subroutine:  extract
modules/DIGS/Pipeline.pm:# Subroutine:  assign
modules/DIGS/Pipeline.pm:# Subroutine:  index previously extracted loci
modules/DIGS/Pipeline.pm:# Subroutine:  check if locus previously extracted
modules/DIGS/Pipeline.pm:# Subroutine:  reassign
modules/DIGS/Pipeline.pm:# Subroutine:  initialise_reassign 
modules/DIGS/Pipeline.pm:# Subroutine:  retrieve 
modules/DIGS/Pipeline.pm:# Subroutine:  check_process_dir_status
modules/DIGS/Pipeline.pm:# Subroutine:  show_title

modules/DIGS/GenomeControl.pm:# Subroutine:  new
modules/DIGS/GenomeControl.pm:# Subroutine:  summarise_genomes
modules/DIGS/GenomeControl.pm:# Subroutine:  refresh_genomes
modules/DIGS/GenomeControl.pm:# Subroutine:  read_genome_directory
modules/DIGS/GenomeControl.pm:# Subroutine:  check_genome_formatting
modules/DIGS/GenomeControl.pm:# Subroutine:  format_genome
modules/DIGS/GenomeControl.pm:# Subroutine:  get_genome_chunk_stats
modules/DIGS/GenomeControl.pm:# Subroutine:  split_genome_chunk
modules/DIGS/GenomeControl.pm:# Subroutine:  split_longline_contig
modules/DIGS/GenomeControl.pm:# Subroutine:  by number

modules/DIGS/ScreenBuild.pm:# Subroutine:  new
modules/DIGS/ScreenBuild.pm:# Subroutine:  set_up_screen
modules/DIGS/ScreenBuild.pm:# Subroutine:  set_screening_db
modules/DIGS/ScreenBuild.pm:# Subroutine:  load_aa_fasta_reference_library
modules/DIGS/ScreenBuild.pm:# Subroutine:  load_nt_fasta_reference_library
modules/DIGS/ScreenBuild.pm:# Subroutine:  create_blast_aa_lib
modules/DIGS/ScreenBuild.pm:# Subroutine:  create_blast_nt_lib
modules/DIGS/ScreenBuild.pm:# Subroutine:  set_targets
modules/DIGS/ScreenBuild.pm:# Subroutine:  read genome files
modules/DIGS/ScreenBuild.pm:# Subroutine:  get_path_elements
modules/DIGS/ScreenBuild.pm:# Subroutine:  load_aa_fasta_probes
modules/DIGS/ScreenBuild.pm:# Subroutine:  load_nt_fasta_probes
modules/DIGS/ScreenBuild.pm:# Subroutine:  parse_fasta_header_data
modules/DIGS/ScreenBuild.pm:# Subroutine:  add_aa_probe
modules/DIGS/ScreenBuild.pm:# Subroutine:  add_na_probe
modules/DIGS/ScreenBuild.pm:# Subroutine:  set_queries
modules/DIGS/ScreenBuild.pm:# Subroutine:  create output directories
modules/DIGS/ScreenBuild.pm:# Subroutine:  parse control file

modules/DIGS/DB.pm:# Subroutine:  new
modules/DIGS/DB.pm:# Subroutine:  load_screening_db 
modules/DIGS/DB.pm:# Subroutine:  load_blast_results_table
modules/DIGS/DB.pm:# Subroutine:  load_extracted_table
modules/DIGS/DB.pm:# Subroutine:  load_status_table
modules/DIGS/DB.pm:# Subroutine:  create_screening_db
modules/DIGS/DB.pm:# Subroutine:  create_blast_results_table
modules/DIGS/DB.pm:# Subroutine:  create_extracted_table
modules/DIGS/DB.pm:# Subroutine:  create_status_table
modules/DIGS/DB.pm:# Subroutine:  index_previously_executed_queries 
modules/DIGS/DB.pm:# Subroutine:  summarise_db
modules/DIGS/DB.pm:# Subroutine:  summarise_status_table
modules/DIGS/DB.pm:# Subroutine:  summarise BLAST_results table
modules/DIGS/DB.pm:# Subroutine:  summarise Extracted table
modules/DIGS/DB.pm:# Subroutine:  retrieve_sequences
modules/DIGS/DB.pm:# Subroutine:  drop_screening_db
modules/DIGS/DB.pm:# Subroutine:  flush_screening_db 

Interface

modules/Interface/BLAST.pm:# Subroutine:  new
modules/Interface/BLAST.pm:# Subroutine:  BLAST - used with PIPELINE screens
modules/Interface/BLAST.pm:# Subroutine:  parse_tab_format_results
modules/Interface/BLAST.pm:# Subroutine:  sort_hits_into_fwd_and_rev 
modules/Interface/BLAST.pm:# Subroutine:  convert_evalue


modules/Interface/MySQLtable.pm:# Subroutine:  new
modules/Interface/MySQLtable.pm:# Subroutine:  insert_row
modules/Interface/MySQLtable.pm:# Subroutine:  select rows
modules/Interface/MySQLtable.pm:# Subroutine:  select distinct
modules/Interface/MySQLtable.pm:# Subroutine:  update
modules/Interface/MySQLtable.pm:# Subroutine:  delete_rows
modules/Interface/MySQLtable.pm:# Subroutine:  flush
modules/Interface/MySQLtable.pm:# Subroutine:  reset_primary_key

Base

modules/Base/Console.pm:# Subroutine:  new
modules/Base/Console.pm:# Subroutine:  refresh_console
modules/Base/Console.pm:# Subroutine:  show_about_box 
modules/Base/Console.pm:# Subroutine:  ask_yes_no_question
modules/Base/Console.pm:# Subroutine:  enclose_box_text


modules/Base/DevTools.pm:# Subroutine:  new
modules/Base/DevTools.pm:# Subroutine:  print_hash
modules/Base/DevTools.pm:# Subroutine:  print_array


modules/Base/SeqIO.pm:# Subroutine:  new
modules/Base/SeqIO.pm:# Subroutine:  read_fasta


modules/Base/FileIO.pm:# Subroutine:  new
modules/Base/FileIO.pm:# Subroutine:  check_directory_exists
modules/Base/FileIO.pm:# Subroutine:  check_file_exists
modules/Base/FileIO.pm:# Subroutine:  get infile type
modules/Base/FileIO.pm:# Subroutine:  read_directory_to_array
modules/Base/FileIO.pm:# Subroutine:  read_directory_tree_leaves
modules/Base/FileIO.pm:# Subroutine:  recursive_read
modules/Base/FileIO.pm:# Subroutine:  read_directory_tree_leaves_simple
modules/Base/FileIO.pm:# Subroutine:  recursive_read2
modules/Base/FileIO.pm:# Subroutine:  read_file
modules/Base/FileIO.pm:# Subroutine:  write_file
modules/Base/FileIO.pm:# Subroutine:  write_text_to_file
modules/Base/FileIO.pm:# Subroutine:  append_text_to_file
modules/Base/FileIO.pm:# Subroutine:  read_sql_block
modules/Base/FileIO.pm:# Subroutine:  read_standard_field_value_block
modules/Base/FileIO.pm:# Subroutine:  extract_text_blocks
modules/Base/FileIO.pm:# Subroutine:  extract_text_block
modules/Base/FileIO.pm:# Subroutine:  create_unique_directory 


modules/Base/Sequence.pm:# Subroutine:  new
modules/Base/Sequence.pm:# Subroutine:  translate
modules/Base/Sequence.pm:# Subroutine:  reverse and complement
modules/Base/Sequence.pm:# Subroutine:  extract_subsequence
modules/Base/Sequence.pm:# Subroutine:  get_translations 
modules/Base/Sequence.pm:# Subroutine:  get_codon_list
modules/Base/Sequence.pm:# Subroutine:  codon2aa