Class: Bioroebe::FetchFastaSequenceFromPdb

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/pdb_and_protein_structure/fetch_fasta_sequence_from_pdb.rb

Overview

Bioroebe::FetchFastaSequenceFromPdb

Constant Summary collapse

URL_FOR_FASTA_ENTRIES_AT_THE_PDB =
#

URL_FOR_FASTA_ENTRIES_AT_THE_PDB

#
'https://www.rcsb.org/fasta/entry/'

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

Instance Method Summary collapse

Methods inherited from CommandlineApplication

#all_aminoacids?, #append_what_into, #at_home?, #be_silent, #be_verbose?, #cat, #ccliner, #change_directory, #cliner, #codon_table_dataset?, #codon_to_aminoacid, #codons_for?, #colourize_this_dna_sequence, #complement, #cp, #disable_warnings, #download_dir?, #editor?, #enable_warnings, #ensure_that_the_base_directories_exist, #esystem, #extract, #is_this_a_start_codon?, #is_this_a_stop_codon?, #leading_five_prime, #load_bioroebe_yaml_file, #log_directory?, #one_letter_to_long_name, #one_to_three, #only_numbers?, #open_in_browser, #opnerev, #opnn, #pad_with_double_quotes, #pad_with_single_quotes, #partner_nucleotide, #remove_numbers, #remove_trailing_ansii_escape_code, #return_all_possible_start_codons, #return_array_of_one_letter_aminoacids, #return_cheerful_person, #return_chunked_display, #return_ubiquitin_sequence, #runmode?, #set_be_verbose, #set_runmode, #start_codon?, #stop_codons?, #strict_filter_away_invalid_aminoacids, #taxonomy_download_directory?, #three_to_one, #to_rna, #trailing_three_prime, #use_opn?, #verbose_truth, #was_or_were, #without_extname, #write_what_into

Methods included from BaseModule

#absolute_path, #default_file_read, #file_readlines

Methods included from CommandlineArguments

#commandline_arguments?, #commandline_arguments_that_are_files?, #e, #first?, #first_non_hyphen_argument?, #remove_hyphens_from_the_commandline_arguments, #return_commandline_arguments_as_string, #return_commandline_arguments_that_are_not_files, #return_entries_without_two_leading_hyphens, #select_commandline_arguments, #select_entries_starting_with_two_hyphens, #set_commandline_arguments

Methods included from ColoursForBase

#colourize_this_aminoacid_sequence_for_the_commandline, #colourize_this_nucleotide_sequence, #disable_colours, #ecomment, #efancy, #egold, #enable_colours, #eorange, #eparse, #erev, #red, #remove_trailing_escape_part, #return_colour_for_nucleotides, #rev, #sdir, #set_will_we_use_colours, #sfancy, #sfile, #simp, #swarn, #use_colours?, #use_colours_within_the_bioroebe_namespace?

Methods inherited from Base

#append_what_into, #can_base_pair?, #convert_global_env, #delete_file, #directory_to_the_codon_tables?, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #no_file_exists_at, #no_newlines, #project_yaml_directory?, #rds, #register_sigint, #return_pwd, #return_the_first_line_of_this_file, #word_wrap, #write_what_into

Methods included from InternalHashModule

#internal_hash?, #reset_the_internal_hash

Methods included from InferTheNamespaceModule

#infer_the_namespace, #namespace?

Constructor Details

#initialize(i = ARGV, run_already = true) ⇒ FetchFastaSequenceFromPdb

#

initialize

#


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# File 'lib/bioroebe/pdb_and_protein_structure/fetch_fasta_sequence_from_pdb.rb', line 33

def initialize(
    i           = ARGV,
    run_already = true
  )
  reset
  set_commandline_arguments(i)
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :be_silent
    # ===================================================================== #
    when :be_silent
      set_be_silent
    end
  end
  run if run_already
end

Instance Method Details

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/pdb_and_protein_structure/fetch_fasta_sequence_from_pdb.rb', line 55

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @result
  # ======================================================================= #
  @result = ''.dup
end

#result? ⇒ Boolean Also known as: aminoacid_sequence?

#

result?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/pdb_and_protein_structure/fetch_fasta_sequence_from_pdb.rb', line 87

def result?
  @result
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/pdb_and_protein_structure/fetch_fasta_sequence_from_pdb.rb', line 105

def run
  commandline_arguments?.each {|this_file|
    set_search_for_this_file(this_file)
    if File.exist? this_file
      data_from_the_remote_webpage = File.read(this_file)
    else # else download it
      remote_url = "#{URL_FOR_FASTA_ENTRIES_AT_THE_PDB}#{@search_for_this_file}/display"
      erev "Working on #{steelblue(remote_url)} #{rev}next." if be_verbose?
      data_from_the_remote_webpage = URI.open(remote_url).read
    end
    set_result(data_from_the_remote_webpage)
    store_this_dataset(@result)
    @result # Return it here too, just in case.
  }
end

#set_result(i) ⇒ Object

#

set_result

#


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# File 'lib/bioroebe/pdb_and_protein_structure/fetch_fasta_sequence_from_pdb.rb', line 77

def set_result(i)
  if i.is_a? Array
    i = i.first
  end
  @result = i
end

#set_search_for_this_file(i) ⇒ Object

#

set_search_for_this_file

#


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# File 'lib/bioroebe/pdb_and_protein_structure/fetch_fasta_sequence_from_pdb.rb', line 67

def set_search_for_this_file(i)
  if i.include? '.'
    i = i.split('.').first
  end
  @search_for_this_file = i.upcase
end

#store_this_dataset(what = @result) ⇒ Object

#

store_this_dataset

#


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# File 'lib/bioroebe/pdb_and_protein_structure/fetch_fasta_sequence_from_pdb.rb', line 94

def store_this_dataset(
    what = @result
  )
  into = log_dir?+'pdb/'+@search_for_this_file+'.fasta'
  erev 'Next storing into `'+sfile(into)+'`.' if be_verbose?
  write_what_into(what, into)
end