Module: Bioroebe::Taxonomy::Constants

Included in:
Bioroebe::Taxonomy, Info, Shared
Defined in:
lib/bioroebe/taxonomy/constants.rb

Overview

Bioroebe::Taxonomy::Constants

Constant Summary collapse

FILE_USE_THIS_DATABASE =
#

FILE_USE_THIS_DATABASE

#
"#{::Bioroebe::Taxonomy.project_base_dir?}yaml/use_this_database.yml"
BE_VERBOSE =
#

BE_VERBOSE

#
true
POSTGRESQL_QUERY_SIZE =
#

POSTGRESQL_QUERY_SIZE

We want to query the size of the postgresql database - the following string achieves precisely that.

#
<<-EOF

SELECT nspname || '.' || relname AS "relation",
    pg_size_pretty(pg_total_relation_size(C.oid)) AS "total_size"
  FROM pg_class C
  LEFT JOIN pg_namespace N ON (N.oid = C.relnamespace)
  WHERE nspname NOT IN ('pg_catalog', 'information_schema')
    AND C.relkind <> 'i'
    AND nspname !~ '^pg_toast'
  ORDER BY pg_total_relation_size(C.oid) DESC
  LIMIT 20;

EOF
ARRAY_PROJECT_FILES =
#

ARRAY_PROJECT_FILES

We list, at the least the more important, project files here.

#
%w(
  info.rb
  interactive.rb
  parse_fasta.rb
  shared.rb
  taxonomy.rb
  INSTRUCTIONS.md
)
POSTGRE_LOGIN_COMMAND =
#

POSTGRE_LOGIN_COMMAND

#
'
  psql --host=bunuel.imp.univie.ac.at --port=5471 --username=dummy --dbname=dummy_db --quiet
'.delete("\n").strip
SHARED_HOME =
#

SHARED_HOME

#
::Bioroebe.log_dir?
TMP_DIR =
#

TMP_DIR

#
::Bioroebe.log_dir?
TEMP_DIR = 
TMP_DIR
NODES_SQL =
#

NODES_SQL

#
AUTOGENERATED_SQL_FILES_DIR+'nodes.sql'
NAMES_SQL =
#

NAMES_SQL

#
AUTOGENERATED_SQL_FILES_DIR+'names.sql'
DATA_DIR =
#

DATA_DIR

#
'/data/'
LOCAL_MIRROR =

Here we have the local nodes.dmp and names.dmp

DATA_DIR+'ncbi/taxonomy/'
CURATED_DIR = 
DATA_DIR+'curated/'
SEQUENCES_DIR = 
CURATED_DIR+'sequences/'
INFO_DIR =
#

INFO_DIR

#
SEQUENCES_DIR+'INFO/'
AA_DIR =

The various .INFO files.

SEQUENCES_DIR+'aa/'
NT_DIR = 
SEQUENCES_DIR+'nt/'
LOCALOME_DIR = 
SEQUENCES_DIR+'localome/'
INCOMING_DIR = 
LOCALOME_DIR+'incoming/'
TEST_DIR = 
LOCALOME_DIR+'test/'
GEM_DIR =
#

GEM_DIR

#
HOME_DIR+'.gem/ruby/2.7.1/gems/'
MODULE_PATH =
#

MODULE_PATH

#
GEM_DIR+'lib/taxonomy/'
BASE = 
BASE_DIR = TAXONOMY_DIR = HOME_DIR+'taxonomy/'
LAST_INTERACTIVE_COMMAND =
#

LAST_INTERACTIVE_COMMAND

The following line must come after Shared was included.

#
TEMP_DIR+'LAST_INTERACTIVE_COMMAND.md'
PROJECT_DOC_DIR =
#

PROJECT_DOC_DIR

Where we will keep our docs.

#
File.absolute_path(
  ::Bioroebe::Taxonomy.project_base_dir?+'../../doc/'
)+'/'
NCBI_BASE =
#

NCBI_BASE

#
'https://www.ncbi.nlm.nih.gov/'
TAXONOMY_BROWSER =
#

TAXONOMY_BROWSER

#
NCBI_BASE+'Taxonomy/Browser/'
BASE_URL =
#

BASE_URL

#
NCBI_CGI_SCRIPT = TAXONOMY_BROWSER+'wwwtax.cgi?'
URL1 =
#

URL1

#
NCBI_CGI_SCRIPT+
'mode=Undef&name=Arabidopsis+thaliana&lvl=0&srchmode=1&keep=1&unlock'
Bacteria_Taxonomy_ID =
#

Taxonomy entries

Some hardcoded Taxonomy ID entries come next - these can be used to find out which entries are Eukarya and which ones are Prokarya. This will then provide us with the starting point to build a rooted taxonomic tree.

#
2
Archaea_Taxonomy_ID = 
2157
Eukaryota_Taxonomy_ID = 
2759
DELNODES = 
_DOWNLOAD_DIR+'delnodes.dmp'
MERGED = 
_DOWNLOAD_DIR+'merged.dmp'
CITATIONS = 
_DOWNLOAD_DIR+'citations.dmp'
DIVISION = 
_DOWNLOAD_DIR+'division.dmp'
GENCODE = 
_DOWNLOAD_DIR+'gencode.dmp'
NODES = 
_DOWNLOAD_DIR+'nodes.dmp'
NAMES = 
_DOWNLOAD_DIR+'names.dmp'

Instance Method Summary collapse

Instance Method Details

#info_dir? ⇒ Boolean

#

info_dir?

#

Returns:

  • (Boolean) 


205
206
207
 
# File 'lib/bioroebe/taxonomy/constants.rb', line 205

def info_dir?
  INFO_DIR
end

#work_directory? ⇒ Boolean Also known as: working_directory?, working_dir?

#

work_directory?

For now, the work-directory defaults to the TEMP_DIR value.

#

Returns:

  • (Boolean) 


214
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216
 
# File 'lib/bioroebe/taxonomy/constants.rb', line 214

def work_directory?
  TEMP_DIR
end