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
-
#info_dir? ⇒ Boolean
# === info_dir? ========================================================================= #.
-
#work_directory? ⇒ Boolean
(also: #working_directory?, #working_dir?)
# === work_directory?.
Instance Method Details
#info_dir? ⇒ Boolean
#
info_dir?
#
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.
#
214 215 216 |
# File 'lib/bioroebe/taxonomy/constants.rb', line 214 def work_directory? TEMP_DIR end |