gb_build: Read and add .seq files to database
In AntonelliLab/restez: Create and Query a Local Copy of 'GenBank' in R

gb_build

R Documentation

Read and add .seq files to database

Description

Given a list of seq_files, read and add the contents of the files to a SQL-like database. If any errors during the process, FALSE is returned.

Usage

gb_build(
  dpth,
  seq_files,
  max_length,
  min_length,
  acc_filter = NULL,
  invert = FALSE,
  scan = FALSE
)

Arguments

`dpth`	Download path (where seq_files are stored)
`seq_files`	.seq.tar seq file names
`max_length`	Maximum sequence length, default NULL.
`min_length`	Minimum sequence length, default 0.
`acc_filter`	Character vector; accessions to include or exclude from the database as specified by `invert`.
`invert`	Logical vector of length 1; if TRUE, accessions in `acc_filter` will be excluded from the database; if FALSE, only accessions in `acc_filter` will be included in the database. Default FALSE.
`scan`	Logical vector of length 1; should the sequence file be scanned for accessions in `acc_filter` prior to processing? Requires zgrep to be installed (so does not work on Windows). Only used if `acc_filter` is not NULL and `invert` is FALSE. Default FALSE.

Details

This function will automatically connect to the restez database.

Value

Logical

Other private: add_rcrd_log(), cat_line(), char(), check_connection(), cleanup(), connected(), connection_get(), db_download_intern(), db_sqlngths_get(), db_sqlngths_log(), dir_size(), dwnld_path_get(), dwnld_rcrd_log(), entrez_fasta_get(), entrez_gb_get(), extract_accession(), extract_by_patterns(), extract_clean_sequence(), extract_definition(), extract_features(), extract_inforecpart(), extract_keywords(), extract_locus(), extract_organism(), extract_seqrecpart(), extract_sequence(), extract_version(), file_download(), filename_log(), flatfile_read(), gb_df_create(), gb_df_generate(), gb_sql_add(), gb_sql_query(), gbrelease_check(), gbrelease_get(), gbrelease_log(), has_data(), identify_downloadable_files(), last_add_get(), last_dwnld_get(), last_entry_get(), latest_genbank_release(), latest_genbank_release_notes(), message_missing(), mock_def(), mock_gb_df_generate(), mock_org(), mock_rec(), mock_seq(), predict_datasizes(), readme_log(), restez_connect(), restez_disconnect(), restez_path_check(), restez_rl(), search_gz(), seshinfo_log(), setup(), slctn_get(), slctn_log(), sql_path_get(), stat(), status_class(), testdatadir_get()