For a list of records, construct a data.frame for insertion into SQL database.
gb_df_generate(
records,
min_length = 0,
max_length = NULL,
acc_filter = NULL,
invert = FALSE
)data.frame, or NULL if no records pass filters
character, vector of GenBank records in text format
Minimum sequence length, default 0.
Maximum sequence length, default NULL.
Character vector; accessions to include or exclude from
the database as specified by 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.
The resulting data.frame has five columns: accession, organism, raw_definition, raw_sequence, raw_record. The prefix 'raw_' indicates the data has been converted to the raw format, see ?charToRaw, in order to save on RAM. The raw_record contains the entire GenBank record in text format.
Use acc_filter and max and min sequence lengths to minimize the size of the
database. All sequences have to be at least as long as min and less than or
equal in length to max, unless max is NULL in which there is no maximum
length. The final selection of sequences is the result of applying all
filters (acc_filter, min_length, max_length) in combination.
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_build(),
gb_df_create(),
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()