Function reference • padlocdev

Read

Read padloc-db files.

read_hmm(): Read an HMMER3 formatted profile HMM

multi_read_hmm(): Read all HMMs in a directory into a list

read_hmm_header(): Read the header section from a profile HMM into a list.

multi_read_hmm_header(): Read the headers from a profile HMM into a list.

read_padloc_model(): Read in a padloc model (*.yaml) file

multi_read_padloc_model(): Read the filename, NAME and ACC identifiers from a profile HMM into a list.

read_hmm_meta(): Read a padloc-db hmm_meta.txt file.

read_sys_meta(): Read a padloc-db sys_meta.txt file.

read_sys_groups(): Read a padloc-db sys_groups.txt file.

Operate

Perform modifications on padloc-db objects.

expand_gene_groups(): Expand gene groups

expand_gene_groups_all(): Expand all gene groups in a list of padloc models

pull_genes(): Pull the genes from a list of system models

expand_hmm_meta(): Expand HMM metadata table multi-name assignments

collapse_hmm_meta(): Collapse HMM metadata table multi-name assignments

Validate

“Validate padloc-db data and identify inconsistencies.”

valid_padloc_model(): Validity checker for a padloc model

report_padloc_model_validity(): Generate a validity report for a list of padloc models

why_invalid(): Determine why padloc models are invalid

compare_hmm_files_hmm_meta(): Compare HMM files against those listed in hmm_meta.txt

compare_sys_files_sys_meta(): Compare system model files against those listed in sys_meta.txt

compare_sys_meta_sys_groups(): Compare system model files against those listed in sys_meta.txt

compare_sys_files_hmm_meta(): Compare system model files against the hmm metadata table.

Everything else

padloc_model(): Padloc model

padlocdev_example(): Get path to padlocdev example

a_vs_b(): Compare two dataframes / tibbles

system_cp_files(): Copy a list of files on the system

system_cp_hmm(): Copy profile HMM files from one directory to another

system_cp_sys(): Copy system description files from one directory to another

system_mv_deprecated(): Move system description files to deprecated directory

which_uses(): Find out which system models use particular proteins

build_generic_hmm_meta(): Build a generic system metadata table from a list of padloc models

build_generic_padloc_models(): Build a list of generic padloc models from a list of loci

build_generic_sys_meta(): Build a generic system metadata table from a list of padloc models

divide_database(): divide_database

filter_hmm_meta(): filter_hmm_meta

filter_models(): filter_models

filter_sys_meta(): filter_sys_meta

group_models(): group_models

group_overlap(): group_overlap

multi_write_padloc_model(): Write out a list of padloc model (*.yaml) files

padloc_model_to_chr(): Convert a padloc model to a glue::glue() character vector

pull_intersect(): pull_intersect

summarise_groups(): summarise_groups

verify_hmm_names(): verify_hmm_names

write_padloc_model(): Write out a padloc model (*.yaml) file

crossref_data_pull_author(): Create a clean 'author' column

crossref_data_pull_date(): Create a clean 'date' column

crossref_data_pull_journal(): Create a clean 'journal' column

crossref_data_pull_title(): Create a clean 'title' column

doi_to_long(): Convert a short doi to the corresponding long doi

doi_to_long_df(): Convert a dataframe of short dois to long dois

doi_to_short(): Convert a long doi to the corresponding short doi

get_crossref_data(): Get a table of crossref data.

read_sys_master(): Read a padloc-db sys_master.txt file.