Package 'dbpq'

Count lines matching a pattern in a FASTA file

Description

Count lines (sequences if fasta file) matching a pattern. Accepts gzip files. May not work on Windows.

Usage

count_pattern_db(file, pattern = ">")

Arguments

file	(Character, required) Path to a file (plain or gzip), often a FASTA file.
pattern	(Character, default ">") A pattern to search for.

Value

An integer, the number of matching lines.

Author(s)

Adrien Taudière

See Also

filter_db(), count_seq_db()

Examples

# count_pattern_db("my_database.fasta", "Fungi")

---

Count sequences in a FASTA file

Description

Counts the number of sequences in a FASTA file by counting header lines (lines starting with >). Accepts gzip files.

Usage

count_seq_db(file)

Arguments

file	(Character, required) Path to a FASTA file (plain or gzip).

Value

An integer, the number of sequences.

Author(s)

Adrien Taudière

See Also

count_pattern_db()

Examples

# count_seq_db("my_database.fasta")

---

Remove primers from a FASTA database using cutadapt

Description

Removes pairs of primers and flanking regions from a FASTA reference database using cutadapt. Uses linked adapters to trim between forward and reverse primers.

Usage

cutadapt_rm_primers_db(
  ref_fasta,
  output = NULL,
  primer_fw = NULL,
  primer_rev = NULL,
  discard_untrimmed = TRUE,
  nproc = 1,
  verbose = TRUE,
  cmd_is_run = TRUE,
  return_file_path = FALSE,
  start_with_fw = FALSE,
  output_json = FALSE,
  error_tolerance = 0.1,
  args_before_cutadapt = paste0("source ~/miniforge3/etc/profile.d/conda.sh ",
    "&& conda activate cutadaptenv && ")
)

Arguments

ref_fasta	(Character, required) Path to a FASTA file (plain or gzip).
output	(Character) Path to the output FASTA file. If NULL, defaults to ⁠{basename}_cutadapted.fasta⁠.
primer_fw	(Character, required) The forward primer DNA sequence.
primer_rev	(Character, required) The reverse primer DNA sequence.
discard_untrimmed	(Logical, default TRUE) Discard sequences where primers were not found.
nproc	(Integer, default 1) Number of CPU cores for cutadapt.
verbose	(Logical, default TRUE) Print summary statistics.
cmd_is_run	(Logical, default TRUE) If FALSE, return the command string without executing it.
return_file_path	(Logical, default FALSE) If TRUE, return the output file path instead of the command.
start_with_fw	(Logical, default FALSE) If TRUE, the forward primer must be anchored at the start of the sequence.
output_json	(Logical, default FALSE) If TRUE, write a JSON summary of the cutadapt process.
error_tolerance	(Numeric, default 0.1) Maximum error rate for primer matching.
args_before_cutadapt	(Character) Shell commands to run before cutadapt (e.g., conda activation).

Details

This function is mainly a wrapper of the work of others. Please cite cutadapt (doi:10.14806/ej.17.1.200).

Value

The cutadapt command string, or the output file path if return_file_path = TRUE.

Author(s)

Adrien Taudière

Examples

## Not run: 
cutadapt_rm_primers_db(
  "database.fasta.gz",
  output = "db_cutadapted.fasta",
  primer_fw = "GCATCGATGAAGAACGCAGC",
  primer_rev = "TCCTCCGCTTATTGATATGC"
)

## End(Not run)

---

Download a BOLD reference database

Description

Downloads reference sequences from BOLD Systems (Barcode of Life Data).

Usage

download_bold_db(dest_dir = ".", marker = "COI-5P", verbose = TRUE)

Arguments

dest_dir	(Character, default ".") Directory to save the downloaded file.
marker	(Character, default "COI-5P") The barcode marker to download.
verbose	(Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly).

Author(s)

Adrien Taudière

Examples

## Not run: 
download_bold_db()

## End(Not run)

---

Download the Eukaryome reference database

Description

Downloads the Eukaryome database.

Usage

download_eukaryome_db(dest_dir = ".", verbose = TRUE)

Arguments

dest_dir	(Character, default ".") Directory to save the downloaded file.
verbose	(Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly).

Author(s)

Adrien Taudière

Examples

## Not run: 
download_eukaryome_db()

## End(Not run)

---

Download the MaarjAM reference database

Description

Downloads the MaarjAM database for arbuscular mycorrhizal fungi (AMF).

Usage

download_marjaam_db(dest_dir = ".", verbose = TRUE)

Arguments

dest_dir	(Character, default ".") Directory to save the downloaded file.
verbose	(Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly).

Author(s)

Adrien Taudière

Examples

## Not run: 
download_marjaam_db()

## End(Not run)

---

Download a PR2 reference database

Description

Downloads the PR2 protist ribosomal reference database.

Usage

download_pr2_db(dest_dir = ".", version = NULL, verbose = TRUE)

Arguments

dest_dir	(Character, default ".") Directory to save the downloaded file.
version	(Character) PR2 version number.
verbose	(Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly).

Author(s)

Adrien Taudière

Examples

## Not run: 
download_pr2_db()

## End(Not run)

---

Download a SILVA reference database

Description

Downloads the SILVA ribosomal RNA database (16S/18S).

Usage

download_silva_db(
  dest_dir = ".",
  version = NULL,
  target = c("SSU", "LSU"),
  verbose = TRUE
)

Arguments

dest_dir	(Character, default ".") Directory to save the downloaded file.
version	(Character) SILVA version number (e.g., "138.2").
target	(Character, default "SSU") One of "SSU" or "LSU".
verbose	(Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly).

Author(s)

Adrien Taudière

Examples

## Not run: 
download_silva_db()

## End(Not run)

---

Download a UNITE reference database

Description

Downloads the latest UNITE fungal ITS database for taxonomic assignment.

Usage

download_unite_db(
  dest_dir = ".",
  type = c("dynamic", "static"),
  taxon_group = c("fungi", "eukaryotes"),
  verbose = TRUE
)

Arguments

dest_dir	(Character, default ".") Directory to save the downloaded file.
type	(Character, default "dynamic") One of "dynamic" or "static". Dynamic files include singletons, static do not.
taxon_group	(Character, default "fungi") One of "fungi" or "eukaryotes".
verbose	(Logical, default TRUE) Print progress messages.

Value

The path to the downloaded file (invisibly).

Author(s)

Adrien Taudière

Examples

## Not run: 
download_unite_db()

## End(Not run)

---

Filter a FASTA database by taxonomic pattern

Description

Filters sequences from a FASTA database whose header lines match a given pattern. Accepts gzip files. May not work on Windows.

Usage

filter_db(
  ref_fasta,
  pattern,
  output = NULL,
  force_two_lines_per_seq = TRUE,
  keep_temporary_files = FALSE
)

Arguments

ref_fasta	(Character, required) Path to a FASTA file (plain or gzip).
pattern	(Character, required) A pattern to search for in sequence headers.
output	(Character, required) Path to the output FASTA file (must not be gzipped).
force_two_lines_per_seq	(Logical, default TRUE) Force the FASTA file to have exactly two lines per sequence (one header, one nucleotide line). If FALSE, the input must already be in this format.
keep_temporary_files	(Logical, default FALSE) If TRUE and force_two_lines_per_seq is TRUE, keep intermediate temporary files.

Value

The path to the output file (invisibly).

Author(s)

Adrien Taudière

See Also

count_pattern_db()

Examples

# filter_db("database.fasta.gz", "Rhizophydiales", "output.fasta")

---

Format taxonomy headers for dada2::assignTaxonomy

Description

Converts taxonomy headers to the format expected by dada2::assignTaxonomy(): ⁠Kingdom;Phylum;Class;Order;Family;Genus;⁠.

Usage

format2dada2(
  fasta_db = NULL,
  taxnames = NULL,
  output_path = NULL,
  from_sintax = TRUE,
  pattern_to_remove = NULL,
  ...
)

Arguments

fasta_db	(Character) Path to a FASTA file. Mutually exclusive with taxnames.
taxnames	(Character vector) Taxonomy header strings. Mutually exclusive with fasta_db.
output_path	(Character) If provided and fasta_db is used, write the reformatted FASTA to this path.
from_sintax	(Logical, default TRUE) If TRUE, input is in SINTAX format. If FALSE, input is converted from standard format via format2sintax() first.
pattern_to_remove	(Character) Optional regex pattern to remove from the reformatted names.
...	Additional arguments passed to format2sintax() when from_sintax = FALSE.

Value

If taxnames is used, a character vector. If fasta_db is used, a DNAStringSet with reformatted names. When output_path is provided, the FASTA file is written and the DNAStringSet is returned invisibly.

Author(s)

Adrien Taudière

See Also

format2sintax(), format2dada2_species()

Examples

format2dada2(
  taxnames = "AB123;tax=k:Fungi,p:Ascomycota,c:Sordariomycetes",
  from_sintax = TRUE
)

---

Format taxonomy headers for dada2::addSpecies

Description

Converts taxonomy headers to the format expected by dada2::addSpecies(): ⁠AccessionID Genus Species⁠.

Usage

format2dada2_species(
  fasta_db = NULL,
  taxnames = NULL,
  from_sintax = FALSE,
  output_path = NULL,
  ...
)

Arguments

fasta_db	(Character) Path to a FASTA file. Mutually exclusive with taxnames.
taxnames	(Character vector) Taxonomy header strings. Mutually exclusive with fasta_db.
from_sintax	(Logical, default FALSE) If TRUE, input is in SINTAX format. If FALSE, input uses standard k__ format.
output_path	(Character) If provided and fasta_db is used, write the reformatted FASTA to this path.
...	Additional arguments passed to internal functions.

Value

If taxnames is used, a character vector. If fasta_db is used, a DNAStringSet with reformatted names.

Author(s)

Adrien Taudière

See Also

format2dada2(), format2sintax()

Examples

format2dada2_species(
  taxnames = "AB123;k__Fungi;g__Aspergillus;s__fumigatus",
  from_sintax = FALSE
)

---

Format taxonomy headers to SINTAX format

Description

Converts taxonomy headers from the common ⁠k__Kingdom;p__Phylum;...⁠ format to the VSEARCH SINTAX format (⁠tax=k:Kingdom,p:Phylum,...⁠).

Usage

format2sintax(
  fasta_db = NULL,
  taxnames = NULL,
  pattern_tax = "k__",
  pattern_sintax = "tax=k:",
  output_path = NULL
)

Arguments

fasta_db	(Character) Path to a FASTA file. Mutually exclusive with taxnames.
taxnames	(Character vector) Taxonomy header strings. Mutually exclusive with fasta_db.
pattern_tax	(Character, default "k__") Pattern identifying the start of taxonomy in the original format.
pattern_sintax	(Character, default "tax=k:") Pattern for the start of taxonomy in SINTAX format.
output_path	(Character) If provided and fasta_db is used, write the reformatted FASTA to this path.

Value

If taxnames is used, a character vector of reformatted names. If fasta_db is used, a DNAStringSet with reformatted names.

Author(s)

Adrien Taudière

See Also

format2dada2(), format2dada2_species()

Examples

format2sintax(taxnames = "AB123;k__Fungi;p__Ascomycota;c__Sordariomycetes")

---

Get file extension(s)

Description

Get file extension(s)

Usage

get_file_extension(file_path)

Arguments

file_path

(Character, required) Path to a file.

Value

A character vector of file extensions.

Examples

get_file_extension("my_database.fasta")
get_file_extension("my_database.fasta.gz")

---

List and count taxonomic ranks from a FASTA database

Description

Extracts and counts occurrences of a given taxonomic rank from FASTA sequence headers. Requires taxonomy encoded in headers following the convention ⁠k__Kingdom;p__Phylum;...⁠ or similar.

Usage

list_ranks_db(file, rank_prefix = "k__")

Arguments

file	(Character, required) Path to a FASTA file (plain or gzip).
rank_prefix	(Character, default "k__") The prefix identifying the taxonomic rank to extract (e.g., "k__" for kingdom, "p__" for phylum, "c__" for class, "o__" for order, "f__" for family, "g__" for genus, "s__" for species).

Value

A named integer vector of counts, sorted in decreasing order. Names are the taxonomic rank values.

Author(s)

Adrien Taudière

Examples

# list_ranks_db("my_database.fasta", rank_prefix = "p__")

---

Summarize a FASTA reference database

Description

Provides an overview of a FASTA reference database: number of sequences, sequence length distribution, and taxonomic coverage at each rank.

Usage

summarize_db(
  file,
  rank_prefixes = c("k__", "p__", "c__", "o__", "f__", "g__", "s__")
)

Arguments

file	(Character, required) Path to a FASTA file (plain or gzip).
rank_prefixes	(Character vector) Taxonomic rank prefixes to summarize. Defaults to kingdom through species.

Value

A list with components:

• n_sequences: total number of sequences

• length_summary: summary statistics of sequence lengths

• ranks: a named list of unique count per rank

Author(s)

Adrien Taudière

Examples

# summarize_db("my_database.fasta")

---