combineFASTA

Combine multiple FASTA files into a single file

catGenes::combineFASTA()

Description

This function reads multiple FASTA files and combines them into a single FASTA file. It saves the combined sequences to a specified output directory.

Details

The function performs the following steps:

Validates that all specified input files exist
Creates an output directory with date stamp if
save = TRUE
Reads each specified FASTA file using
ape::read.FASTA()
Combines all sequences into a single DNAbin object
Saves the combined sequences to the output file if
save = TRUE
Returns summary statistics

Note: This function does not remove duplicate sequences. All sequences from all input files are included in the output.

Arguments

Argument	Description
input_files	Character vector specifying the paths to FASTA files to be combined. This parameter is required - users must specify exactly which files they want to combine.
output_file	Character string specifying the name of the output combined FASTA file. Default is “combined_sequences.fasta”.
save	Logical. If `TRUE` (default), the combined sequences are saved to disk in the specified directory. If `FALSE`, the combined sequences are only returned as an R object without saving.
verbose	Logical. If `TRUE` (default), progress messages are printed to the console.
dir	Character string specifying the directory path for saving results. Default is “RESULTS_combineFASTA”. A subdirectory with current date will be created within this directory when `save = TRUE`.

Value

A list containing:

sequences
: DNAbin object with all combined sequences
summary
: Data frame with summary statistics
output_path
: Path to the saved combined FASTA file (if saved)

Examples

# Basic usage: combine specific FASTA files
result <- combineFASTA(input_files = c("file1.fasta", "file2.fasta", "file3.fasta"))

# Combine files with custom output name
result <- combineFASTA(
  input_files = c("data/gene1.fasta", "data/gene2.fasta"),
  output_file = "all_genes.fasta"
)

# Return results without saving to disk
result <- combineFASTA(
  input_files = c("temp1.fasta", "temp2.fasta"),
  save = FALSE,
  verbose = TRUE
)

# Access results
sequences <- result$sequences
summary_stats <- result$summary
print(summary_stats)

--- title: 'combineFASTA' description: 'Combine multiple FASTA files into a single file' toc: true toc-depth: 3 --- ```{r} #| eval: false catGenes::combineFASTA() ``` ### Description This function reads multiple FASTA files and combines them into a single FASTA file. It saves the combined sequences to a specified output directory. ### Details The function performs the following steps: 1. 2. 3. Validates that all specified input files exist 4. 5. Creates an output directory with date stamp if 6. `save = TRUE` 7. 8. 9. Reads each specified FASTA file using 10. `ape::read.FASTA()` 11. 12. 13. Combines all sequences into a single DNAbin object 14. 15. Saves the combined sequences to the output file if 16. `save = TRUE` 17. 18. 19. Returns summary statistics Note: This function does not remove duplicate sequences. All sequences from all input files are included in the output. ### Arguments | Argument | Description | |---|---| | input_files | Character vector specifying the paths to FASTA files to be combined. This parameter is required - users must specify exactly which files they want to combine. | | output_file | Character string specifying the name of the output combined FASTA file. Default is "combined_sequences.fasta". | | save | Logical. If `TRUE` (default), the combined sequences are saved to disk in the specified directory. If `FALSE`, the combined sequences are only returned as an R object without saving. | | verbose | Logical. If `TRUE` (default), progress messages are printed to the console. | | dir | Character string specifying the directory path for saving results. Default is "RESULTS_combineFASTA". A subdirectory with current date will be created within this directory when `save = TRUE`. | ### Value A list containing: - - - - `sequences` - : DNAbin object with all combined sequences - - - `summary` - : Data frame with summary statistics - - - `output_path` - : Path to the saved combined FASTA file (if saved) ### Examples ```r # Basic usage: combine specific FASTA files result <- combineFASTA(input_files = c("file1.fasta", "file2.fasta", "file3.fasta")) # Combine files with custom output name result <- combineFASTA( input_files = c("data/gene1.fasta", "data/gene2.fasta"), output_file = "all_genes.fasta" ) # Return results without saving to disk result <- combineFASTA( input_files = c("temp1.fasta", "temp2.fasta"), save = FALSE, verbose = TRUE ) # Access results sequences <- result$sequences summary_stats <- result$summary print(summary_stats) ```