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Synchronize FASTA and FASTQ files or objects

Source: R/fastx_synchronize.R
fastx_synchronize.Rd

fastx_synchronize synchronizes sequences between two FASTA/FASTQ files or objects by retaining only the common sequences present in both.

Usage

fastx_synchronize(
  file1,
  file2 = NULL,
  file_format = "fastq",
  file1_out = NULL,
  file2_out = NULL
)

Arguments

file1

(Required). A FASTQ file path, a FASTQ tibble, or a paired-end tibble of class "pe_df". See Details.

file2

(Optional). A FASTQ file path or a FASTQ tibble. Optional if file1 is a "pe_df" object. See Details.

file_format

(Optional). Format of the input (file1 and file2) and the desired output format: "fasta" or "fastq" (default). This determines the format for both outputs.

file1_out

(Optional). Name of the output file for synchronized reads from file1. The file is in either FASTA or FASTQ format, depending on file_format. If NULL (default), no sequences are written to a file. See Details.

file2_out

(Optional). Name of the output file for synchronized reads from file2. The file is in either FASTA or FASTQ format, depending on file_format. If NULL (default), no sequences are written to a file. See Details.

Value

A tibble or NULL.

If both file1_out and file2_out are NULL, a tibble containing the synchronized reads from file1 is returned. The synchronized reads from file2 are accessible via the "reverse" attribute of the returned tibble.

If both file1_out and file2_out are specified, the synchronized sequences are written to the specified output files, and no tibble is returned.

Details

file1 and file2 can either be paths to FASTA/FASTQ files or tibble objects containing the sequences. FASTA objects are tibbles that contain the columns Header and Sequence, see readFasta. FASTQ objects are tibbles that contain the columns Header, Sequence, and Quality, see readFastq.

If file1 is an object of class "pe_df", the second read tibble is automatically extracted from its "reverse" attribute unless explicitly provided via the file2 argument. This allows streamlined input handling for paired-end tibbles created by vs_fastx_trim_filt.

Sequence IDs in the Header fields must be identical for each read pair in both file1 and file2 for synchronization to work correctly.

If file1_out and file2_out are specified, the synchronized sequences are written to these files in the format specified by file_format.

If file1_out and file2_out are NULL, the function returns a FASTA/FASTQ object containing synchronized reads from file1. The synchronized reads from file2 are included as an attribute named "reverse" in the returned tibble.

The returned tibble is assigned the S3 class "pe_df", indicating that it represents paired-end sequence data. Downstream functions can use this class tag to distinguish paired-end tibbles from other tibbles.

Both file1_out and file2_out must either be NULL or both must be character strings specifying the file paths.

Examples

# Define arguments
file1 <- system.file("extdata/small_R1.fq", package = "Rsearch")
file2 <- system.file("extdata/small_R1.fq", package = "Rsearch")
file_format <- "fastq"
file1_out <- NULL
file2_out <- NULL

# Synchronize files and return as a tibble
sync_seqs <- fastx_synchronize(file1 = file1,
                               file2 = file2,
                               file_format = file_format,
                               file1_out = file1_out,
                               file2_out = file2_out)

# Extract tibbles with synchronized sequences
R1_sync <- sync_seqs
R2_sync <- attr(sync_seqs, "reverse")

# Synchronize files and write to output files

# Define output file names
out1 <- tempfile(fileext = ".fastq")
out2 <- tempfile(fileext = ".fastq")

fastx_synchronize(file1 = file1,
                  file2 = file2,
                  file_format = file_format,
                  file1_out = out1,
                  file2_out = out2)