ggDNAvis (version 0.3.2)

write_fastq: Write sequence and quality information to FASTQ

Description

This function simply writes a FASTQ file from a dataframe containing columns for read ID, sequence, and quality scores.

See fastq_quality_scores for an explanation of quality.

Said dataframe can be produced from FASTQ via read_fastq(). To read/write a modified FASTQ containing modification information (SAM/BAM MM and ML tags) in the header lines, use read_modified_fastq() and write_modified_fastq().

Usage

write_fastq(
  dataframe,
  filename = NA,
  read_id_colname = "read",
  sequence_colname = "sequence",
  quality_colname = "quality",
  return = FALSE
)

Value

character vector. The resulting FASTQ file as a character vector of its constituent lines (or invisible(NULL) if return is FALSE). This is probably mostly useful for debugging, as setting filename within this function directly writes to FASTQ via writeLines(). Therefore, defaults to returning invisible(NULL).

Arguments

dataframe

dataframe. Dataframe containing modification information to write back to modified FASTQ. Must have columns for unique read ID and DNA sequence. Should also have a column for quality, unless wanting to fill in qualities with "B".

filename

character. File to write the FASTQ to. Recommended to end with .fastq (warns but works if not). If set to NA (default), no file will be output, which may be useful for testing/debugging.

read_id_colname

character. The name of the column within the dataframe that contains the unique ID for each read. Defaults to "read".

sequence_colname

character. The name of the column within the dataframe that contains the DNA sequence for each read. Defaults to "sequence".

The values within this column must be DNA sequences e.g. "GGCGGC".

quality_colname

character. The name of the column within the dataframe that contains the FASTQ quality scores for each read. Defaults to "quality". If scores are not known, can be set to NA to fill in quality with "B".

If not NA, must correspond to a column where the values are the FASTQ quality scores e.g. "$12\">/2C;4:9F8:816E,6C3*," - see fastq_quality_scores.

return

logical. Boolean specifying whether this function should return the FASTQ (as a character vector of each line in the FASTQ), otherwise it will return invisible(NULL). Defaults to FALSE.

Examples

## Write to FASTQ (using filename = NA, return = FALSE
## to view as char vector rather than writing to file)
write_fastq(
    example_many_sequences,
    filename = NA,
    read_id_colname = "read",
    sequence_colname = "sequence",
    quality_colname = "quality",
    return = TRUE
)

## quality_colname = NA fills in quality with "B"
write_fastq(
    example_many_sequences,
    filename = NA,
    read_id_colname = "read",
    sequence_colname = "sequence",
    quality_colname = NA,
    return = TRUE
)