fetch_reads_from_fastq: Fetch reads from fastq files

In chimeraviz: Visualization tools for gene fusions

Description

This function will fetch read sequences from fastq files and put them into new fastq files.

Usage

fetch_reads_from_fastq(
  reads,
  fastq_file_in1,
  fastq_file_in2,
  fastq_file_out1,
  fastq_file_out2
)

Arguments

reads	List of read IDs that is to be fetched.
fastq_file_in1	First fastq file to search in.
fastq_file_in2	Second fastq file to seach in.
fastq_file_out1	First fastq file with results.
fastq_file_out2	Second fastq file with results.

Details

Note: This function runs (read only) bash commands on your system. Therefore the function will only work on a unix system.

Value

The files fastqFileOut1 and fastqFileOut2 populated with the specified reads.

Examples

## Not run: 
# fastq files that has the supporting reads
fastq1 <- system.file("extdata", "reads.1.fq", package="chimeraviz")
fastq2 <- system.file("extdata", "reads.2.fq", package="chimeraviz")
# Which read ids to extract
reads <- c(
  "13422259", "19375605", "29755061",
  "31632876", "32141428", "33857245")
# Extract the actual reads and put them in the tmp files "fastqFileOut1" and
# "fastqFileOut2"
fastqFileOut1 <- tempfile(pattern = "fq1", tmpdir = tempdir())
fastqFileOut2 <- tempfile(pattern = "fq2", tmpdir = tempdir())
fetch_reads_from_fastq(reads, fastq1, fastq2,
    fastqFileOut1, fastqFileOut2)
# We now have the reads supporting fusion 5267 in the two files.

## End(Not run)

chimeraviz documentation built on Jan. 19, 2021, 2 a.m.