fetchReadsFromFastq {chimeraviz}R Documentation

Fetch reads from fastq files

Description

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

Usage

fetchReadsFromFastq(reads, fastqFileIn1, fastqFileIn2, fastqFileOut1,
  fastqFileOut2)

Arguments

reads

List of read IDs that is to be fetched.

fastqFileIn1

First fastq file to search in.

fastqFileIn2

Second fastq file to seach in.

fastqFileOut1

First fastq file with results.

fastqFileOut2

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())
fetchReadsFromFastq(reads, fastq1, fastq2,
    fastqFileOut1, fastqFileOut2)
# We now have the reads supporting fusion 5267 in the two files.

## End(Not run)


[Package chimeraviz version 1.4.3 Index]