#' Create fastqc reports
#' @importFrom glue glue
#' @inheritParams param_general
#' @export
glue_fastqc <-
function(in_dir = "./fastq", out_dir = "./fastqc_out", core_num = 4){
fq_ext <- get_file_ext()$fastq
glue("
mkdir {out_dir}
fastqc --extract -t {core_num} -o {out_dir} {in_dir}/*.{fq_ext}.gz
")
}
#' Calculate genome coverage
#' @importFrom glue glue
#' @param head_label .tar file path
#' @param in_dir .tar file path
#' @param out_dir .tar file path
#' @export
glue_genomecov <-
function(head_label, in_dir, out_dir = in_dir){
le <- "\\"
glue("
mkdir {out_dir}/genomecov
bedtools genomecov -bga -split {le}
-ibam {in_dir}/{head_label}.sort.bam > {out_dir}/genomecov/{head_label}.bedgraph
")
}
#' Convert gff3 file to bed file
#' @importFrom glue glue
#' @param head_label .tar file path
#' @param in_dir .tar file path
#' @param out_dir .tar file path
#' @export
glue_gff2bed <-
function(head_label, in_dir = ".", out_dir = "."){
glue("
gff2bed < {in_dir}/{head_label}.gff > {out_dir}/{head_label}.bed
")
}
glue_samtools_view <-
function(head_label, bedfile, out_label, in_dir = ".", out_dir = "."){
lineend <- "\\"
glue(
"
samtools view -@ 2 -b -L {bedfile} {in_dir}/{head_label}.sort.bam {lineend}
| {lineend}
samtools sort -@ 2 > {out_dir}/{head_label}_{out_label}.sort.bam
samtools index {out_dir}/{head_label}_{out_label}.sort.bam
"
)
}
glue_rseqc_clipping_profile <-
function(
head_label,
in_dir,
out_dir = in_dir,
seq_layout = '"SE"'
){
le <- "\\"
seq_layout <- '"SE"'
glue("
mkdir {out_dir}/clip_prof
clipping_profile.py {le}
-i {in_dir}/{head_label}.sort.bam {le}
-s {seq_layout} {le}
-o {out_dir}/clip_prof/{head_label}
")
}
glue_rseqc_deletion_profile <-
function(
head_label,
in_dir,
out_dir = in_dir
){
le <- "\\"
seq_layout <- '"SE"'
glue("
mkdir {out_dir}/clip_prof
clipping_profile.py {le}
-i {in_dir}/{head_label}.sort.bam {le}
-s {seq_layout} {le}
-o {out_dir}/clip_prof/{head_label}
")
}
glue_multiqc <-
function(
out_dir = "."
){
glue("
multiqc -f -o {out_dir} .
")
}
glue_sra2fastq <-
function(
head_label,
is_pe = F,
in_dir = "./sra",
out_dir = "./fastq"
){
le <- "\\"
pe_option <- ifelse(is_pe, "\n --split-files \\", "")
glue("
fastq-dump {le}{pe_option}
-O {out_dir} {le}
--gzip {le}
{in_dir}/{head_label}.sra
")
}
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