PRESEQ LC_EXTRAP

preseq estimates the library complexity of existing sequencing data to then estimate the yield of future experiments based on their design. For usage information, please see preseq’s command line help (this seems more up to date than the available documentation from 2014 ). For more information about preseq, also see the source code.

URL:

Example

This wrapper can be used in the following way:

rule preseq_lc_extrap_bam:
    input:
        "samples/{sample}.sorted.bam"
    output:
        "test_bam/{sample}.lc_extrap"
    params:
        "-v"   #optional parameters
    log:
        "logs/test_bam/{sample}.log"
    wrapper:
        "v1.2.1/bio/preseq/lc_extrap"

rule preseq_lc_extrap_bed:
    input:
        "samples/{sample}.sorted.bed"
    output:
        "test_bed/{sample}.lc_extrap"
    params:
        "-v"   #optional parameters
    log:
        "logs/test_bed/{sample}.log"
    wrapper:
        "v1.2.1/bio/preseq/lc_extrap"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Software dependencies

• preseq==2.0.3

Input/Output

Input:

• bed files containing duplicates and sorted by chromosome, start position, strand position and finally strand OR
• bam files containing duplicates and sorted by using bamtools or samtools sort.

Output:

• lc_extrap (.lc_extrap)

Authors

• Antonie Vietor

Code

__author__ = "Antonie Vietor"
__copyright__ = "Copyright 2020, Antonie Vietor"
__email__ = "antonie.v@gmx.de"
__license__ = "MIT"

import os
from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

params = ""
if (os.path.splitext(snakemake.input[0])[-1]) == ".bam":
    if "-bam" not in (snakemake.input[0]):
        params = "-bam "

shell(
    "(preseq lc_extrap {params} {snakemake.params} {snakemake.input[0]} -output {snakemake.output[0]}) {log}"
)