BISMARK2SUMMARY

Generate summary graphical HTML report from several Bismark text report files reports (see https://github.com/FelixKrueger/Bismark/blob/master/bismark2summary).

Software dependencies

• bowtie2 == 2.3.4.3
• bismark == 0.22.1
• samtools == 1.9

Example

This wrapper can be used in the following way:

import  os

rule bismark2summary:
    input:
        bam=["bams/a_genome_pe.bam", "bams/b_genome.bam"],

        # Bismark `bismark2summary` discovers reports automatically based
        # on files available in bam file containing folder
        #
        # If your per BAM file reports aren't in the same folder
        # you will need an additional task which symlinks all reports
        # (E.g. your splitting report generated by `bismark_methylation_extractor`
        # tool is in `meth` folder, and alignment related reports in `bams` folder)

        # These dependencies are here just to ensure that corresponding rules
        # has already finished at rule execution time, otherwise some reports
        # will be missing.
        dependencies=[
            "bams/a_genome_PE_report.txt",
            "bams/a_genome_pe.deduplication_report.txt",
            # for example splitting report is missing for 'a' sample

            "bams/b_genome_SE_report.txt",
            "bams/b_genome.deduplication_report.txt",
            "bams/b_genome.deduplicated_splitting_report.txt"
        ]
    output:
        html="qc/{experiment}.bismark2summary.html",
        txt="qc/{experiment}.bismark2summary.txt"
    log:
        "logs/qc/{experiment}.bismark2summary.log"
    wrapper:
        "0.67.0/bio/bismark/bismark2summary"

rule bismark2summary_prepare_symlinks:
    input:
        "meth/b_genome.deduplicated_splitting_report.txt",
    output:
        temp("bams/b_genome.deduplicated_splitting_report.txt"),
    log:
        "qc/bismark2summary_prepare_symlinks.symlinks.log"
    run:
        wd = os.getcwd()
        shell("echo 'Making symlinks' > {log}")
        for source, target in zip(input, output):
           target_dir = os.path.dirname(target)
           target_name = os.path.basename(target)
           log_path = os.path.join(wd, log[0])
           abs_src_path = os.path.abspath(source)
           shell("cd {target_dir} && ln -f -s {abs_src_path} {target_name} >> {log_path} 2>&1")

        shell("echo 'Done' >> {log}")

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.

Authors

• Roman Cherniatchik

Code

"""Snakemake wrapper to generate summary graphical HTML report from several Bismark text report files."""
# https://github.com/FelixKrueger/Bismark/blob/master/bismark2summary

__author__ = "Roman Chernyatchik"
__copyright__ = "Copyright (c) 2019 JetBrains"
__email__ = "roman.chernyatchik@jetbrains.com"
__license__ = "MIT"

import os
from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
cmds = ["bismark2summary {extra}"]

# basename
bam = snakemake.input.get("bam", None)
if not bam:
    raise ValueError(
        "bismark/bismark2summary: Please specify aligned BAM file path"
        " (one or several) using 'bam=..'"
    )

html = snakemake.output.get("html", None)
txt = snakemake.output.get("txt", None)
if not html or not txt:
    raise ValueError(
        "bismark/bismark2summary: Please specify both 'html=..' and"
        " 'txt=..' paths in output section"
    )

basename, ext = os.path.splitext(html)
if ext.lower() != ".html":
    raise ValueError(
        "bismark/bismark2summary: HTML report file should end"
        " with suffix '.html' but was {} ({})".format(ext, html)
    )

suggested_txt = basename + ".txt"
if suggested_txt != txt:
    raise ValueError(
        "bismark/bismark2summary: Expected '{}' TXT report, "
        "but was: '{}'".format(suggested_txt, txt)
    )

cmds.append("--basename {basename:q}")

# title
title = snakemake.params.get("title", None)
if title:
    cmds.append("--title {title:q}")

cmds.append("{bam}")

# log
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
cmds.append("{log}")

# run shell command:
shell(" ".join(cmds))