PRETEXT MAP¶
Embeds bedgraph data into Pretext contact maps.
URL: https://github.com/wtsi-hpag/PretextGraph
Example¶
This wrapper can be used in the following way:
rule pretext_graph:
input:
bedgraph="{a}.bedgraph",
map="map.pretext",
output:
"{a}.pretext",
log:
"logs/{a}.pretext_graph.log",
params:
graph_name="graph_name",
extra="",
wrapper:
"v1.12.2/bio/pretext/graph"
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.
Notes¶
- The extra param allows for additional arguments.
Software dependencies¶
pretextgraph==0.0.6
Authors¶
- Filipe G. Vieira
Code¶
__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2022, Filipe G. Vieira"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")
if snakemake.input[0].endswith(".gz"):
pipe = "gunzip -c"
elif snakemake.input[0].endswith(".bz2"):
pipe = "bunzip2 -c"
else:
pipe = "cat"
shell(
"({pipe}"
" {snakemake.input.bedgraph} | "
"PretextGraph"
" -i {snakemake.input.map}"
" -n {snakemake.params.graph_name}"
" {extra}"
" -o {snakemake.output}"
") {log}"
)