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fix: remove NA string replacement, fixed upstream #2940

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May 22, 2024
Merged

fix: remove NA string replacement, fixed upstream #2940

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125d4d9
fix: remove NA string replacement, fixed upstream
lparsons May 21, 2024
25c9513
Use params.extra
fgvieira May 21, 2024
4df668a
fix: deeptools use params.extra consistently
lparsons May 22, 2024
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11 changes: 5 additions & 6 deletions bio/deeptools/plotfingerprint/test/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -2,21 +2,20 @@ rule plot_fingerprint:
input:
bam_files=expand("samples/{sample}.bam", sample=["a", "b"]),
bam_idx=expand("samples/{sample}.bam.bai", sample=["a", "b"]),
jsd_sample="samples/b.bam" # optional, requires qc_metrics output
jsd_sample="samples/b.bam", # optional, requires qc_metrics output
output:
# Please note that --plotFile and --outRawCounts are exclusively defined via output files.
# Usable output variables, their extensions and which option they implicitly call are listed here:
# https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/deeptools/plotfingerprint.html.
fingerprint="plot_fingerprint/plot_fingerprint.png", # required
# optional output
counts="plot_fingerprint/raw_counts.tab",
qc_metrics="plot_fingerprint/qc_metrics.txt"
qc_metrics="plot_fingerprint/qc_metrics.txt",
log:
"logs/deeptools/plot_fingerprint.log"
"logs/deeptools/plot_fingerprint.log",
params:
# optional parameters
"--numberOfSamples 200 "
threads:
8
"--numberOfSamples 200 ",
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threads: 8
wrapper:
"master/bio/deeptools/plotfingerprint"
16 changes: 3 additions & 13 deletions bio/deeptools/plotfingerprint/wrapper.py
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Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
__author__ = "Antonie Vietor"
__copyright__ = "Copyright 2020, Antonie Vietor"
__copyright__ = "Copyright 2024, Antonie Vietor, Lance Parsons"
__email__ = "[email protected]"
__license__ = "MIT"

from snakemake.shell import shell
import re

from snakemake.shell import shell

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

jsd_sample = snakemake.input.get("jsd_sample")
Expand All @@ -32,14 +33,3 @@
"{jsd} "
"{snakemake.params}) {log}"
)
# ToDo: remove the 'NA' string replacement when fixed in deepTools, see:
# https://github.com/deeptools/deepTools/pull/999
regex_passes = 2

with open(out_metrics, "rt") as f:
metrics = f.read()
for i in range(regex_passes):
metrics = re.sub("\tNA(\t|\n)", "\tnan\\1", metrics)

with open(out_metrics, "wt") as f:
f.write(metrics)
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