Commit 5e93608f authored by bow's avatar bow
Browse files

Update flt3 coord param handling

parent 320b7f2d
......@@ -10,6 +10,10 @@ RUN.set_default_setting("extract_sc_flt3",
RUN.set_default_setting("plot_sc_linear_flt3",
srcdir(path.join("scripts", "plot_sc_linear_flt3.py")))
# Region of interest ~ exon 14-15 in transcript coordinates.
RUN.set_default_setting("flt3_start", 1787)
RUN.set_default_setting("flt3_end", 2024)
rule all_flt3:
input:
......@@ -54,7 +58,10 @@ rule plot_sc_linear_flt3:
bg=RUN.settings["bg_soft_clip_csv"],
output:
png=RUN.output("{sample}/itd-flt3/{sample}.flt3-sc.png"),
params:
start=RUN.settings["flt3_start"],
end=RUN.settings["flt3_end"],
conda: srcdir("envs/plot_sc_linear_flt3.yml")
shell:
"python {input.scr} --sc-bg {input.bg} --min-scl-count 2 --min-insert-count 2"
" --fuzziness 12 --padding 0 {input.counts} 1787 2024 {output.png}"
" --fuzziness 12 --padding 0 {input.counts} {params.start} {params.end} {output.png}"
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