Commit 6fcd8adc authored by Blaise Li's avatar Blaise Li
Browse files

DESeq2 and bigwig files for unique mappers.

parent 5946a7a6
Pipeline #7136 failed with stages
in 46 seconds
...@@ -371,7 +371,9 @@ if contrasts_dict["ip"]: ...@@ -371,7 +371,9 @@ if contrasts_dict["ip"]:
expand( expand(
OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}", "fold_boxplots_{mapped_type}", OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}", "fold_boxplots_{mapped_type}",
"{contrast_type}_{orientation}_{biotype}_{fold_type}_{id_list}_boxplots.pdf"), "{contrast_type}_{orientation}_{biotype}_{fold_type}_{id_list}_boxplots.pdf"),
counter=COUNTERS, mapped_type=[f"on_{genome}"], contrast_type=["ip"], #counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"],
counter=COUNTERS, mapped_type=[f"on_{genome}"],
contrast_type=["ip"],
orientation=ORIENTATIONS, biotype=DE_BIOTYPES, orientation=ORIENTATIONS, biotype=DE_BIOTYPES,
fold_type=["mean_log2_RPM_fold"], id_list=ID_LISTS),] fold_type=["mean_log2_RPM_fold"], id_list=ID_LISTS),]
else: else:
...@@ -382,7 +384,8 @@ if contrasts_dict["de"]: ...@@ -382,7 +384,8 @@ if contrasts_dict["de"]:
expand( expand(
OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}", "fold_boxplots_{mapped_type}", OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}", "fold_boxplots_{mapped_type}",
"{contrast_type}_{orientation}_{biotype}_{fold_type}_{id_list}_boxplots.pdf"), "{contrast_type}_{orientation}_{biotype}_{fold_type}_{id_list}_boxplots.pdf"),
counter=COUNTERS, mapped_type=[f"on_{genome}"], contrast_type=["de"], counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"],
contrast_type=["de"],
orientation=ORIENTATIONS, biotype=DE_BIOTYPES, orientation=ORIENTATIONS, biotype=DE_BIOTYPES,
fold_type=["log2FoldChange"], id_list=ID_LISTS),] fold_type=["log2FoldChange"], id_list=ID_LISTS),]
else: else:
...@@ -392,16 +395,19 @@ de_files = [ ...@@ -392,16 +395,19 @@ de_files = [
expand( expand(
OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}", OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}",
"deseq2_{mapped_type}", "{contrast}", "{orientation}_{biotype}", "{contrast}_counts_and_res.txt"), "deseq2_{mapped_type}", "{contrast}", "{orientation}_{biotype}", "{contrast}_counts_and_res.txt"),
counter=COUNTERS, mapped_type=[f"on_{genome}"], contrast=DE_CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES), counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"],
contrast=DE_CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES),
expand( expand(
OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}", OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}",
"deseq2_{mapped_type}", "{contrast}", "{orientation}_{biotype}", "{contrast}_{fold_type}_distribution.pdf"), "deseq2_{mapped_type}", "{contrast}", "{orientation}_{biotype}", "{contrast}_{fold_type}_distribution.pdf"),
counter=COUNTERS, mapped_type=[f"on_{genome}"], contrast=DE_CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES, counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"],
contrast=DE_CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES,
fold_type=["log2FoldChange"]), fold_type=["log2FoldChange"]),
expand( expand(
OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}", OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}",
"deseq2_{mapped_type}", "{contrast}", "{orientation}_{biotype}", "{contrast}_MA_with_{id_list}.pdf"), "deseq2_{mapped_type}", "{contrast}", "{orientation}_{biotype}", "{contrast}_MA_with_{id_list}.pdf"),
counter=COUNTERS, mapped_type=[f"on_{genome}"], contrast=DE_CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES, counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"],
contrast=DE_CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES,
id_list=ID_LISTS + ["lfc_statuses"]), id_list=ID_LISTS + ["lfc_statuses"]),
de_fold_boxplots] de_fold_boxplots]
...@@ -420,11 +426,13 @@ bigwig_files = [ ...@@ -420,11 +426,13 @@ bigwig_files = [
OPJ(output_dir, aligner, f"mapped_{genome}", "{lib}_{rep}", OPJ(output_dir, aligner, f"mapped_{genome}", "{lib}_{rep}",
"{lib}_{rep}_{orientation}_{mapped_type}_by_{norm_type}.bw"), "{lib}_{rep}_{orientation}_{mapped_type}_by_{norm_type}.bw"),
lib=LIBS, rep=REPS, orientation=ORIENTATIONS, lib=LIBS, rep=REPS, orientation=ORIENTATIONS,
#mapped_type=[f"on_{genome}", f"unique_on_{genome}"], norm_type=NORM_TYPES),
mapped_type=[f"on_{genome}"], norm_type=NORM_TYPES), mapped_type=[f"on_{genome}"], norm_type=NORM_TYPES),
expand( expand(
OPJ(output_dir, aligner, f"mapped_{genome}", "{lib}_mean", OPJ(output_dir, aligner, f"mapped_{genome}", "{lib}_mean",
"{lib}_mean_{orientation}_{mapped_type}_by_{norm_type}.bw"), "{lib}_mean_{orientation}_{mapped_type}_by_{norm_type}.bw"),
lib=LIBS, orientation=ORIENTATIONS, lib=LIBS, orientation=ORIENTATIONS,
#mapped_type=[f"on_{genome}", f"unique_on_{genome}"], norm_type=NORM_TYPES),]
mapped_type=[f"on_{genome}"], norm_type=NORM_TYPES),] mapped_type=[f"on_{genome}"], norm_type=NORM_TYPES),]
if spikein_microliter_equivalent: if spikein_microliter_equivalent:
...@@ -610,6 +618,8 @@ def source_sam(wildcards): ...@@ -610,6 +618,8 @@ def source_sam(wildcards):
## ##
elif mapped_type == f"polyU_on_{genome}": elif mapped_type == f"polyU_on_{genome}":
return rules.remap_on_genome.output.sam return rules.remap_on_genome.output.sam
elif mapped_type == f"unique_on_{genome}":
raise NotImplementedError(f"{mapped_type} only handled from count level on.")
else: else:
raise NotImplementedError(f"{mapped_type} not handled (yet?)") raise NotImplementedError(f"{mapped_type} not handled (yet?)")
......
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