Commit 783a77ac authored by Blaise Li's avatar Blaise Li
Browse files

Compute TPM and "efficiencies" on protein_coding.

parent 23c1b898
......@@ -130,7 +130,7 @@ rule all:
# lib=LIBS, biotype=["alltypes"], orientation=ORIENTATIONS),
expand(
OPJ(counts_dir, "diff_%s" % eff_name, "{contrast}", "{orientation}_{biotype}", "{contrast}_diff_%s.txt" % eff_name),
contrast=DD_CONTRASTS, orientation=["fwd"], biotype=["alltypes"]),
contrast=DD_CONTRASTS, orientation=["fwd"], biotype=["alltypes", "protein_coding"]),
include: ensure_relative(irules["link_raw_data"], workflow.basedir)
......
......@@ -357,7 +357,7 @@ rule all:
expand(OPJ(
"{trimmer}", aligner, "mapped_C_elegans", "{counter}",
"all_on_C_elegans", "{biotype}_{orientation}_TPM.txt"),
trimmer=TRIMMERS, counter=COUNTERS, biotype=["alltypes"], orientation=ORIENTATIONS),
trimmer=TRIMMERS, counter=COUNTERS, biotype=["alltypes", "protein_coding"], orientation=ORIENTATIONS),
#expand(OPJ("{trimmer}", "figures", aligner, "{lib}_mean", "{orientation}_on_merged_isolated_%d_{biotype}_min_%d_meta_profile.pdf" % (MIN_DIST, META_MIN_LEN)), trimmer=TRIMMERS, lib=LIBS, orientation=["all"], biotype=["protein_coding"]),
#expand(OPJ("{trimmer}", "figures", aligner, "{lib}_mean", "{orientation}_on_merged_isolated_%d_{biotype}_min_%d_meta_profile.pdf" % (MIN_DIST, META_MIN_LEN)), trimmer=TRIMMERS, lib=LIBS, orientation=["all"], biotype=METAGENE_BIOTYPES),
# TODO: Add metagene profiles similar to small RNA-seq
......
......@@ -318,7 +318,7 @@ counts_files = [
OPJ(aligner, f"mapped_{genome}", "{counter}",
"all_{mapped_type}", "{biotype}_{orientation}_TPM.txt"),
counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"],
biotype=["alltypes"], orientation=ORIENTATIONS),
biotype=["alltypes", "protein_coding"], orientation=ORIENTATIONS),
expand(
OPJ(aligner, f"mapped_{genome}", "{counter}",
"all_{mapped_type}", "{biotype}_{orientation}_RPK.txt"),
......
......@@ -579,7 +579,7 @@ rule all:
# translation_efficiency
expand(
OPJ(counts_dir, "{lib}_mean_{read_type}_on_%s" % genome, "{lib}_{biotype}_{orientation}_%s.txt" % eff_name),
lib=EFF_LIBS, read_type=["RPF"], biotype=["alltypes"], orientation=["fwd"]),
lib=EFF_LIBS, read_type=["RPF"], biotype=["alltypes", "protein_coding"], orientation=["fwd"]),
# DESeq2 results
expand(
OPJ(
......@@ -599,7 +599,7 @@ rule all:
counts_dir,
"diff_%s_{read_type}" % eff_name,
"{contrast}", "{orientation}_{biotype}", "{contrast}_diff_%s.txt" % eff_name),
read_type=["RPF"], contrast=DT_CONTRASTS, orientation=["fwd"], biotype=["alltypes"]),
read_type=["RPF"], contrast=DT_CONTRASTS, orientation=["fwd"], biotype=["alltypes", "protein_coding"]),
# rule future_all:
# meta_profiles,
......
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