Commit 0160ee2f authored by Blaise Li's avatar Blaise Li
Browse files

Relax wildcard constraints for TPM.

The goal is to also allow TPM computed on protein-coding genes only.
parent 783a77ac
......@@ -413,7 +413,7 @@ rule compute_TPM:
f"all_on_{genome}", "{biotype}_{orientation}_TPM.txt"),
# The sum must be done over all counted features
wildcard_constraints:
biotype = "alltypes"
biotype = "|".join(["alltypes", "protein_coding"]),
# run:
# rpk = pd.read_table(input.rpk_file, index_col="gene")
# tpm = 1000000 * rpk / rpk.sum()
......
......@@ -992,7 +992,7 @@ rule compute_TPM:
"all_on_C_elegans", "{biotype}_{orientation}_TPM.txt"),
# The sum must be done over all counted features
wildcard_constraints:
biotype = "|".join(["alltypes"])
biotype = "|".join(["alltypes", "protein_coding"])
# run:
# rpk = pd.read_table(input.rpk_file, index_col="gene")
# tpm = 1000000 * rpk / rpk.sum()
......
......@@ -1143,7 +1143,7 @@ rule compute_TPM:
"all_{mapped_type}", "{biotype}_{orientation}_TPM.txt"),
# The sum must be done over all counted features
wildcard_constraints:
biotype = "|".join(["alltypes"])
biotype = "|".join(["alltypes", "protein_coding"])
# run:
# rpk = pd.read_table(input.rpk_file, index_col="gene")
# tpm = 1000000 * rpk / rpk.sum()
......
......@@ -1292,7 +1292,7 @@ rule compute_TPM:
"all_{read_type}_on_%s" % genome, "{biotype}_{orientation}_TPM.txt"),
# The sum must be done over all counted features
wildcard_constraints:
biotype = "alltypes"
biotype = "|".join(["alltypes", "protein_coding"]),
run:
rpk = pd.read_table(input.rpk_file, index_col="gene")
tpm = 1000000 * rpk / rpk.sum()
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment