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Commit 54d37c8f authored by Blaise Li's avatar Blaise Li
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Only one config for normalizers.

This applies for both bigwig files and RPM-based stuff, and maybe
also for other outputs.
parent 184c47b8
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...@@ -515,9 +515,10 @@ TESTED_SIZE_FACTORS = ["mapped", "non_structural", "all_sisiuRNA", "piRNA", "miR ...@@ -515,9 +515,10 @@ TESTED_SIZE_FACTORS = ["mapped", "non_structural", "all_sisiuRNA", "piRNA", "miR
# and then substraction of a pseudocount, in order to deal with zero counts. # and then substraction of a pseudocount, in order to deal with zero counts.
# This seems to perform well (see "test_size_factor" results). # This seems to perform well (see "test_size_factor" results).
DE_SIZE_FACTORS = ["non_structural", "median_ratio_to_pseudo_ref"] DE_SIZE_FACTORS = ["non_structural", "median_ratio_to_pseudo_ref"]
SIZE_FACTORS = ["non_structural", "piRNA"] SIZE_FACTORS = config.get("size_factors", ["non_structural"])
#NORMALIZER = "median_ratio_to_pseudo_ref" #NORMALIZER = "median_ratio_to_pseudo_ref"
RPM_NORMS = config.get("rpm_norms", SIZE_FACTORS) # Do we really need distinct lists of normalizers?
RPM_NORMS = SIZE_FACTORS
RPM_FOLD_TYPES = [ RPM_FOLD_TYPES = [
f"mean_log2_RPM_by_{norm}_fold" f"mean_log2_RPM_by_{norm}_fold"
for norm in RPM_NORMS] for norm in RPM_NORMS]
......
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