Commit 01a0ddec authored by Blaise Li's avatar Blaise Li
Browse files

Missing explicit handling of rRNA.

parent bc19760e
......@@ -552,7 +552,7 @@ def sum_counts(fname):
p = Popen(
# ['awk', '$1 ~ /^piRNA$|^miRNA$|^pseudogene$|^satellites_rmsk$|^simple_repeats_rmsk$|^protein_coding_|^.NA_transposons_rmsk$/ {sum += $2} END {print sum}', fname],
# slightly faster
['mawk', '$1 ~ /^piRNA$|^miRNA$|^pseudogene$|^satellites_rmsk$|^simple_repeats_rmsk$|^protein_coding_|^.NA_transposons_rmsk$/ {sum += $2} END {print sum}', fname],
['mawk', '$1 ~ /^piRNA$|^miRNA$|^pseudogene$|^satellites_rmsk$|^simple_repeats_rmsk$|^rRNA$|^protein_coding_|^.NA_transposons_rmsk$/ {sum += $2} END {print sum}', fname],
stdout=PIPE,
stderr=PIPE)
(result, err) = p.communicate()
......@@ -1828,6 +1828,10 @@ rule gather_small_RNA_counts:
*{f"simrep_si_{suffix}" for suffix in SI_SUFFIXES},
*{f"simrep_siu_{suffix}" for suffix in SI_SUFFIXES}}:
drop = ["simple_repeats_rmsk"]
elif wildcards.small_type in {
*{f"ri_si_{suffix}" for suffix in SI_SUFFIXES},
*{f"ri_siu_{suffix}" for suffix in SI_SUFFIXES}}:
drop = ["rRNA"]
elif wildcards.small_type in {
*{f"all_si_{suffix}" for suffix in SI_SUFFIXES},
*{f"all_siu_{suffix}" for suffix in SI_SUFFIXES}}:
......
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