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Blaise LI
bioinfo_utils
Commits
fc3f65ef
Commit
fc3f65ef
authored
7 years ago
by
Blaise Li
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Reverting, siRNA can start with any nucleotide.
parent
5bc3c6ce
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master
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libsmallrna/libsmallrna/libsmallrna.pyx
+7
-2
7 additions, 2 deletions
libsmallrna/libsmallrna/libsmallrna.pyx
with
7 additions
and
2 deletions
libsmallrna/libsmallrna/libsmallrna.pyx
+
7
−
2
View file @
fc3f65ef
...
...
@@ -355,8 +355,13 @@ def count_sis(annot_infos, write_queue):
# Eliminate most common non-siRNA target cases based on annotation name.
# Also eliminate the reads with no signature
# (the annot_name should be "no_signature")
if
(
annot_name
in
COMMON_NO_TARGET
or
annot_name
[:
3
]
==
"
no_
"
):
# if (annot_name in COMMON_NO_TARGET
# or annot_name[:3] == "no_"):
# continue
# Actually, we do accept reads that do not start with G
# Provided they are not plain "no_signature"
# (that is: without other annotations)
if
annot_name
in
COMMON_NO_TARGET
:
continue
# annotations: set of tuples
# (attrs["gene_biotype"], gtf.strand, gtf.start, gtf.end, attrs["gene_id"])
...
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