From fc3f65efd5a22b57fd646fa2a71ae342b85dd56d Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Thu, 1 Feb 2018 16:22:30 +0100
Subject: [PATCH] Reverting, siRNA can start with any nucleotide.
---
libsmallrna/libsmallrna/libsmallrna.pyx | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/libsmallrna/libsmallrna/libsmallrna.pyx b/libsmallrna/libsmallrna/libsmallrna.pyx
index 62a6cae..b0326e0 100755
--- a/libsmallrna/libsmallrna/libsmallrna.pyx
+++ b/libsmallrna/libsmallrna/libsmallrna.pyx
@@ -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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