Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
B
bioinfo_utils
Manage
Activity
Members
Labels
Plan
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Container registry
Model registry
Operate
Environments
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
GitLab community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Blaise LI
bioinfo_utils
Commits
fc3f65ef
Commit
fc3f65ef
authored
7 years ago
by
Blaise Li
Browse files
Options
Downloads
Patches
Plain Diff
Reverting, siRNA can start with any nucleotide.
parent
5bc3c6ce
No related branches found
No related tags found
No related merge requests found
Changes
1
Show whitespace changes
Inline
Side-by-side
Showing
1 changed file
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):
...
@@ -355,8 +355,13 @@ def count_sis(annot_infos, write_queue):
# Eliminate most common non-siRNA target cases based on annotation name.
# Eliminate most common non-siRNA target cases based on annotation name.
# Also eliminate the reads with no signature
# Also eliminate the reads with no signature
# (the annot_name should be "no_signature")
# (the annot_name should be "no_signature")
if
(
annot_name
in
COMMON_NO_TARGET
# if (annot_name in COMMON_NO_TARGET
or
annot_name
[:
3
]
==
"
no_
"
):
# 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
continue
# annotations: set of tuples
# annotations: set of tuples
# (attrs["gene_biotype"], gtf.strand, gtf.start, gtf.end, attrs["gene_id"])
# (attrs["gene_biotype"], gtf.strand, gtf.start, gtf.end, attrs["gene_id"])
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment