filter_reads_by_softclip bugfixes

bugfix - do not treat quality-filtered gaps as splice junctions
Gregor-Mendel-Institute · Sep 25, 2023 · cd192ad · cd192ad
1 parent 8cd3b8a
commit cd192ad
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Showing 14 changed files with 6,870 additions and 5,647 deletions.
diff --git a/bookend/__init__.py b/bookend/__init__.py
@@ -1,3 +1,3 @@
-__version__ = '1.2.0'
-__updated__ = '09.19.2023'
-__date__ = '09.19.2023'
+__version__ = '1.2.1'
+__updated__ = '09.25.2023'
+__date__ = '09.25.2023'
diff --git a/bookend/core/bam_to_elr.py b/bookend/core/bam_to_elr.py
@@ -109,9 +109,11 @@ def __init__(self, args):
             if self.data_type.upper() in ['ONT','NANOPORE','OXFORD']:
                 """Reads are from Oxford Nanopore cDNA or PCR-cDNA kits, trimmed and oriented by bookend label or pychopper."""
                 self.config_dict['stranded'] = True
+                self.config_dict['s_tag'] = True
+                self.config_dict['e_tag'] = True
                 self.config_dict['max_headclip'] = 10
                 self.config_dict['quality_filter'] = False
-                self.config_dict['error_rate'] = 0.4
+                self.config_dict['error_rate'] = 0.2
                 self.config_dict['remove_noncanonical'] = True
                 self.config_dict['remove_gapped_termini'] = True
                 if self.untrimmed:

diff --git a/bookend/core/cython_utils/_rnaseq_utils.c b/bookend/core/cython_utils/_rnaseq_utils.c
diff --git a/bookend/core/cython_utils/_rnaseq_utils.pyx b/bookend/core/cython_utils/_rnaseq_utils.pyx
diff --git a/bookend/core/gtf_to_bed.py b/bookend/core/gtf_to_bed.py
@@ -66,6 +66,7 @@ def __init__(self, args):
             gtf_config=gtf_defaults, 
             gff_config=gff_defaults
         )
+        # print(gff_defaults)
         self.dataset.source_array = [self.source]
         self.generator = self.dataset.generator
         self.locus_counter = 0

diff --git a/bookend_rna.egg-info/PKG-INFO b/bookend_rna.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bookend-rna
-Version: 1.2.0
+Version: 1.2.1
 Summary: End-guided transcript assembler for short and long RNA-seq reads.
 Home-page: https://github.com/Gregor-Mendel-Institute/bookend
 Author: Michael A. Schon

diff --git a/build/lib.linux-x86_64-3.7/bookend/__init__.py b/build/lib.linux-x86_64-3.7/bookend/__init__.py
@@ -1,3 +1,3 @@
-__version__ = '1.2.0'
-__updated__ = '09.19.2023'
-__date__ = '09.19.2023'
+__version__ = '1.2.1'
+__updated__ = '09.25.2023'
+__date__ = '09.25.2023'
diff --git a/build/lib.linux-x86_64-3.7/bookend/core/bam_to_elr.py b/build/lib.linux-x86_64-3.7/bookend/core/bam_to_elr.py
@@ -109,9 +109,11 @@ def __init__(self, args):
             if self.data_type.upper() in ['ONT','NANOPORE','OXFORD']:
                 """Reads are from Oxford Nanopore cDNA or PCR-cDNA kits, trimmed and oriented by bookend label or pychopper."""
                 self.config_dict['stranded'] = True
+                self.config_dict['s_tag'] = True
+                self.config_dict['e_tag'] = True
                 self.config_dict['max_headclip'] = 10
                 self.config_dict['quality_filter'] = False
-                self.config_dict['error_rate'] = 0.4
+                self.config_dict['error_rate'] = 0.2
                 self.config_dict['remove_noncanonical'] = True
                 self.config_dict['remove_gapped_termini'] = True
                 if self.untrimmed:

diff --git a/....linux-x86_64-3.7/bookend/core/cython_utils/_rnaseq_utils.cpython-37m-x86_64-linux-gnu.so b/....linux-x86_64-3.7/bookend/core/cython_utils/_rnaseq_utils.cpython-37m-x86_64-linux-gnu.so
diff --git a/build/lib.linux-x86_64-3.7/bookend/core/gtf_to_bed.py b/build/lib.linux-x86_64-3.7/bookend/core/gtf_to_bed.py
@@ -66,6 +66,7 @@ def __init__(self, args):
             gtf_config=gtf_defaults, 
             gff_config=gff_defaults
         )
+        # print(gff_defaults)
         self.dataset.source_array = [self.source]
         self.generator = self.dataset.generator
         self.locus_counter = 0

diff --git a/build/temp.linux-x86_64-3.7/bookend/core/cython_utils/_rnaseq_utils.o b/build/temp.linux-x86_64-3.7/bookend/core/cython_utils/_rnaseq_utils.o
diff --git a/dist/bookend_rna-1.2.0-py3.7-linux-x86_64.egg b/dist/bookend_rna-1.2.0-py3.7-linux-x86_64.egg
diff --git a/dist/bookend_rna-1.2.1-py3.7-linux-x86_64.egg b/dist/bookend_rna-1.2.1-py3.7-linux-x86_64.egg
diff --git a/setup.py b/setup.py
@@ -38,7 +38,7 @@ def run(self):
 
 setup(
     name="bookend_rna", # Replace with your own username
-    version="1.2.0",
+    version="1.2.1",
     author="Michael A. Schon",
     author_email="[email protected]",
     description="End-guided transcript assembler for short and long RNA-seq reads.",