REDItools3 3.2a0__py3-none-any.whl → 3.3__py3-none-any.whl

reditools/analyze.py

@@ -89,7 +89,8 @@ def setup_rtools(options):  # noqa:WPS213,WPS231
         )
 
     if options.bed_file:
-        rtools.load_target_positions(options.bed_file)
+        regions = file_utils.read_bed_file(options.bed_file)
+        rtools.target_positions = regions
     if options.exclude_regions:
         for fname in options.exclude_regions:
             regions = file_utils.read_bed_file(fname)
@@ -208,7 +209,7 @@ def run(options, in_queue, out_queue):
     except Exception as exc:
         if options.debug:
             traceback.print_exception(*sys.exc_info())
-        sys.stderr.write(f'[ERROR] {exc}\n')
+        sys.stderr.write(f'[ERROR] ({type(exc)}) {exc}\n')
 
 
 def parse_options():  # noqa:WPS213

reditools/rtchecks.py

@@ -149,12 +149,14 @@ class RTChecks(object):
         Returns:
             (bool): True if there are sufficient edits
         """
-        for num_edits in bases.get_min_edits():
-            if 0 < num_edits < rtools.min_edits_per_nucleotide:
+        for base in "ATCG":
+            if base == bases.ref:
+                continue
+            if bases[base] < rtools.min_edits_per_nucleotide:
                 rtools.log(
                     Logger.debug_level,
                     'DISCARDING COLUMN edits={} < {}',
-                    num_edits,
+                    bases[base],
                     rtools.min_edits_per_nucleotide,
                 )
                 return False

{REDItools3-3.2a0.dist-info → reditools3-3.3.dist-info}/METADATA

@@ -1,13 +1,13 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: REDItools3
-Version: 3.2a0
+Version: 3.3
 Author: Ernesto Picardi
 Author-email: Adam Handen <adam.handen@gmail.com>
 Project-URL: homepage, https://github.com/BioinfoUNIBA/REDItools3
 Project-URL: repository, https://github.com/BioinfoUNIBA/REDItools3
 Project-URL: issues, https://github.com/BioinfoUNIBA/REDItools3/issues
 Keywords: bioinformatics,RNA,RNA-editing
-Classifier: Development Status :: 3 - Alpha
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License (GPL)
@@ -18,8 +18,8 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: pysam >=0.22.0
-Requires-Dist: sortedcontainers >=2.4.0
+Requires-Dist: pysam>=0.22.0
+Requires-Dist: sortedcontainers>=2.4.0
 
 # REDItools3
 A new REDItools implementation to speed-up the RNA editing profiling in massive RNAseq data

{REDItools3-3.2a0.dist-info → reditools3-3.3.dist-info}/RECORD

@@ -2,7 +2,7 @@ reditools/__init__.py,sha256=7nSB0hrQznxrn6l95cv_pSonJTG6jZCQdbn7aT1TtvY,46
 reditools/__main__.py,sha256=mWJ9O2LDiOpBWDBJJUN7OiM4SyltW-kVXXAGBe_JxgQ,842
 reditools/alignment_file.py,sha256=YFyCEhMek2t93DpmpwEst5v3gDZkmRotbd6Fy_mP0aE,4258
 reditools/alignment_manager.py,sha256=_FXwvqGWoXRdzVrwBxki2heaVZA2cQbGXqCopr-g1Hs,4138
-reditools/analyze.py,sha256=tW9Rz-R_8R-mJ2uQP5fpGFTH7TEv-2pOsigtbKqwYDY,14649
+reditools/analyze.py,sha256=7J_arZX2Sc-lFuFdjjGq_G7QQ8s2hQ1paWqqUBXoftQ,14711
 reditools/compiled_position.py,sha256=v540uUEie_HHUwsYQmBqeeOkUvtYlcnWj1v8gAhLUiE,3858
 reditools/compiled_reads.py,sha256=7Hm5f7g1T8q1zDOOxZUD7aZax9b7SdQ0PlmT93hmcaE,4154
 reditools/fasta_file.py,sha256=KBsJBs7OnBpew2PGWGp0mTxPLlpBmRrtXL4uvQw4t34,2212
@@ -12,10 +12,10 @@ reditools/index.py,sha256=jLgWwKXIA_e-bqVu74SDZXmrdWch_syDSmMnFZPbqz4,7537
 reditools/logger.py,sha256=u4L2SYxy4vJ4KDHEymd0b1sCa8BXXHchx8LR_wcFq1A,1210
 reditools/reditools.py,sha256=RNH7aKC2QnbafA7T9E6UpV5Llv3FjfDIabjPCuwDgW0,13111
 reditools/region.py,sha256=_BiKDc5lCl1snjkokRiUWOgzA57ME3yLydEIwK9ku7U,3780
-reditools/rtchecks.py,sha256=TmCow38fCRwSICvx3nlOxy6Q216BcDXESGhM7bB_ixo,8878
+reditools/rtchecks.py,sha256=q_-8iAV51mGrqN30blSgMD_htF3CGrPyrI4PD3CSCLQ,8917
 reditools/utils.py,sha256=a2qfhMcrH2QlK-JoR-HHF6_bnlo5v3jihAqqknvVIjc,2733
-REDItools3-3.2a0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-REDItools3-3.2a0.dist-info/METADATA,sha256=NRwZTGGmlHBkP6XiQ4Sdql-XXRR2Ii27beCDf_jCt90,1288
-REDItools3-3.2a0.dist-info/WHEEL,sha256=R06PA3UVYHThwHvxuRWMqaGcr-PuniXahwjmQRFMEkY,91
-REDItools3-3.2a0.dist-info/top_level.txt,sha256=wrvvbFXhmNg7s6LQqjlV_fVQYUZOOpF93IcMu_hBCx4,10
-REDItools3-3.2a0.dist-info/RECORD,,
+reditools3-3.3.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+reditools3-3.3.dist-info/METADATA,sha256=Toc23YEA7V-dWeNWbNay_vtq_ycxWLHKtstCbsIp9yg,1296
+reditools3-3.3.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+reditools3-3.3.dist-info/top_level.txt,sha256=wrvvbFXhmNg7s6LQqjlV_fVQYUZOOpF93IcMu_hBCx4,10
+reditools3-3.3.dist-info/RECORD,,

{REDItools3-3.2a0.dist-info → reditools3-3.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.5.0)
+Generator: setuptools (76.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any