Release 3.5

Author: uchicago-handena

REDItools3.egg-info/PKG-INFO

@@ -1,16 +1,16 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: REDItools3
-Version: 3.3
+Version: 3.5
 Author: Ernesto Picardi
 Author-email: Adam Handen <adam.handen@gmail.com>
+License-Expression: GPL-3.0-or-later
 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 :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: GNU General Public License (GPL)
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: Unix
 Classifier: Programming Language :: Python :: 3.7
@@ -20,6 +20,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pysam>=0.22.0
 Requires-Dist: sortedcontainers>=2.4.0
+Dynamic: license-file
 
 # REDItools3
 A new REDItools implementation to speed-up the RNA editing profiling in massive RNAseq data
@@ -34,3 +35,65 @@ Use the whl file under the dist directory.
 # Usage
 Once installed, reditools can be run from the commandline.
 `python -m reditools`
+
+## Tools
+
+### analyze
+This is the core reditools function: detecting editing events from one or more BAM file.
+
+The output is a tab separated table with these columns:
+| Field | Description |
+| --- | --- |
+| Region        | Chromosome or contig |
+| Position      | Position in the region |
+| Reference     | Base from the reference sequence |
+| Strand        | DNA strand (+, -, or \*) |
+| Coverage-q30  | How many reads had a quality of at least 30 |
+| MeanQ         | Mean read quality |
+| BaseCount[A,C,G,T] | Total count of each base found |
+| AllSubs       | All the detected substitutions |
+| Frequency     | Ratio of non-reference bases to reference bases |
+| gCoverage-q30 | Genomic Coverage-q30 (see `annotate`) |
+| gMeanQ        | Genomic MeanQ (see `annotate`) |
+| gBaseCount[A,C,G,T] | Genomic BaseCount (see `annotate`) |
+| gAllSubs      | Genomic variants (see `annotate`) |
+| gFrequency    | Genomic variant frequency (see `annotate`) |
+
+The last 5 columns will always be blank (`-`). They are reserved for output
+from the `annotate` tool.
+
+### annotate
+Annotate RNA editing output with variant detection from genomic data.
+
+`annotate` takes two reditools output files and fills in the last five columns
+of the first file with positional matches from the second.
+
+For example, this RNA file:
+```
+Region	Position	Reference	Strand	Coverage-q30	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage-q30	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency
+chr1	1115715	C	*	2	38.00	[0, 2, 0, 0]	-	0.00	-	-	-	-	-
+chr1	1115716	A	*	2	38.00	[2, 0, 0, 0]	-	0.00	-	-	-	-	-
+```
+
+With this DNA file:
+```
+Region	Position	Reference	Strand	Coverage-q30	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage-q30	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency
+chr1	1115716	A	*	2	38.00	[2, 0, 0, 0]	-	0.00	-	-	-	-	-
+chr1	1115717	C	*	2	38.00	[0, 2, 0, 0]	-	0.00	-	-	-	-	-
+```
+
+Produces:
+```
+Region	Position	Reference	Strand	Coverage-q30	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage-q30	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency
+chr1	1115715	C	*	2	38.00	[0, 2, 0, 0]	-	0.00	-	-	-	-	-
+chr1    1115716 A       *       2       38.00   [2, 0, 0, 0]    -       0.00    2       38.00   [2, 0, 0, 0]    -       0.00
+```
+
+### find-repeats
+Identify repetitive elements in a FASTQ file.
+
+### index
+Compute RNA editing index from reditools `analyze` output
+([PMDI: 31636457](https://pubmed.ncbi.nlm.nih.gov/31636457/)).
+The `index` tool computes the editing indices for all possible variants, not
+just A-to-I (listed as A-G in the output).

REDItools3.egg-info/SOURCES.txt

@@ -11,6 +11,7 @@ reditools/__main__.py
 reditools/alignment_file.py
 reditools/alignment_manager.py
 reditools/analyze.py
+reditools/annotate.py
 reditools/compiled_position.py
 reditools/compiled_reads.py
 reditools/fasta_file.py
@@ -20,5 +21,6 @@ reditools/index.py
 reditools/logger.py
 reditools/reditools.py
 reditools/region.py
+reditools/region_collection.py
 reditools/rtchecks.py
 reditools/utils.py

dist/reditools3-3.3-py3-none-any.whl

@@ -4,10 +4,11 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "REDItools3"
-version = "v3.3"
+version = "v3.5"
+license = "GPL-3.0-or-later"
 authors = [
-  { name="Adam Handen", email="adam.handen@gmail.com" },
   { name="Ernesto Picardi" },
+  { name="Adam Handen", email="adam.handen@gmail.com" },
 ]
 readme = "README.md"
 dependencies = [
@@ -20,7 +21,6 @@ classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: GNU General Public License (GPL)",
     "Operating System :: MacOS :: MacOS X",
     "Operating System :: Unix",
     "Programming Language :: Python :: 3.7",