bookend 1.2.0 update

Finalized setup files for 1.2.0

README.md

@@ -9,7 +9,7 @@ Take a look at the [Bookend publication](https://genomebiology.biomedcentral.com
 ## Installation  
 Bookend can be installed through the Python Package Index (PyPI) on UNIX systems with Python 3.6+ using the command:
 ```
-pip install bookend-rna
+pip install bookend-rna --upgrade
 ```
 
 If installing from the GitHub source code, perform the following steps:
@@ -23,15 +23,16 @@ Once installed, all utilities can be accessed on the command as bookend subcomma
 
     usage: bookend [subcommand] [options] [input file(s)]
     Subcommands (use -h/--help for more info):
-
+    
         label    (Label 5' and 3' ends in a FASTQ file)
         elr      (Convert a BAM/SAM file to the end-labeled read format)
         assemble (Assemble transcripts from aligned end-labeled reads)
         condense (Partial assembly that leaves keeps all fragments; use for meta-assembly)
         classify (Compare an assembly to the transcripts of a reference annotation)
+        merge    (Combine GTF files into a unified annotation)
         bedgraph (Write a coverage Bedgraph file of end-labeled reads)
         fasta    (Write a transcript FASTA file from an annotation and genome)
-
+    
         --end-labeled read (ELR) operations--
         elr-sort
         elr-subset
@@ -44,4 +45,4 @@ Once installed, all utilities can be accessed on the command as bookend subcomma
         elr-to-bed
         sam-to-sj
         sj-to-bed
-        sj-merge
+        sj-merge  

bookend/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '1.1.0'
-__updated__ = '04.20.2023'
-__date__ = '04.20.2023'
+__version__ = '1.2.0'
+__updated__ = '09.19.2023'
+__date__ = '09.19.2023'

bookend_rna.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bookend-rna
-Version: 1.1.2
+Version: 1.2.0
 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
@@ -26,7 +26,7 @@ Take a look at the [Bookend publication](https://genomebiology.biomedcentral.com
 ## Installation  
 Bookend can be installed through the Python Package Index (PyPI) on UNIX systems with Python 3.6+ using the command:
 ```
-pip install bookend-rna
+pip install bookend-rna --upgrade
 ```
 
 If installing from the GitHub source code, perform the following steps:
@@ -40,15 +40,16 @@ Once installed, all utilities can be accessed on the command as bookend subcomma
 
     usage: bookend [subcommand] [options] [input file(s)]
     Subcommands (use -h/--help for more info):
-
+    
         label    (Label 5' and 3' ends in a FASTQ file)
         elr      (Convert a BAM/SAM file to the end-labeled read format)
         assemble (Assemble transcripts from aligned end-labeled reads)
         condense (Partial assembly that leaves keeps all fragments; use for meta-assembly)
         classify (Compare an assembly to the transcripts of a reference annotation)
+        merge    (Combine GTF files into a unified annotation)
         bedgraph (Write a coverage Bedgraph file of end-labeled reads)
         fasta    (Write a transcript FASTA file from an annotation and genome)
-
+    
         --end-labeled read (ELR) operations--
         elr-sort
         elr-subset
@@ -61,6 +62,6 @@ Once installed, all utilities can be accessed on the command as bookend subcomma
         elr-to-bed
         sam-to-sj
         sj-to-bed
-        sj-merge
+        sj-merge  
 
 

build/lib.linux-x86_64-3.7/bookend/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '1.1.0'
-__updated__ = '04.20.2023'
-__date__ = '04.20.2023'
+__version__ = '1.2.0'
+__updated__ = '09.19.2023'
+__date__ = '09.19.2023'

setup.py

@@ -38,7 +38,7 @@ def run(self):
 
 setup(
     name="bookend_rna", # Replace with your own username
-    version="1.1.2",
+    version="1.2.0",
     author="Michael A. Schon",
     author_email="[email protected]",
     description="End-guided transcript assembler for short and long RNA-seq reads.",