PyPI - ORForise - Versions diffs - 1.4.2__tar.gz → 1.4.3__tar.gz - Mend

ORForise 1.4.2tar.gz → 1.4.3tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (73) hide show

{orforise-1.4.2 → orforise-1.4.3}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: ORForise
-Version: 1.4.2
+Version: 1.4.3
 Summary: ORForise - Platform for analysing and comparing Prokaryote CoDing Sequence (CDS) Gene Predictions.
 Home-page: https://github.com/NickJD/ORForise
 Author: Nicholas Dimonaco
@@ -13,6 +13,7 @@ Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
+Dynamic: license-file
 # ORForise - Prokaryote Genome Annotation Analysis and Comparison Platform
 ## Published in Bioinformatics :   https://academic.oup.com/bioinformatics/article/38/5/1198/6454948
@@ -62,7 +63,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: Annotation_Compare.py [-h] -dna GENOME_DNA -ref REFERENCE_ANNOTATION -t TOOL -tp TOOL_PREDICTION
                              [-rt REFERENCE_TOOL] [-o OUTNAME] [-v {True,False}]
-ORForise v1.4.2: Annotatione-Compare Run Parameters.
+ORForise v1.4.3: Annotatione-Compare Run Parameters.
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -112,7 +113,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: Aggregate_Compare.py [-h] -dna GENOME_DNA -t TOOLS -tp TOOL_PREDICTIONS -ref REFERENCE_ANNOTATION
                             [-rt REFERENCE_TOOL] [-o OUTNAME] [-v {True,False}]
-ORForise v1.4.2: Aggregate-Compare Run Parameters.
+ORForise v1.4.3: Aggregate-Compare Run Parameters.
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -266,7 +267,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: GFF_Adder.py [-h] -dna GENOME_DNA -ref REFERENCE_ANNOTATION -at ADDITIONAL_TOOL -add ADDITIONAL_ANNOTATION -o
                     OUTPUT_FILE [-rt REFERENCE_TOOL] [-gi GENE_IDENT] [-gene_ident GENE_IDENT] [-olap OVERLAP]
-ORForise v1.4.2: GFF-Adder Run Parameters.
+ORForise v1.4.3: GFF-Adder Run Parameters.
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -328,7 +329,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: GFF_Intersector.py [-h] -dna GENOME_DNA -ref REFERENCE_ANNOTATION -at ADDITIONAL_TOOL -add
                           ADDITIONAL_ANNOTATION -o OUTPUT_FILE [-rt REFERENCE_TOOL] [-gi GENE_IDENT] [-cov COVERAGE]
-ORForise v1.4.2: GFF-Intersector Run Parameters.
+ORForise v1.4.3: GFF-Intersector Run Parameters.
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on

{orforise-1.4.2 → orforise-1.4.3}/README.md RENAMED Viewed

@@ -46,7 +46,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: Annotation_Compare.py [-h] -dna GENOME_DNA -ref REFERENCE_ANNOTATION -t TOOL -tp TOOL_PREDICTION
                              [-rt REFERENCE_TOOL] [-o OUTNAME] [-v {True,False}]
-ORForise v1.4.2: Annotatione-Compare Run Parameters.
+ORForise v1.4.3: Annotatione-Compare Run Parameters.
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -96,7 +96,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: Aggregate_Compare.py [-h] -dna GENOME_DNA -t TOOLS -tp TOOL_PREDICTIONS -ref REFERENCE_ANNOTATION
                             [-rt REFERENCE_TOOL] [-o OUTNAME] [-v {True,False}]
-ORForise v1.4.2: Aggregate-Compare Run Parameters.
+ORForise v1.4.3: Aggregate-Compare Run Parameters.
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -250,7 +250,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: GFF_Adder.py [-h] -dna GENOME_DNA -ref REFERENCE_ANNOTATION -at ADDITIONAL_TOOL -add ADDITIONAL_ANNOTATION -o
                     OUTPUT_FILE [-rt REFERENCE_TOOL] [-gi GENE_IDENT] [-gene_ident GENE_IDENT] [-olap OVERLAP]
-ORForise v1.4.2: GFF-Adder Run Parameters.
+ORForise v1.4.3: GFF-Adder Run Parameters.
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -312,7 +312,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: GFF_Intersector.py [-h] -dna GENOME_DNA -ref REFERENCE_ANNOTATION -at ADDITIONAL_TOOL -add
                           ADDITIONAL_ANNOTATION -o OUTPUT_FILE [-rt REFERENCE_TOOL] [-gi GENE_IDENT] [-cov COVERAGE]
-ORForise v1.4.2: GFF-Intersector Run Parameters.
+ORForise v1.4.3: GFF-Intersector Run Parameters.
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on

{orforise-1.4.2 → orforise-1.4.3}/setup.cfg RENAMED Viewed

@@ -1,6 +1,6 @@
 [metadata]
 name = ORForise
-version = 1.4.2
+version = 1.4.3
 author = Nicholas Dimonaco
 author_email = nicholas@dimonaco.co.uk
 description = ORForise - Platform for analysing and comparing Prokaryote CoDing Sequence (CDS) Gene Predictions.

{orforise-1.4.2 → orforise-1.4.3}/src/ORForise/Comparator.py RENAMED Viewed

@@ -230,7 +230,8 @@ def candidate_ORF_Selection(gene_Set,
     for c_Pos, c_ORF_Details in candidate_ORFs.items():
         o_Start = int(c_Pos.split(',')[0])
         o_Stop = int(c_Pos.split(',')[1])
-        coverage = c_ORF_Details[3]
+        # Below is not a long term fix
+        coverage = c_ORF_Details[-1]
         orf_Set = set(range(o_Start, o_Stop + 1))
         if coverage > current_Coverage:
             current_Coverage = coverage

{orforise-1.4.2 → orforise-1.4.3}/src/ORForise/utils.py RENAMED Viewed

@@ -4,7 +4,7 @@ import collections
 # Constants
 SHORT_ORF_LENGTH = 300
 MIN_COVERAGE = 75
-ORForise_Version = 'v1.4.2'
+ORForise_Version = 'v1.4.3'
 def revCompIterative(watson):  # Gets Reverse Complement

{orforise-1.4.2 → orforise-1.4.3}/src/ORForise.egg-info/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: ORForise
-Version: 1.4.2
+Version: 1.4.3
 Summary: ORForise - Platform for analysing and comparing Prokaryote CoDing Sequence (CDS) Gene Predictions.
 Home-page: https://github.com/NickJD/ORForise
 Author: Nicholas Dimonaco
@@ -13,6 +13,7 @@ Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
+Dynamic: license-file
 # ORForise - Prokaryote Genome Annotation Analysis and Comparison Platform
 ## Published in Bioinformatics :   https://academic.oup.com/bioinformatics/article/38/5/1198/6454948
@@ -62,7 +63,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: Annotation_Compare.py [-h] -dna GENOME_DNA -ref REFERENCE_ANNOTATION -t TOOL -tp TOOL_PREDICTION
                              [-rt REFERENCE_TOOL] [-o OUTNAME] [-v {True,False}]
-ORForise v1.4.2: Annotatione-Compare Run Parameters.
+ORForise v1.4.3: Annotatione-Compare Run Parameters.
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -112,7 +113,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: Aggregate_Compare.py [-h] -dna GENOME_DNA -t TOOLS -tp TOOL_PREDICTIONS -ref REFERENCE_ANNOTATION
                             [-rt REFERENCE_TOOL] [-o OUTNAME] [-v {True,False}]
-ORForise v1.4.2: Aggregate-Compare Run Parameters.
+ORForise v1.4.3: Aggregate-Compare Run Parameters.
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -266,7 +267,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: GFF_Adder.py [-h] -dna GENOME_DNA -ref REFERENCE_ANNOTATION -at ADDITIONAL_TOOL -add ADDITIONAL_ANNOTATION -o
                     OUTPUT_FILE [-rt REFERENCE_TOOL] [-gi GENE_IDENT] [-gene_ident GENE_IDENT] [-olap OVERLAP]
-ORForise v1.4.2: GFF-Adder Run Parameters.
+ORForise v1.4.3: GFF-Adder Run Parameters.
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -328,7 +329,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: GFF_Intersector.py [-h] -dna GENOME_DNA -ref REFERENCE_ANNOTATION -at ADDITIONAL_TOOL -add
                           ADDITIONAL_ANNOTATION -o OUTPUT_FILE [-rt REFERENCE_TOOL] [-gi GENE_IDENT] [-cov COVERAGE]
-ORForise v1.4.2: GFF-Intersector Run Parameters.
+ORForise v1.4.3: GFF-Intersector Run Parameters.
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on