ORForise 1.4.2__py3-none-any.whl → 1.4.3__py3-none-any.whl

ORForise/Comparator.py

@@ -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/utils.py

@@ -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.dist-info → orforise-1.4.3.dist-info}/METADATA

@@ -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.dist-info → orforise-1.4.3.dist-info}/RECORD

@@ -1,11 +1,11 @@
 ORForise/Aggregate_Compare.py,sha256=cY0PdA_SnywPcqwPomXmEHaZ6OUDS9k_QeLtXnewjiA,10648
 ORForise/Annotation_Compare.py,sha256=6y_RiJg0q9g4Bcwy8Lxi5gSDkMLwm6uYJG2evxnKAhU,10228
-ORForise/Comparator.py,sha256=AEpZQ8IURgYrWLKRRQEBUp3nFWKsxTb0f3O6XdHfRAc,45041
+ORForise/Comparator.py,sha256=kGRn7_CYKULI5xV7IH2RpRIP0xpj_OfPxO4iGdLBnKQ,45081
 ORForise/GFF_Adder.py,sha256=-BlF6DQWcbhyYT88M0ZkoaWA2YDDxsby-7jksfeJN1Q,14057
 ORForise/GFF_Intersector.py,sha256=EcDKyJr_47066kma2CguMf3uwzB2tYomPDFjmoX8IoU,9900
 ORForise/StORForise.py,sha256=2QU6q3wPK6iqtyKg2jEVwFTB4bSymyc-mSpk7T8yNaY,5431
 ORForise/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/utils.py,sha256=BeYOERE3UfBXpazmLDOQDzXj-bGbXd9oooWyPC1Ts1s,1099
+ORForise/utils.py,sha256=39OeKjNTRkyoEqxsTCrcwucbrkKOq3CTd6wEm1p7MOA,1099
 ORForise/ORForise_Analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/ORForise_Analysis/cds_checker.py,sha256=x838-PDd8HxZ3uhfW7wPzaJdiVwomNaYOZzMe-09f_0,2643
 ORForise/ORForise_Analysis/gene_Lenghts.py,sha256=eDmJqVjBJYkBMuLr4s4XDA-E-fv0eEITpWAPySOynow,939
@@ -60,9 +60,9 @@ ORForise/Tools/StORF_Undetected/unvitiated_Genes/__init__.py,sha256=47DEQpj8HBSa
 ORForise/Tools/StORF_Undetected/unvitiated_Genes/unvitiated_Missed_Genes.py,sha256=notWaFx7AG8BZjBhnGuSyitxa1cRK_7rygOPp9keGfM,1863
 ORForise/Tools/TransDecoder/TransDecoder.py,sha256=utnL52il6BGbbBxoizYPnY1qwBGeslYDCa5xU9RGWPg,1384
 ORForise/Tools/TransDecoder/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise-1.4.2.dist-info/LICENSE,sha256=eAL1bBUjSMCdvudcn9E3sbujCBCa839cqXxauONDbSU,32476
-ORForise-1.4.2.dist-info/METADATA,sha256=kv8pem6rn0yrjNtc9Gkm-RZvWsafVx866aCjUIdti5c,36457
-ORForise-1.4.2.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-ORForise-1.4.2.dist-info/entry_points.txt,sha256=ss2cbLmljRmLIeZ3t48p_06NuQuRiKeA11IOUYg_uiY,246
-ORForise-1.4.2.dist-info/top_level.txt,sha256=7kmFicUFY65FJmioc0cpZtXVz93V7KSKvZVWpGz5Hyk,9
-ORForise-1.4.2.dist-info/RECORD,,
+orforise-1.4.3.dist-info/licenses/LICENSE,sha256=eAL1bBUjSMCdvudcn9E3sbujCBCa839cqXxauONDbSU,32476
+orforise-1.4.3.dist-info/METADATA,sha256=7JZBTCxggexbQcUsHTNdZBKUQ1laUnINv0vIGq_6k0k,36479
+orforise-1.4.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orforise-1.4.3.dist-info/entry_points.txt,sha256=ss2cbLmljRmLIeZ3t48p_06NuQuRiKeA11IOUYg_uiY,246
+orforise-1.4.3.dist-info/top_level.txt,sha256=7kmFicUFY65FJmioc0cpZtXVz93V7KSKvZVWpGz5Hyk,9
+orforise-1.4.3.dist-info/RECORD,,

{ORForise-1.4.2.dist-info → orforise-1.4.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any