ORForise 1.6.2__py3-none-any.whl → 1.6.3__py3-none-any.whl

ORForise/Tools/StORF-Reporter/StORF-Reporter.py

@@ -13,8 +13,8 @@ def StORF_Reporter(*args):
     dna_regions = args[1]
     if not dna_regions: # This triggers if dna_regions is an empty dict (GFF_Intersect passed nothing)
         dna_regions = collections.OrderedDict()
-        with open(tool_pred, 'r') as StORF-Reporter_input:
-            for line in StORF-Reporter_input:
+        with open(tool_pred, 'r') as StORF_Reporter_input:
+            for line in StORF_Reporter_input:
                 line = line.split()
                 if 'StORF-Reporter' in line[1] or 'StoRF_Reporter' in line[1]  or 'StORF' in line[1] or 'StORF-Reporter' in line[1] and line[0] not in dna_regions:
                     dna_regions[line[0]] = []  # Placeholder for genome sequence

{orforise-1.6.2.dist-info → orforise-1.6.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ORForise
-Version: 1.6.2
+Version: 1.6.3
 Summary: ORForise - A platform for analysing and comparing genome annotations.
 Author-email: Nicholas Dimonaco <nicholas@dimonaco.co.uk>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -662,7 +662,7 @@ Example output files from ```Annotation-Compare```, ```Aggregate-Compare```, ```
 For Help: ```Annotation-Compare -h ```
 
 ```python
-ORForise v1.6.2: Annotatione-Compare Run Parameters.
+ORForise v1.6.3: Annotatione-Compare Run Parameters.
 
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -730,7 +730,7 @@ ORForise can be used as the example below.
 For Help: ```Aggregate-Compare -h ```
 
 ```python
-ORForise v1.6.2: Aggregate-Compare Run Parameters.
+ORForise v1.6.3: Aggregate-Compare Run Parameters.
 
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -811,7 +811,7 @@ GFF-Adder combines two existing annotations (GFF or other tool formats).
 For Help: ```GFF-Adder -h ```
 
 ```python
-ORForise v1.6.2: GFF-Adder Run Parameters.
+ORForise v1.6.3: GFF-Adder Run Parameters.
 
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -868,7 +868,7 @@ usage: Annotation_Intersector.py [-h] -ref REFERENCE_ANNOTATION -at
                                  [-cov COVERAGE] [--report-discordance]
                                  [--report-discordance-file REPORT_DISCORDANCE_FILE]
 
-ORForise v1.6.2: Annotation-Intersector Run Parameters
+ORForise v1.6.3: Annotation-Intersector Run Parameters
 
 options:
   -h, --help            show this help message and exit
@@ -947,7 +947,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 #####
 usage: Convert_To_GFF.py [-h] [-dna GENOME_DNA] -i INPUT_ANNOTATION -fmt FORMAT -o OUTPUT_DIR [-gi GENE_IDENT] [--verbose]
 
-ORForise v1.6.2: Convert-To-GFF Run Parameters
+ORForise v1.6.3: Convert-To-GFF Run Parameters
 
 Required Arguments:
   -dna GENOME_DNA      Genome DNA file (.fa)
@@ -1026,7 +1026,7 @@ Defaults options were used.
 **MetaGeneMark - Version '2020'** - http://exon.gatech.edu/meta_gmhmmp.cgi  
 GFF was chosen as output type.
 
-**Prodigal - Version 2.6.3** - https://github.com/hyattpd/Prodigal  
+**Prodigal (Includes Pyrodigal) - Version 2.6.3** - https://github.com/hyattpd/Prodigal  
 GFF was chosen as output type.
 
 **TransDecoder - Version 5.5.0** - https://github.com/TransDecoder/TransDecoder/wiki  

{orforise-1.6.2.dist-info → orforise-1.6.3.dist-info}/RECORD

@@ -61,13 +61,13 @@ ORForise/Tools/Prodigal/Prodigal.py,sha256=1KVkTL3gHp8iSNFt_CvPnLZUr66x1AfE0ZKxo
 ORForise/Tools/Prodigal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/Tools/Prokka/Prokka.py,sha256=Kcl1ocVj6hPOfEEwf8bBAWhzWX_XAe55kwNUeM8EUKg,2468
 ORForise/Tools/Prokka/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/StORF-Reporter/StORF-Reporter.py,sha256=mbpoCuzVDVVFZgSd3TDzgjbp-JsrxIDB-DL2qjQwq-U,2647
+ORForise/Tools/StORF-Reporter/StORF-Reporter.py,sha256=BQpFfpXtcNC4C_P4Bk5IZZ9__Xy2VNcbh7zzSDnrNOE,2647
 ORForise/Tools/StORF-Reporter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/Tools/TransDecoder/TransDecoder.py,sha256=l9y4OFxhSdPRBhUprs0yt2fxtSwyNCOv7oKO-aTvpDk,2381
 ORForise/Tools/TransDecoder/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-orforise-1.6.2.dist-info/licenses/LICENSE,sha256=eAL1bBUjSMCdvudcn9E3sbujCBCa839cqXxauONDbSU,32476
-orforise-1.6.2.dist-info/METADATA,sha256=xqVn0TcMdZkrKeyVbjENidxxhN6PKuHZkb0WC2nx5pE,59554
-orforise-1.6.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-orforise-1.6.2.dist-info/entry_points.txt,sha256=_HaBzKQFXCkxHIIgBH_XIOng92-GWJ5FC29LmNaSpR0,670
-orforise-1.6.2.dist-info/top_level.txt,sha256=7kmFicUFY65FJmioc0cpZtXVz93V7KSKvZVWpGz5Hyk,9
-orforise-1.6.2.dist-info/RECORD,,
+orforise-1.6.3.dist-info/licenses/LICENSE,sha256=eAL1bBUjSMCdvudcn9E3sbujCBCa839cqXxauONDbSU,32476
+orforise-1.6.3.dist-info/METADATA,sha256=09DL7OYqHk_CnvgvGF1676j6Vf-RdTDXInf0fX8cZro,59575
+orforise-1.6.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orforise-1.6.3.dist-info/entry_points.txt,sha256=_HaBzKQFXCkxHIIgBH_XIOng92-GWJ5FC29LmNaSpR0,670
+orforise-1.6.3.dist-info/top_level.txt,sha256=7kmFicUFY65FJmioc0cpZtXVz93V7KSKvZVWpGz5Hyk,9
+orforise-1.6.3.dist-info/RECORD,,