ORForise 1.6.2__tar.gz → 1.6.3__tar.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 (77) hide show
  1. {orforise-1.6.2 → orforise-1.6.3}/PKG-INFO +7 -7
  2. {orforise-1.6.2 → orforise-1.6.3}/README.md +6 -6
  3. {orforise-1.6.2 → orforise-1.6.3}/pyproject.toml +1 -1
  4. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/StORF-Reporter/StORF-Reporter.py +2 -2
  5. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise.egg-info/PKG-INFO +7 -7
  6. {orforise-1.6.2 → orforise-1.6.3}/LICENSE +0 -0
  7. {orforise-1.6.2 → orforise-1.6.3}/setup.cfg +0 -0
  8. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Aggregate_Compare.py +0 -0
  9. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Annotation_Compare.py +0 -0
  10. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Annotation_Intersector.py +0 -0
  11. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Aux/StORF_Undetected/Completely_Undetected/Completey_Undetected.py +0 -0
  12. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Aux/StORF_Undetected/Completely_Undetected/__init__.py +0 -0
  13. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Aux/StORF_Undetected/StORF_Undetected.py +0 -0
  14. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Aux/StORF_Undetected/__init__.py +0 -0
  15. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Aux/StORF_Undetected/unvitiated_Genes/__init__.py +0 -0
  16. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Aux/StORF_Undetected/unvitiated_Genes/unvitiated_Missed_Genes.py +0 -0
  17. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Aux/TabToGFF/TabToGFF.py +0 -0
  18. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Aux/TabToGFF/__init__.py +0 -0
  19. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Aux/__init__.py +0 -0
  20. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Comparator.py +0 -0
  21. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Convert_To_GFF.py +0 -0
  22. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/GFF_Adder.py +0 -0
  23. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/List_Tools.py +0 -0
  24. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/ORForise_Analysis/__init__.py +0 -0
  25. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/ORForise_Analysis/cds_checker.py +0 -0
  26. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/ORForise_Analysis/gene_Lenghts.py +0 -0
  27. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/ORForise_Analysis/genome_Metrics.py +0 -0
  28. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/ORForise_Analysis/hypothetical_gene_predictions.py +0 -0
  29. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/ORForise_Analysis/missed_Gene_Metrics.py +0 -0
  30. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/ORForise_Analysis/parital_Match_Analysis.py +0 -0
  31. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/ORForise_Analysis/result_File_Analysis.py +0 -0
  32. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/ORForise_Analysis/start_Codon_Substitution.py +0 -0
  33. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/StORForise.py +0 -0
  34. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/Augustus/Augustus.py +0 -0
  35. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/Augustus/__init__.py +0 -0
  36. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/Balrog/Balrog.py +0 -0
  37. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/Balrog/__init__.py +0 -0
  38. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/EasyGene/EasyGene.py +0 -0
  39. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/EasyGene/__init__.py +0 -0
  40. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/FGENESB/FGENESB.py +0 -0
  41. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/FGENESB/__init__.py +0 -0
  42. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/FragGeneScan/FragGeneScan.py +0 -0
  43. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/FragGeneScan/__init__.py +0 -0
  44. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GFF/GFF.py +0 -0
  45. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GFF/__init__.py +0 -0
  46. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GLIMMER3/GLIMMER3.py +0 -0
  47. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GLIMMER3/__init__.py +0 -0
  48. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GeneMark/GeneMark.py +0 -0
  49. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GeneMark/__init__.py +0 -0
  50. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GeneMarkHA/GeneMarkHA.py +0 -0
  51. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GeneMarkHA/__init__.py +0 -0
  52. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GeneMarkHMM/GeneMarkHMM.py +0 -0
  53. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GeneMarkHMM/__init__.py +0 -0
  54. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GeneMarkS/GeneMarkS.py +0 -0
  55. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GeneMarkS/__init__.py +0 -0
  56. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GeneMarkS2/GeneMarkS2.py +0 -0
  57. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/GeneMarkS2/__init__.py +0 -0
  58. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/MetaGene/MetaGene.py +0 -0
  59. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/MetaGene/__init__.py +0 -0
  60. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/MetaGeneAnnotator/MetaGeneAnnotator.py +0 -0
  61. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/MetaGeneAnnotator/__init__.py +0 -0
  62. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/MetaGeneMark/MetaGeneMark.py +0 -0
  63. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/MetaGeneMark/__init__.py +0 -0
  64. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/Prodigal/Prodigal.py +0 -0
  65. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/Prodigal/__init__.py +0 -0
  66. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/Prokka/Prokka.py +0 -0
  67. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/Prokka/__init__.py +0 -0
  68. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/StORF-Reporter/__init__.py +0 -0
  69. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/TransDecoder/TransDecoder.py +0 -0
  70. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/TransDecoder/__init__.py +0 -0
  71. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/__init__.py +0 -0
  72. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/__init__.py +0 -0
  73. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise/utils.py +0 -0
  74. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise.egg-info/SOURCES.txt +0 -0
  75. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise.egg-info/dependency_links.txt +0 -0
  76. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise.egg-info/entry_points.txt +0 -0
  77. {orforise-1.6.2 → orforise-1.6.3}/src/ORForise.egg-info/top_level.txt +0 -0
{orforise-1.6.2 → orforise-1.6.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: ORForise
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- Version: 1.6.2
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+ Version: 1.6.3
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  Summary: ORForise - A platform for analysing and comparing genome annotations.
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  Author-email: Nicholas Dimonaco <nicholas@dimonaco.co.uk>
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  License: GNU GENERAL PUBLIC LICENSE
@@ -662,7 +662,7 @@ Example output files from ```Annotation-Compare```, ```Aggregate-Compare```, ```
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  For Help: ```Annotation-Compare -h ```
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  ```python
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- ORForise v1.6.2: Annotatione-Compare Run Parameters.
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+ ORForise v1.6.3: Annotatione-Compare Run Parameters.
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  Required Arguments:
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  -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.
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  For Help: ```Aggregate-Compare -h ```
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  ```python
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- ORForise v1.6.2: Aggregate-Compare Run Parameters.
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+ ORForise v1.6.3: Aggregate-Compare Run Parameters.
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  Required Arguments:
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  -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).
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  For Help: ```GFF-Adder -h ```
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  ```python
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- ORForise v1.6.2: GFF-Adder Run Parameters.
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+ ORForise v1.6.3: GFF-Adder Run Parameters.
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  Required Arguments:
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  -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
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  [-cov COVERAGE] [--report-discordance]
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  [--report-discordance-file REPORT_DISCORDANCE_FILE]
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871
- ORForise v1.6.2: Annotation-Intersector Run Parameters
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+ ORForise v1.6.3: Annotation-Intersector Run Parameters
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  options:
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  -h, --help show this help message and exit
@@ -947,7 +947,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
947
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  #####
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  usage: Convert_To_GFF.py [-h] [-dna GENOME_DNA] -i INPUT_ANNOTATION -fmt FORMAT -o OUTPUT_DIR [-gi GENE_IDENT] [--verbose]
949
949
 
950
- ORForise v1.6.2: Convert-To-GFF Run Parameters
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+ ORForise v1.6.3: Convert-To-GFF Run Parameters
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952
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  Required Arguments:
953
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  -dna GENOME_DNA Genome DNA file (.fa)
@@ -1026,7 +1026,7 @@ Defaults options were used.
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  **MetaGeneMark - Version '2020'** - http://exon.gatech.edu/meta_gmhmmp.cgi
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  GFF was chosen as output type.
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- **Prodigal - Version 2.6.3** - https://github.com/hyattpd/Prodigal
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+ **Prodigal (Includes Pyrodigal) - Version 2.6.3** - https://github.com/hyattpd/Prodigal
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  GFF was chosen as output type.
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  **TransDecoder - Version 5.5.0** - https://github.com/TransDecoder/TransDecoder/wiki
{orforise-1.6.2 → orforise-1.6.3}/README.md RENAMED
@@ -21,7 +21,7 @@ Example output files from ```Annotation-Compare```, ```Aggregate-Compare```, ```
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  For Help: ```Annotation-Compare -h ```
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  ```python
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- ORForise v1.6.2: Annotatione-Compare Run Parameters.
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+ ORForise v1.6.3: Annotatione-Compare Run Parameters.
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  Required Arguments:
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  -dna GENOME_DNA Genome DNA file (.fa) which both annotations are based on
@@ -89,7 +89,7 @@ ORForise can be used as the example below.
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  For Help: ```Aggregate-Compare -h ```
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  ```python
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- ORForise v1.6.2: Aggregate-Compare Run Parameters.
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+ ORForise v1.6.3: Aggregate-Compare Run Parameters.
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  Required Arguments:
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  -dna GENOME_DNA Genome DNA file (.fa) which both annotations are based on
@@ -170,7 +170,7 @@ GFF-Adder combines two existing annotations (GFF or other tool formats).
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  For Help: ```GFF-Adder -h ```
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  ```python
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- ORForise v1.6.2: GFF-Adder Run Parameters.
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+ ORForise v1.6.3: GFF-Adder Run Parameters.
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  Required Arguments:
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  -dna GENOME_DNA Genome DNA file (.fa) which both annotations are based on
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  [-cov COVERAGE] [--report-discordance]
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  [--report-discordance-file REPORT_DISCORDANCE_FILE]
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- ORForise v1.6.2: Annotation-Intersector Run Parameters
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+ ORForise v1.6.3: Annotation-Intersector Run Parameters
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  options:
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  -h, --help show this help message and exit
@@ -306,7 +306,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
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  #####
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  usage: Convert_To_GFF.py [-h] [-dna GENOME_DNA] -i INPUT_ANNOTATION -fmt FORMAT -o OUTPUT_DIR [-gi GENE_IDENT] [--verbose]
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- ORForise v1.6.2: Convert-To-GFF Run Parameters
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+ ORForise v1.6.3: Convert-To-GFF Run Parameters
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  Required Arguments:
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  -dna GENOME_DNA Genome DNA file (.fa)
@@ -385,7 +385,7 @@ Defaults options were used.
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  **MetaGeneMark - Version '2020'** - http://exon.gatech.edu/meta_gmhmmp.cgi
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  GFF was chosen as output type.
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- **Prodigal - Version 2.6.3** - https://github.com/hyattpd/Prodigal
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+ **Prodigal (Includes Pyrodigal) - Version 2.6.3** - https://github.com/hyattpd/Prodigal
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  GFF was chosen as output type.
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  **TransDecoder - Version 5.5.0** - https://github.com/TransDecoder/TransDecoder/wiki
{orforise-1.6.2 → orforise-1.6.3}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "ORForise"
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- version = "1.6.2"
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+ version = "1.6.3"
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  authors = [
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  {name = "Nicholas Dimonaco", email = "nicholas@dimonaco.co.uk"}
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  ]
{orforise-1.6.2 → orforise-1.6.3}/src/ORForise/Tools/StORF-Reporter/StORF-Reporter.py RENAMED
@@ -13,8 +13,8 @@ def StORF_Reporter(*args):
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  dna_regions = args[1]
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  if not dna_regions: # This triggers if dna_regions is an empty dict (GFF_Intersect passed nothing)
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  dna_regions = collections.OrderedDict()
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- with open(tool_pred, 'r') as StORF-Reporter_input:
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- for line in StORF-Reporter_input:
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+ with open(tool_pred, 'r') as StORF_Reporter_input:
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+ for line in StORF_Reporter_input:
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  line = line.split()
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  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:
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  dna_regions[line[0]] = [] # Placeholder for genome sequence
{orforise-1.6.2 → orforise-1.6.3}/src/ORForise.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
2
2
  Name: ORForise
3
- Version: 1.6.2
3
+ Version: 1.6.3
4
4
  Summary: ORForise - A platform for analysing and comparing genome annotations.
5
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  Author-email: Nicholas Dimonaco <nicholas@dimonaco.co.uk>
6
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  License: GNU GENERAL PUBLIC LICENSE
@@ -662,7 +662,7 @@ Example output files from ```Annotation-Compare```, ```Aggregate-Compare```, ```
662
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  For Help: ```Annotation-Compare -h ```
663
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664
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  ```python
665
- ORForise v1.6.2: Annotatione-Compare Run Parameters.
665
+ ORForise v1.6.3: Annotatione-Compare Run Parameters.
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667
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  Required Arguments:
668
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  -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.
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  For Help: ```Aggregate-Compare -h ```
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  ```python
733
- ORForise v1.6.2: Aggregate-Compare Run Parameters.
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+ ORForise v1.6.3: Aggregate-Compare Run Parameters.
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735
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  Required Arguments:
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  -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).
811
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  For Help: ```GFF-Adder -h ```
812
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  ```python
814
- ORForise v1.6.2: GFF-Adder Run Parameters.
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+ ORForise v1.6.3: GFF-Adder Run Parameters.
815
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816
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  Required Arguments:
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  -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
868
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  [-cov COVERAGE] [--report-discordance]
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  [--report-discordance-file REPORT_DISCORDANCE_FILE]
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- ORForise v1.6.2: Annotation-Intersector Run Parameters
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+ ORForise v1.6.3: Annotation-Intersector Run Parameters
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  options:
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  -h, --help show this help message and exit
@@ -947,7 +947,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
947
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  #####
948
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  usage: Convert_To_GFF.py [-h] [-dna GENOME_DNA] -i INPUT_ANNOTATION -fmt FORMAT -o OUTPUT_DIR [-gi GENE_IDENT] [--verbose]
949
949
 
950
- ORForise v1.6.2: Convert-To-GFF Run Parameters
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+ ORForise v1.6.3: Convert-To-GFF Run Parameters
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951
 
952
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  Required Arguments:
953
953
  -dna GENOME_DNA Genome DNA file (.fa)
@@ -1026,7 +1026,7 @@ Defaults options were used.
1026
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  **MetaGeneMark - Version '2020'** - http://exon.gatech.edu/meta_gmhmmp.cgi
1027
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  GFF was chosen as output type.
1028
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1029
- **Prodigal - Version 2.6.3** - https://github.com/hyattpd/Prodigal
1029
+ **Prodigal (Includes Pyrodigal) - Version 2.6.3** - https://github.com/hyattpd/Prodigal
1030
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  GFF was chosen as output type.
1031
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  **TransDecoder - Version 5.5.0** - https://github.com/TransDecoder/TransDecoder/wiki
{orforise-1.6.2 → orforise-1.6.3}/LICENSE RENAMED
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{orforise-1.6.2 → orforise-1.6.3}/setup.cfg RENAMED
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{orforise-1.6.2 → orforise-1.6.3}/src/ORForise/utils.py RENAMED
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