PyamilySeq 1.3.1__tar.gz → 1.3.2__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 (27) hide show
  1. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/PKG-INFO +9 -9
  2. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/README.md +8 -8
  3. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/pyproject.toml +5 -5
  4. pyamilyseq-1.3.2/src/PyamilySeq/constants.py +2 -0
  5. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq.egg-info/PKG-INFO +9 -9
  6. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq.egg-info/SOURCES.txt +2 -3
  7. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq.egg-info/entry_points.txt +4 -4
  8. pyamilyseq-1.3.1/src/PyamilySeq/constants.py +0 -2
  9. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/LICENSE +0 -0
  10. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/setup.cfg +0 -0
  11. /pyamilyseq-1.3.1/src/PyamilySeq/Cluster_Compare.py → /pyamilyseq-1.3.2/src/PyamilySeq/Group_Compare.py +0 -0
  12. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/Group_Extractor.py +0 -0
  13. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/Group_Sizes.py +0 -0
  14. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/Group_Splitter.py +0 -0
  15. /pyamilyseq-1.3.1/src/PyamilySeq/Cluster_Summary.py → /pyamilyseq-1.3.2/src/PyamilySeq/Group_Summary.py +0 -0
  16. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/PyamilySeq.py +0 -0
  17. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/PyamilySeq_Genus.py +0 -0
  18. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/PyamilySeq_Species.py +0 -0
  19. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/Seq_Combiner.py +0 -0
  20. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/Seq_Extractor.py +0 -0
  21. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/Seq_Finder.py +0 -0
  22. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/__init__.py +0 -0
  23. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/clusterings.py +0 -0
  24. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/config.py +0 -0
  25. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq/utils.py +0 -0
  26. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq.egg-info/dependency_links.txt +0 -0
  27. {pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq.egg-info/top_level.txt +0 -0
{pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: PyamilySeq
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- Version: 1.3.1
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+ Version: 1.3.2
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  Summary: PyamilySeq - A a tool to investigate sequence-based gene groups identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.
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  Author-email: Nicholas Dimonaco <nicholas@dimonaco.co.uk>
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  License: GNU GENERAL PUBLIC LICENSE
@@ -720,7 +720,7 @@ To update to the newest version add '-U' to end of the pip install command.
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  ```commandline
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  usage: PyamilySeq.py [-h] {Full,Partial} ...
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- PyamilySeq v1.3.1: A tool for gene clustering and analysis.
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+ PyamilySeq v1.3.2: A tool for gene clustering and analysis.
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  positional arguments:
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  {Full,Partial} Choose a mode: 'Full' or 'Partial'.
@@ -750,7 +750,7 @@ Escherichia_coli_110957|ENSB_TIZS9kbTvShDvyX Escherichia_coli_110957|ENSB_TIZS9k
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  ```
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  ### Example output:
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  ```
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- Running PyamilySeq v1.3.1
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+ Running PyamilySeq v1.3.2
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  Calculating Groups
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  Number of Genomes: 10
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  Gene Groups
@@ -895,7 +895,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split_gff .gff3 -output_dir
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  ```
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  usage: Seq_Combiner.py [-h] -input_dir INPUT_DIR -input_type {separate,combined,fasta} [-name_split_gff NAME_SPLIT_GFF] [-name_split_fasta NAME_SPLIT_FASTA] -output_dir OUTPUT_DIR -output_name OUTPUT_FILE [-gene_ident GENE_IDENT] [-translate] [-v]
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- PyamilySeq v1.3.1: Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.
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+ PyamilySeq v1.3.2: Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.
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  options:
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  -h, --help show this help message and exit
@@ -938,7 +938,7 @@ usage: Group_Splitter.py [-h] -input_fasta INPUT_FASTA -sequence_type {AA,DNA}
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  [-M CLUSTERING_MEMORY] [-no_delete_temp_files]
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  [-verbose] [-v]
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- PyamilySeq v1.3.1: Group-Splitter - A tool to split multi-copy gene groups
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+ PyamilySeq v1.3.2: Group-Splitter - A tool to split multi-copy gene groups
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  identified by PyamilySeq.
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  options:
@@ -981,17 +981,17 @@ Misc Parameters:
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  ```
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- ## Cluster-Summary menu: This tool can be used to summarise CD-HIT .clstr files:
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+ ## Group-Summary menu: This tool can be used to summarise CD-HIT .clstr files:
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  ### Example:
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  ```bash
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- Cluster-Summary -genome_num 10 -input_clstr .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80.clstr -output_tsv .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80_Summary.tsv
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+ Group-Summary -genome_num 10 -input_clstr .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80.clstr -output_tsv .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80_Summary.tsv
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  ```
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- ### Cluster-Summary Menu:
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+ ### Group-Summary Menu:
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  ```
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  usage: Cluster_Summary.py [-h] -input_clstr INPUT_CLSTR -output OUTPUT -genome_num GENOME_NUM
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  [-output_dir OUTPUT_DIR] [-verbose] [-v]
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- PyamilySeq v1.3.1: Cluster-Summary - A tool to summarise CD-HIT clustering files.
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+ PyamilySeq v1.3.2: Group-Summary - A tool to summarise CD-HIT clustering files.
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  options:
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  -h, --help show this help message and exit
{pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/README.md RENAMED
@@ -29,7 +29,7 @@ To update to the newest version add '-U' to end of the pip install command.
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  ```commandline
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  usage: PyamilySeq.py [-h] {Full,Partial} ...
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- PyamilySeq v1.3.1: A tool for gene clustering and analysis.
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+ PyamilySeq v1.3.2: A tool for gene clustering and analysis.
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  positional arguments:
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  {Full,Partial} Choose a mode: 'Full' or 'Partial'.
@@ -59,7 +59,7 @@ Escherichia_coli_110957|ENSB_TIZS9kbTvShDvyX Escherichia_coli_110957|ENSB_TIZS9k
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  ```
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  ### Example output:
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  ```
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- Running PyamilySeq v1.3.1
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+ Running PyamilySeq v1.3.2
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  Calculating Groups
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  Number of Genomes: 10
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  Gene Groups
@@ -204,7 +204,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split_gff .gff3 -output_dir
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  ```
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  usage: Seq_Combiner.py [-h] -input_dir INPUT_DIR -input_type {separate,combined,fasta} [-name_split_gff NAME_SPLIT_GFF] [-name_split_fasta NAME_SPLIT_FASTA] -output_dir OUTPUT_DIR -output_name OUTPUT_FILE [-gene_ident GENE_IDENT] [-translate] [-v]
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- PyamilySeq v1.3.1: Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.
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+ PyamilySeq v1.3.2: Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.
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  options:
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  -h, --help show this help message and exit
@@ -247,7 +247,7 @@ usage: Group_Splitter.py [-h] -input_fasta INPUT_FASTA -sequence_type {AA,DNA}
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  [-M CLUSTERING_MEMORY] [-no_delete_temp_files]
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  [-verbose] [-v]
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- PyamilySeq v1.3.1: Group-Splitter - A tool to split multi-copy gene groups
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+ PyamilySeq v1.3.2: Group-Splitter - A tool to split multi-copy gene groups
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  identified by PyamilySeq.
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  options:
@@ -290,17 +290,17 @@ Misc Parameters:
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  ```
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- ## Cluster-Summary menu: This tool can be used to summarise CD-HIT .clstr files:
293
+ ## Group-Summary menu: This tool can be used to summarise CD-HIT .clstr files:
294
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  ### Example:
295
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  ```bash
296
- Cluster-Summary -genome_num 10 -input_clstr .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80.clstr -output_tsv .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80_Summary.tsv
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+ Group-Summary -genome_num 10 -input_clstr .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80.clstr -output_tsv .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80_Summary.tsv
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  ```
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- ### Cluster-Summary Menu:
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+ ### Group-Summary Menu:
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  ```
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  usage: Cluster_Summary.py [-h] -input_clstr INPUT_CLSTR -output OUTPUT -genome_num GENOME_NUM
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  [-output_dir OUTPUT_DIR] [-verbose] [-v]
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- PyamilySeq v1.3.1: Cluster-Summary - A tool to summarise CD-HIT clustering files.
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+ PyamilySeq v1.3.2: Group-Summary - A tool to summarise CD-HIT clustering files.
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  options:
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  -h, --help show this help message and exit
{pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "PyamilySeq"
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- version = "1.3.1"
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+ version = "1.3.2"
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  authors = [
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  {name = "Nicholas Dimonaco", email = "nicholas@dimonaco.co.uk"}
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  ]
@@ -33,10 +33,10 @@ Homepage = "https://github.com/NickJD/PyamilySeq"
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  seq-combiner = "PyamilySeq.Seq_Combiner:main"
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  Group-Splitter = "PyamilySeq.Group_Splitter:main"
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  group-splitter = "PyamilySeq.Group_Splitter:main"
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- Cluster-Summary = "PyamilySeq.Cluster_Summary:main"
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- cluster-summary = "PyamilySeq.Cluster_Summary:main"
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- Cluster-Extractor = "PyamilySeq.Cluster_Extractor:main"
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- cluster-extractor = "PyamilySeq.Cluster_Extractor:main"
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+ Group-Extractor = "PyamilySeq.Group_Extractor:main"
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+ group-extractor = "PyamilySeq.Group_Extractor:main"
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+ Group-Summary = "PyamilySeq.Group_Summary:main"
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+ group-summary = "PyamilySeq.Group_Summary:main"
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  Seq-Finder = "PyamilySeq.Seq_Finder:main"
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  seq-finder = "PyamilySeq.Seq_Finder:main"
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  Seq-Extractor = "PyamilySeq.Seq_Extractor:main"
pyamilyseq-1.3.2/src/PyamilySeq/constants.py ADDED
@@ -0,0 +1,2 @@
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+ PyamilySeq_Version = 'v1.3.2'
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+
{pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
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  Metadata-Version: 2.4
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  Name: PyamilySeq
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- Version: 1.3.1
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+ Version: 1.3.2
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  Summary: PyamilySeq - A a tool to investigate sequence-based gene groups identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.
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  Author-email: Nicholas Dimonaco <nicholas@dimonaco.co.uk>
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  License: GNU GENERAL PUBLIC LICENSE
@@ -720,7 +720,7 @@ To update to the newest version add '-U' to end of the pip install command.
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  ```commandline
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  usage: PyamilySeq.py [-h] {Full,Partial} ...
722
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723
- PyamilySeq v1.3.1: A tool for gene clustering and analysis.
723
+ PyamilySeq v1.3.2: A tool for gene clustering and analysis.
724
724
 
725
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  positional arguments:
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  {Full,Partial} Choose a mode: 'Full' or 'Partial'.
@@ -750,7 +750,7 @@ Escherichia_coli_110957|ENSB_TIZS9kbTvShDvyX Escherichia_coli_110957|ENSB_TIZS9k
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  ```
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  ### Example output:
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  ```
753
- Running PyamilySeq v1.3.1
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+ Running PyamilySeq v1.3.2
754
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  Calculating Groups
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  Number of Genomes: 10
756
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  Gene Groups
@@ -895,7 +895,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split_gff .gff3 -output_dir
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  ```
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  usage: Seq_Combiner.py [-h] -input_dir INPUT_DIR -input_type {separate,combined,fasta} [-name_split_gff NAME_SPLIT_GFF] [-name_split_fasta NAME_SPLIT_FASTA] -output_dir OUTPUT_DIR -output_name OUTPUT_FILE [-gene_ident GENE_IDENT] [-translate] [-v]
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- PyamilySeq v1.3.1: Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.
898
+ PyamilySeq v1.3.2: Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.
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  options:
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  -h, --help show this help message and exit
@@ -938,7 +938,7 @@ usage: Group_Splitter.py [-h] -input_fasta INPUT_FASTA -sequence_type {AA,DNA}
938
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  [-M CLUSTERING_MEMORY] [-no_delete_temp_files]
939
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  [-verbose] [-v]
940
940
 
941
- PyamilySeq v1.3.1: Group-Splitter - A tool to split multi-copy gene groups
941
+ PyamilySeq v1.3.2: Group-Splitter - A tool to split multi-copy gene groups
942
942
  identified by PyamilySeq.
943
943
 
944
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  options:
@@ -981,17 +981,17 @@ Misc Parameters:
981
981
 
982
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  ```
983
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984
- ## Cluster-Summary menu: This tool can be used to summarise CD-HIT .clstr files:
984
+ ## Group-Summary menu: This tool can be used to summarise CD-HIT .clstr files:
985
985
  ### Example:
986
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  ```bash
987
- Cluster-Summary -genome_num 10 -input_clstr .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80.clstr -output_tsv .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80_Summary.tsv
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+ Group-Summary -genome_num 10 -input_clstr .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80.clstr -output_tsv .../test_data/species/E-coli/E-coli_extracted_pep_cd-hit_80_Summary.tsv
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  ```
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- ### Cluster-Summary Menu:
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+ ### Group-Summary Menu:
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  ```
991
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  usage: Cluster_Summary.py [-h] -input_clstr INPUT_CLSTR -output OUTPUT -genome_num GENOME_NUM
992
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  [-output_dir OUTPUT_DIR] [-verbose] [-v]
993
993
 
994
- PyamilySeq v1.3.1: Cluster-Summary - A tool to summarise CD-HIT clustering files.
994
+ PyamilySeq v1.3.2: Group-Summary - A tool to summarise CD-HIT clustering files.
995
995
 
996
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  options:
997
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  -h, --help show this help message and exit
{pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq.egg-info/SOURCES.txt RENAMED
@@ -1,12 +1,11 @@
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  LICENSE
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  README.md
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  pyproject.toml
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- src/PyamilySeq/Cluster_Compare.py
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- src/PyamilySeq/Cluster_Summary.py
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- src/PyamilySeq/Constants.py
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+ src/PyamilySeq/Group_Compare.py
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  src/PyamilySeq/Group_Extractor.py
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  src/PyamilySeq/Group_Sizes.py
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  src/PyamilySeq/Group_Splitter.py
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+ src/PyamilySeq/Group_Summary.py
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  src/PyamilySeq/PyamilySeq.py
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  src/PyamilySeq/PyamilySeq_Genus.py
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  src/PyamilySeq/PyamilySeq_Species.py
{pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/src/PyamilySeq.egg-info/entry_points.txt RENAMED
@@ -1,17 +1,17 @@
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  [console_scripts]
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- Cluster-Extractor = PyamilySeq.Cluster_Extractor:main
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- Cluster-Summary = PyamilySeq.Cluster_Summary:main
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+ Group-Extractor = PyamilySeq.Group_Extractor:main
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  Group-Splitter = PyamilySeq.Group_Splitter:main
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+ Group-Summary = PyamilySeq.Group_Summary:main
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  PyamilySeq = PyamilySeq.PyamilySeq:main
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  Seq-Combiner = PyamilySeq.Seq_Combiner:main
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  Seq-Extractor = PyamilySeq.Seq_Extractor:main
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  Seq-Finder = PyamilySeq.Seq_Finder:main
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- cluster-extractor = PyamilySeq.Cluster_Extractor:main
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- cluster-summary = PyamilySeq.Cluster_Summary:main
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  compare-contree-singletrees = aux_tools.RF.compare_contree_singletrees:main
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  compare-rf = aux_tools.RF.compare_RF:main
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  compute-singletrees-rf = aux_tools.RF.Compute_SingleTree_RFs:main
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+ group-extractor = PyamilySeq.Group_Extractor:main
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  group-splitter = PyamilySeq.Group_Splitter:main
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+ group-summary = PyamilySeq.Group_Summary:main
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  pyamilyseq = PyamilySeq.PyamilySeq:main
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  seq-combiner = PyamilySeq.Seq_Combiner:main
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  seq-extractor = PyamilySeq.Seq_Extractor:main
pyamilyseq-1.3.1/src/PyamilySeq/constants.py DELETED
@@ -1,2 +0,0 @@
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- PyamilySeq_Version = 'v1.3.1'
2
-
{pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/LICENSE RENAMED
File without changes
{pyamilyseq-1.3.1 → pyamilyseq-1.3.2}/setup.cfg RENAMED
File without changes