PyamilySeq 0.5.0__tar.gz → 0.5.1__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 (19) hide show
  1. {pyamilyseq-0.5.0/src/PyamilySeq.egg-info → pyamilyseq-0.5.1}/PKG-INFO +7 -7
  2. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/README.md +6 -6
  3. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/setup.cfg +1 -1
  4. pyamilyseq-0.5.1/src/PyamilySeq/Constants.py +2 -0
  5. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/src/PyamilySeq/PyamilySeq.py +3 -3
  6. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1/src/PyamilySeq.egg-info}/PKG-INFO +7 -7
  7. pyamilyseq-0.5.0/src/PyamilySeq/Constants.py +0 -2
  8. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/LICENSE +0 -0
  9. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/pyproject.toml +0 -0
  10. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/src/PyamilySeq/CD-Hit_StORF-Reporter_Cross-Genera_Builder.py +0 -0
  11. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/src/PyamilySeq/PyamilySeq_Genus.py +0 -0
  12. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/src/PyamilySeq/PyamilySeq_Species.py +0 -0
  13. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/src/PyamilySeq/Seq_Combiner.py +0 -0
  14. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/src/PyamilySeq/__init__.py +0 -0
  15. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/src/PyamilySeq/utils.py +0 -0
  16. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/src/PyamilySeq.egg-info/SOURCES.txt +0 -0
  17. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/src/PyamilySeq.egg-info/dependency_links.txt +0 -0
  18. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/src/PyamilySeq.egg-info/entry_points.txt +0 -0
  19. {pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/src/PyamilySeq.egg-info/top_level.txt +0 -0
{pyamilyseq-0.5.0/src/PyamilySeq.egg-info → pyamilyseq-0.5.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: PyamilySeq
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- Version: 0.5.0
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+ Version: 0.5.1
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  Summary: PyamilySeq - A a tool to look for sequence-based gene families identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.
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  Home-page: https://github.com/NickJD/PyamilySeq
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  Author: Nicholas Dimonaco
@@ -47,7 +47,7 @@ usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus}
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  [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}]
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  [-v]
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- PyamilySeq v0.5.0: PyamilySeq Run Parameters.
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+ PyamilySeq v0.5.1: PyamilySeq Run Parameters.
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  options:
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  -h, --help show this help message and exit
@@ -56,9 +56,9 @@ Required Arguments:
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  -run_mode {Full,Partial}
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  Run Mode: Should PyamilySeq be run in "Full" or
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  "Partial" mode?
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- -group_mode {Species,Genus}
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+ -group_mode {Species}
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  Group Mode: Should PyamilySeq be run in "Species" or
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- "Genus" mode?
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+ "Genus" mode? - Genus mode not currently functioning
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  -clust_tool {CD-HIT} Clustering tool to use: CD-HIT, DIAMOND, BLAST or
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  MMseqs2.
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  -output_dir OUTPUT_DIR
@@ -119,14 +119,14 @@ Misc:
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  ### Examples: Below are two examples of running PyamilySeq in its two main modes.
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  #### 'Full Mode': Will conduct clustering of sequences as part of PyamilySeq run
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  ```bash
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- PyamilySeq -id .../genomes -it combined -ns _combined.gff3 -pid 0.90 -ld 0.60 -co testing_cd-hit -ct CD-HIT -od .../testing
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+ PyamilySeq -run_mode Full -group_mode Species -output_dir ../../test_data/testing -input_type combined -input_dir .../test_data/genomes -name_split _combined.gff3 -pid 0.99 -len_diff 0.99 -clust_tool CD-HIT -gpa True -con True -w 99 -verbose True
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  ```
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  #### 'Partial Mode': Will take the output of a sequence clustering
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  ```bash
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  PyamilySeq -run_mode Partial -group_mode Species -output_dir .../test_data/testing -cluster_file .../test_data/CD-HIT/combined_Ensmbl_pep_CD_90_60.clstr -clust_tool CD-HIT -original_fasta .../test_data/combined_Ensmbl_cds.fasta -gpa True -con True -w 99 -verbose True
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  ```
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- ```Calculating Groups
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+ ```bash
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  Calculating Groups
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  Gene Groups:
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  first_core_99: 3103
@@ -145,7 +145,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split _combined.gff3 -output
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  ```bash
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  usage: Seq_Combiner.py [-h] -input_dir INPUT_DIR -input_type {separate,combined} -name_split NAME_SPLIT -output_dir OUTPUT_DIR -output_name OUTPUT_FILE
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- Seq-Combiner v0.5.0: Seq-Combiner Run Parameters.
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+ Seq-Combiner v0.5.1: Seq-Combiner Run Parameters.
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  options:
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  -h, --help show this help message and exit
{pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/README.md RENAMED
@@ -32,7 +32,7 @@ usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus}
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  [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}]
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  [-v]
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- PyamilySeq v0.5.0: PyamilySeq Run Parameters.
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+ PyamilySeq v0.5.1: PyamilySeq Run Parameters.
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  options:
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  -h, --help show this help message and exit
@@ -41,9 +41,9 @@ Required Arguments:
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  -run_mode {Full,Partial}
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  Run Mode: Should PyamilySeq be run in "Full" or
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43
  "Partial" mode?
44
- -group_mode {Species,Genus}
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+ -group_mode {Species}
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  Group Mode: Should PyamilySeq be run in "Species" or
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- "Genus" mode?
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+ "Genus" mode? - Genus mode not currently functioning
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  -clust_tool {CD-HIT} Clustering tool to use: CD-HIT, DIAMOND, BLAST or
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  MMseqs2.
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  -output_dir OUTPUT_DIR
@@ -104,14 +104,14 @@ Misc:
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  ### Examples: Below are two examples of running PyamilySeq in its two main modes.
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  #### 'Full Mode': Will conduct clustering of sequences as part of PyamilySeq run
106
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  ```bash
107
- PyamilySeq -id .../genomes -it combined -ns _combined.gff3 -pid 0.90 -ld 0.60 -co testing_cd-hit -ct CD-HIT -od .../testing
107
+ PyamilySeq -run_mode Full -group_mode Species -output_dir ../../test_data/testing -input_type combined -input_dir .../test_data/genomes -name_split _combined.gff3 -pid 0.99 -len_diff 0.99 -clust_tool CD-HIT -gpa True -con True -w 99 -verbose True
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  ```
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  #### 'Partial Mode': Will take the output of a sequence clustering
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  ```bash
111
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  PyamilySeq -run_mode Partial -group_mode Species -output_dir .../test_data/testing -cluster_file .../test_data/CD-HIT/combined_Ensmbl_pep_CD_90_60.clstr -clust_tool CD-HIT -original_fasta .../test_data/combined_Ensmbl_cds.fasta -gpa True -con True -w 99 -verbose True
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  ```
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- ```Calculating Groups
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+ ```bash
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  Calculating Groups
116
116
  Gene Groups:
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  first_core_99: 3103
@@ -130,7 +130,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split _combined.gff3 -output
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  ```bash
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  usage: Seq_Combiner.py [-h] -input_dir INPUT_DIR -input_type {separate,combined} -name_split NAME_SPLIT -output_dir OUTPUT_DIR -output_name OUTPUT_FILE
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- Seq-Combiner v0.5.0: Seq-Combiner Run Parameters.
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+ Seq-Combiner v0.5.1: Seq-Combiner Run Parameters.
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  options:
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  -h, --help show this help message and exit
{pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/setup.cfg RENAMED
@@ -1,6 +1,6 @@
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  [metadata]
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  name = PyamilySeq
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- version = v0.5.0
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+ version = v0.5.1
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  author = Nicholas Dimonaco
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  author_email = nicholas@dimonaco.co.uk
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  description = PyamilySeq - A a tool to look for sequence-based gene families identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.
pyamilyseq-0.5.1/src/PyamilySeq/Constants.py ADDED
@@ -0,0 +1,2 @@
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+ PyamilySeq_Version = 'v0.5.1'
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+
{pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/src/PyamilySeq/PyamilySeq.py RENAMED
@@ -3,7 +3,7 @@ import collections
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  import os
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  import glob
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  import subprocess
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- from PyamilySeq_Species import *
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+
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  try:
@@ -43,8 +43,8 @@ def main():
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  required.add_argument('-run_mode', action='store', dest='run_mode', choices=['Full','Partial'],
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  help='Run Mode: Should PyamilySeq be run in "Full" or "Partial" mode?',
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  required=True)
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- required.add_argument('-group_mode', action='store', dest='group_type', choices=['Species','Genus'],
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- help='Group Mode: Should PyamilySeq be run in "Species" or "Genus" mode?',
46
+ required.add_argument('-group_mode', action='store', dest='group_type', choices=['Species'],
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+ help='Group Mode: Should PyamilySeq be run in "Species" or "Genus" mode? - Genus mode not currently functioning',
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  required=True)
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  required.add_argument("-clust_tool", action="store", dest="clust_tool", choices=['CD-HIT'],
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  help="Clustering tool to use: CD-HIT, DIAMOND, BLAST or MMseqs2.",
{pyamilyseq-0.5.0 → pyamilyseq-0.5.1/src/PyamilySeq.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: PyamilySeq
3
- Version: 0.5.0
3
+ Version: 0.5.1
4
4
  Summary: PyamilySeq - A a tool to look for sequence-based gene families identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.
5
5
  Home-page: https://github.com/NickJD/PyamilySeq
6
6
  Author: Nicholas Dimonaco
@@ -47,7 +47,7 @@ usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus}
47
47
  [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}]
48
48
  [-v]
49
49
 
50
- PyamilySeq v0.5.0: PyamilySeq Run Parameters.
50
+ PyamilySeq v0.5.1: PyamilySeq Run Parameters.
51
51
 
52
52
  options:
53
53
  -h, --help show this help message and exit
@@ -56,9 +56,9 @@ Required Arguments:
56
56
  -run_mode {Full,Partial}
57
57
  Run Mode: Should PyamilySeq be run in "Full" or
58
58
  "Partial" mode?
59
- -group_mode {Species,Genus}
59
+ -group_mode {Species}
60
60
  Group Mode: Should PyamilySeq be run in "Species" or
61
- "Genus" mode?
61
+ "Genus" mode? - Genus mode not currently functioning
62
62
  -clust_tool {CD-HIT} Clustering tool to use: CD-HIT, DIAMOND, BLAST or
63
63
  MMseqs2.
64
64
  -output_dir OUTPUT_DIR
@@ -119,14 +119,14 @@ Misc:
119
119
  ### Examples: Below are two examples of running PyamilySeq in its two main modes.
120
120
  #### 'Full Mode': Will conduct clustering of sequences as part of PyamilySeq run
121
121
  ```bash
122
- PyamilySeq -id .../genomes -it combined -ns _combined.gff3 -pid 0.90 -ld 0.60 -co testing_cd-hit -ct CD-HIT -od .../testing
122
+ PyamilySeq -run_mode Full -group_mode Species -output_dir ../../test_data/testing -input_type combined -input_dir .../test_data/genomes -name_split _combined.gff3 -pid 0.99 -len_diff 0.99 -clust_tool CD-HIT -gpa True -con True -w 99 -verbose True
123
123
  ```
124
124
  #### 'Partial Mode': Will take the output of a sequence clustering
125
125
  ```bash
126
126
  PyamilySeq -run_mode Partial -group_mode Species -output_dir .../test_data/testing -cluster_file .../test_data/CD-HIT/combined_Ensmbl_pep_CD_90_60.clstr -clust_tool CD-HIT -original_fasta .../test_data/combined_Ensmbl_cds.fasta -gpa True -con True -w 99 -verbose True
127
127
  ```
128
128
 
129
- ```Calculating Groups
129
+ ```bash
130
130
  Calculating Groups
131
131
  Gene Groups:
132
132
  first_core_99: 3103
@@ -145,7 +145,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split _combined.gff3 -output
145
145
  ```bash
146
146
  usage: Seq_Combiner.py [-h] -input_dir INPUT_DIR -input_type {separate,combined} -name_split NAME_SPLIT -output_dir OUTPUT_DIR -output_name OUTPUT_FILE
147
147
 
148
- Seq-Combiner v0.5.0: Seq-Combiner Run Parameters.
148
+ Seq-Combiner v0.5.1: Seq-Combiner Run Parameters.
149
149
 
150
150
  options:
151
151
  -h, --help show this help message and exit
pyamilyseq-0.5.0/src/PyamilySeq/Constants.py DELETED
@@ -1,2 +0,0 @@
1
- PyamilySeq_Version = 'v0.5.0'
2
-
{pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/LICENSE RENAMED
File without changes
{pyamilyseq-0.5.0 → pyamilyseq-0.5.1}/pyproject.toml RENAMED
File without changes