PyamilySeq 0.5.0__py3-none-any.whl → 0.5.1__py3-none-any.whl

PyamilySeq/Constants.py

@@ -1,2 +1,2 @@
-PyamilySeq_Version = 'v0.5.0'
+PyamilySeq_Version = 'v0.5.1'
 

PyamilySeq/PyamilySeq.py

@@ -3,7 +3,7 @@ import collections
 import os
 import glob
 import subprocess
-from PyamilySeq_Species import *
+
 
 
 try:
@@ -43,8 +43,8 @@ def main():
     required.add_argument('-run_mode', action='store', dest='run_mode', choices=['Full','Partial'],
                           help='Run Mode: Should PyamilySeq be run in "Full" or "Partial" mode?',
                           required=True)
-    required.add_argument('-group_mode', action='store', dest='group_type', choices=['Species','Genus'],
-                          help='Group Mode: Should PyamilySeq be run in "Species" or "Genus" mode?',
+    required.add_argument('-group_mode', action='store', dest='group_type', choices=['Species'],
+                          help='Group Mode: Should PyamilySeq be run in "Species" or "Genus" mode? - Genus mode not currently functioning',
                           required=True)
     required.add_argument("-clust_tool", action="store", dest="clust_tool", choices=['CD-HIT'],
                           help="Clustering tool to use: CD-HIT, DIAMOND, BLAST or MMseqs2.",

{PyamilySeq-0.5.0.dist-info → PyamilySeq-0.5.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyamilySeq
-Version: 0.5.0
+Version: 0.5.1
 Summary: PyamilySeq - A a tool to look for sequence-based gene families identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.
 Home-page: https://github.com/NickJD/PyamilySeq
 Author: Nicholas Dimonaco
@@ -47,7 +47,7 @@ usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus}
                      [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}]
                      [-v]
 
-PyamilySeq v0.5.0: PyamilySeq Run Parameters.
+PyamilySeq v0.5.1: PyamilySeq Run Parameters.
 
 options:
   -h, --help            show this help message and exit
@@ -56,9 +56,9 @@ Required Arguments:
   -run_mode {Full,Partial}
                         Run Mode: Should PyamilySeq be run in "Full" or
                         "Partial" mode?
-  -group_mode {Species,Genus}
+  -group_mode {Species}
                         Group Mode: Should PyamilySeq be run in "Species" or
-                        "Genus" mode?
+                        "Genus" mode?  - Genus mode not currently functioning
   -clust_tool {CD-HIT}  Clustering tool to use: CD-HIT, DIAMOND, BLAST or
                         MMseqs2.
   -output_dir OUTPUT_DIR
@@ -119,14 +119,14 @@ Misc:
 ### Examples: Below are two examples of running PyamilySeq in its two main modes.
 #### 'Full Mode': Will conduct clustering of sequences as part of PyamilySeq run
 ```bash 
-PyamilySeq -id .../genomes -it combined -ns _combined.gff3 -pid 0.90 -ld 0.60 -co testing_cd-hit -ct CD-HIT -od .../testing
+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
 ```
 #### 'Partial Mode': Will take the output of a sequence clustering
 ```bash
 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
 ```
 
-```Calculating Groups
+```bash
 Calculating Groups
 Gene Groups:
 first_core_99: 3103
@@ -145,7 +145,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split _combined.gff3 -output
 ```bash
 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
 
-Seq-Combiner v0.5.0: Seq-Combiner Run Parameters.
+Seq-Combiner v0.5.1: Seq-Combiner Run Parameters.
 
 options:
   -h, --help            show this help message and exit

{PyamilySeq-0.5.0.dist-info → PyamilySeq-0.5.1.dist-info}/RECORD

@@ -1,14 +1,14 @@
 PyamilySeq/CD-Hit_StORF-Reporter_Cross-Genera_Builder.py,sha256=UzQ5iOKCNfurxmj1pnkowF11YfWBO5vnBCKxQK6goB8,26538
-PyamilySeq/Constants.py,sha256=H1GMMb0WK68bphZPfzCvdvvSi5BeQc80QL4igt17S94,31
-PyamilySeq/PyamilySeq.py,sha256=ONDjQZoR4YCdAoDq2Ufv8mcY_1ek1LPJF-OtS4gzXDs,11276
+PyamilySeq/Constants.py,sha256=mmMeeD5svOnN-Kn7LUd16DY8rWTcU2WajldKlNkuuWY,31
+PyamilySeq/PyamilySeq.py,sha256=7pyBujHmdYR6DVNlKQ2BqX9-AylTpNexrcWN-rtyauk,11275
 PyamilySeq/PyamilySeq_Genus.py,sha256=JpLLu3QaahUHBe7E80xVHtFORGuyeUMOt9eiLN5uazc,31286
 PyamilySeq/PyamilySeq_Species.py,sha256=6LHEdp6Vndoder8dlVSuyUKHdCbo5Rbxea1rnncrceY,35172
 PyamilySeq/Seq_Combiner.py,sha256=bHEIR-MZODSGm8n69ZIN-XzEoct5WZ1kH5Xa6uKCu4Y,1972
 PyamilySeq/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 PyamilySeq/utils.py,sha256=KhEnwzgVZyUu_Q92ukRPUrVD2505xSg9NY6e75nUmPQ,6487
-PyamilySeq-0.5.0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-PyamilySeq-0.5.0.dist-info/METADATA,sha256=II_Elm1hg0nTXjmnEnsct2e4l2KQ1xR2hcXgp1wEiJA,7649
-PyamilySeq-0.5.0.dist-info/WHEEL,sha256=Wyh-_nZ0DJYolHNn1_hMa4lM7uDedD_RGVwbmTjyItk,91
-PyamilySeq-0.5.0.dist-info/entry_points.txt,sha256=QtXD1tmnLvRAkIpGWZgXm1lfLH8GGeCwxmgoHZaTp98,102
-PyamilySeq-0.5.0.dist-info/top_level.txt,sha256=J6JhugUQTq4rq96yibAlQu3o4KCM9WuYfqr3w1r119M,11
-PyamilySeq-0.5.0.dist-info/RECORD,,
+PyamilySeq-0.5.1.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+PyamilySeq-0.5.1.dist-info/METADATA,sha256=FJRNy2WTazUXemY4jHYPmpJEdq5JQMebhfeicagLTCA,7792
+PyamilySeq-0.5.1.dist-info/WHEEL,sha256=Wyh-_nZ0DJYolHNn1_hMa4lM7uDedD_RGVwbmTjyItk,91
+PyamilySeq-0.5.1.dist-info/entry_points.txt,sha256=QtXD1tmnLvRAkIpGWZgXm1lfLH8GGeCwxmgoHZaTp98,102
+PyamilySeq-0.5.1.dist-info/top_level.txt,sha256=J6JhugUQTq4rq96yibAlQu3o4KCM9WuYfqr3w1r119M,11
+PyamilySeq-0.5.1.dist-info/RECORD,,