PyamilySeq 1.3.1__py3-none-any.whl → 1.3.2__py3-none-any.whl

PyamilySeq/constants.py

@@ -1,2 +1,2 @@
-PyamilySeq_Version = 'v1.3.1'
+PyamilySeq_Version = 'v1.3.2'
 

{pyamilyseq-1.3.1.dist-info → pyamilyseq-1.3.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyamilySeq
-Version: 1.3.1
+Version: 1.3.2
 Summary: PyamilySeq - A a tool to investigate sequence-based gene groups identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.
 Author-email: Nicholas Dimonaco <nicholas@dimonaco.co.uk>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -720,7 +720,7 @@ To update to the newest version add '-U' to end of the pip install command.
 ```commandline
 usage: PyamilySeq.py [-h] {Full,Partial} ...
 
-PyamilySeq v1.3.1: A tool for gene clustering and analysis.
+PyamilySeq v1.3.2: A tool for gene clustering and analysis.
 
 positional arguments:
   {Full,Partial}  Choose a mode: 'Full' or 'Partial'.
@@ -750,7 +750,7 @@ Escherichia_coli_110957|ENSB_TIZS9kbTvShDvyX	Escherichia_coli_110957|ENSB_TIZS9k
 ```
 ### Example output:
 ```
-Running PyamilySeq v1.3.1
+Running PyamilySeq v1.3.2
 Calculating Groups
 Number of Genomes: 10
 Gene Groups
@@ -895,7 +895,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split_gff .gff3 -output_dir
 ```
 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]
 
-PyamilySeq v1.3.1: Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.
+PyamilySeq v1.3.2: Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.
 
 options:
   -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}
                          [-M CLUSTERING_MEMORY] [-no_delete_temp_files]
                          [-verbose] [-v]
 
-PyamilySeq v1.3.1: Group-Splitter - A tool to split multi-copy gene groups
+PyamilySeq v1.3.2: Group-Splitter - A tool to split multi-copy gene groups
 identified by PyamilySeq.
 
 options:
@@ -981,17 +981,17 @@ Misc Parameters:
 
 ```
 
-## Cluster-Summary menu: This tool can be used to summarise CD-HIT .clstr files:
+## Group-Summary menu: This tool can be used to summarise CD-HIT .clstr files:
 ### Example:
 ```bash
-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
+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
 ```
-### Cluster-Summary Menu: 
+### Group-Summary Menu: 
 ```
 usage: Cluster_Summary.py [-h] -input_clstr INPUT_CLSTR -output OUTPUT -genome_num GENOME_NUM
                           [-output_dir OUTPUT_DIR] [-verbose] [-v]
 
-PyamilySeq v1.3.1: Cluster-Summary - A tool to summarise CD-HIT clustering files.
+PyamilySeq v1.3.2: Group-Summary - A tool to summarise CD-HIT clustering files.
 
 options:
   -h, --help            show this help message and exit

{pyamilyseq-1.3.1.dist-info → pyamilyseq-1.3.2.dist-info}/RECORD

@@ -1,8 +1,8 @@
-PyamilySeq/Cluster_Compare.py,sha256=2jRXBYN8T9TUDLV9bj3SWFQ2pBUH3BAKW1FYrDYSQBw,4421
-PyamilySeq/Cluster_Summary.py,sha256=efXMfGvATERCTxwaqbauhZwt_5Hrf9KpGKY3EgsHVDk,6720
+PyamilySeq/Group_Compare.py,sha256=2jRXBYN8T9TUDLV9bj3SWFQ2pBUH3BAKW1FYrDYSQBw,4421
 PyamilySeq/Group_Extractor.py,sha256=oe2VmOVxdvTmAcy8NKwD1F27IdN2utAfczxsyxg96yc,2898
 PyamilySeq/Group_Sizes.py,sha256=3snkAN19o3Y4IY6IqSim1qy415FfQe1Wb8vzWTKF0Wo,3028
 PyamilySeq/Group_Splitter.py,sha256=OcMj9GnAyybs_DaNKRyvfL_nl2dB2gUI4BD_EQrBbWo,25653
+PyamilySeq/Group_Summary.py,sha256=efXMfGvATERCTxwaqbauhZwt_5Hrf9KpGKY3EgsHVDk,6720
 PyamilySeq/PyamilySeq.py,sha256=vc_mFuK-Cmqa3elusyIg5DksTHxdwCcFv2ki2ACqXIA,17468
 PyamilySeq/PyamilySeq_Genus.py,sha256=KUC0QkCRpKQ9HEgxyTSD7Nc63wSXtriWyIqt_YOy5ys,12470
 PyamilySeq/PyamilySeq_Species.py,sha256=1P_xbdUrZPykyS44KFyRdyxU-XPX_yKLpJhjhB8VTpg,24029
@@ -12,11 +12,11 @@ PyamilySeq/Seq_Finder.py,sha256=ht-fSQ_opWKydcoWI9D3nTwLt6Rpgevnf2y0KxVjw4M,1881
 PyamilySeq/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 PyamilySeq/clusterings.py,sha256=bfST7_i6qnj9ogclmOSkQhurZaEWBBq0H48FAN7JpOg,22374
 PyamilySeq/config.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-PyamilySeq/constants.py,sha256=rjAhz3KZ8STrueOdZOBvWKZUALDJM0y3QrTZGDE88JU,31
+PyamilySeq/constants.py,sha256=lCsqqBBXsq1Qim8y9ElG9Jm555FZ-brTCk6WuJJtemE,31
 PyamilySeq/utils.py,sha256=1U794Xd5qzmaIz2VujdnPkND729kr7rKjei0Y57f-QE,32972
-pyamilyseq-1.3.1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-pyamilyseq-1.3.1.dist-info/METADATA,sha256=-6Y4VzMdNpsQ7O4WB_xJ6Mxa9y0qovhrbYOwwPeahjQ,58566
-pyamilyseq-1.3.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-pyamilyseq-1.3.1.dist-info/entry_points.txt,sha256=5RkUWIneXu-kCnClJhv0u27lWHAoyoVmospZMU5Cs2U,846
-pyamilyseq-1.3.1.dist-info/top_level.txt,sha256=J6JhugUQTq4rq96yibAlQu3o4KCM9WuYfqr3w1r119M,11
-pyamilyseq-1.3.1.dist-info/RECORD,,
+pyamilyseq-1.3.2.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+pyamilyseq-1.3.2.dist-info/METADATA,sha256=V6DlnSRPx5hiGOzkyJ0GPe0VL--UKQE1V75nmceyq-o,58558
+pyamilyseq-1.3.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+pyamilyseq-1.3.2.dist-info/entry_points.txt,sha256=1P7oCXW1ONiy6LvGZ_Z6LPGDGcCIsZs7r0BIEtP_rmQ,830
+pyamilyseq-1.3.2.dist-info/top_level.txt,sha256=J6JhugUQTq4rq96yibAlQu3o4KCM9WuYfqr3w1r119M,11
+pyamilyseq-1.3.2.dist-info/RECORD,,

{pyamilyseq-1.3.1.dist-info → pyamilyseq-1.3.2.dist-info}/entry_points.txt

@@ -1,17 +1,17 @@
 [console_scripts]
-Cluster-Extractor = PyamilySeq.Cluster_Extractor:main
-Cluster-Summary = PyamilySeq.Cluster_Summary:main
+Group-Extractor = PyamilySeq.Group_Extractor:main
 Group-Splitter = PyamilySeq.Group_Splitter:main
+Group-Summary = PyamilySeq.Group_Summary:main
 PyamilySeq = PyamilySeq.PyamilySeq:main
 Seq-Combiner = PyamilySeq.Seq_Combiner:main
 Seq-Extractor = PyamilySeq.Seq_Extractor:main
 Seq-Finder = PyamilySeq.Seq_Finder:main
-cluster-extractor = PyamilySeq.Cluster_Extractor:main
-cluster-summary = PyamilySeq.Cluster_Summary:main
 compare-contree-singletrees = aux_tools.RF.compare_contree_singletrees:main
 compare-rf = aux_tools.RF.compare_RF:main
 compute-singletrees-rf = aux_tools.RF.Compute_SingleTree_RFs:main
+group-extractor = PyamilySeq.Group_Extractor:main
 group-splitter = PyamilySeq.Group_Splitter:main
+group-summary = PyamilySeq.Group_Summary:main
 pyamilyseq = PyamilySeq.PyamilySeq:main
 seq-combiner = PyamilySeq.Seq_Combiner:main
 seq-extractor = PyamilySeq.Seq_Extractor:main