PyamilySeq 1.3.1__py3-none-any.whl → 1.3.3__py3-none-any.whl

{pyamilyseq-1.3.1.dist-info → pyamilyseq-1.3.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyamilySeq
-Version: 1.3.1
+Version: 1.3.3
 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 v1.3.3: 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 v1.3.3
 Calculating Groups
 Number of Genomes: 10
 Gene Groups
@@ -805,7 +805,7 @@ Total Number of First Gene Groups That Had Additional Second Sequences But Not N
 ## PyamilySeq is separated into two main 'run modes', Full and Partial. They each have their own set of required and optional arguments.
 ### PyamilySeq - Full Menu: 
 ```
-usage: PyamilySeq.py Full [-h] -output_dir OUTPUT_DIR -input_type {separate,combined,fasta} [-input_dir INPUT_DIR] [-input_fasta INPUT_FASTA] [-name_split_gff NAME_SPLIT_GFF] [-name_split_fasta NAME_SPLIT_FASTA] [-sequence_type {AA,DNA}] [-gene_ident GENE_IDENT] [-c PIDENT] [-s LEN_DIFF] [-fast_mode]
+usage: PyamilySeq.py Full [-h] -output_dir OUTPUT_DIR -input_type {separate,combined,fasta} [-input_dir INPUT_DIR] [-input_fasta INPUT_FASTA] [-name_split_gff NAME_SPLIT_GFF] [-name_split_fasta NAME_SPLIT_FASTA] [-seq_type {AA,DNA}] [-gene_ident GENE_IDENT] [-c PIDENT] [-s LEN_DIFF] [-fast_mode]
                           [-group_mode {Species,Genus}] [-species_groups SPECIES_GROUPS] [-genus_groups GENUS_GROUPS] [-write_groups WRITE_GROUPS] [-write_individual_groups] [-align] [-align_aa] [-no_gpa] [-M MEM] [-T THREADS] [-verbose] [-v]
 
 options:
@@ -821,7 +821,7 @@ options:
                         Substring to split filenames and extract genome names for gff files (e.g., '_combined.gff3') - Use with -input_type separate/combined.
   -name_split_fasta NAME_SPLIT_FASTA
                         Substring to split filenames and extract genome names for fasta files if named differently to paired gff files (e.g., '_dna.fasta') - Use with -input_type separate/combined.
-  -sequence_type {AA,DNA}
+  -seq_type {AA,DNA}
                         Clustering mode: 'DNA' or 'AA'.
   -gene_ident GENE_IDENT
                         Gene identifiers to extract sequences (e.g., 'CDS, tRNA').
@@ -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 v1.3.3: 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
@@ -927,18 +927,18 @@ Misc Arguments:
 ## Group-Splitter: This tool can split multi-copy gene groups using CD-HIT after initial PyamilySeq analysis.
 ### Example:
 ```bash
-Group-Splitter -genome_num 10 -input_fasta .../test/species/ -output_dir .../test/species/ -sequence_type AA
+Group-Splitter -genome_num 10 -input_fasta .../test/species/ -output_dir .../test/species/ -seq_type AA
 ```
 ### Group-Splitter Menu:
 ```
-usage: Group_Splitter.py [-h] -input_fasta INPUT_FASTA -sequence_type {AA,DNA}
+usage: Group_Splitter.py [-h] -input_fasta INPUT_FASTA -seq_type {AA,DNA}
                          -genome_num GENOME_NUM -output_dir OUTPUT_DIR
                          [-groups GROUPS] [-group_threshold GROUP_THRESHOLD]
                          [-c PIDENT] [-s LEN_DIFF] [-T CLUSTERING_THREADS]
                          [-M CLUSTERING_MEMORY] [-no_delete_temp_files]
                          [-verbose] [-v]
 
-PyamilySeq v1.3.1: Group-Splitter - A tool to split multi-copy gene groups
+PyamilySeq v1.3.3: Group-Splitter - A tool to split multi-copy gene groups
 identified by PyamilySeq.
 
 options:
@@ -947,7 +947,7 @@ options:
 Required Parameters:
   -input_fasta INPUT_FASTA
                         Input FASTA file containing gene groups.
-  -sequence_type {AA,DNA}
+  -seq_type {AA,DNA}
                         Default - DNA: Are groups "DNA" or "AA" sequences?
   -genome_num GENOME_NUM
                         The total number of genomes must be provide
@@ -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 v1.3.3: Group-Summary - A tool to summarise CD-HIT clustering files.
 
 options:
   -h, --help            show this help message and exit

pyamilyseq-1.3.3.dist-info/RECORD

@@ -0,0 +1,21 @@
+PyamilySeq/Group_Compare.py,sha256=6GdJdrdMqsSG87xR1GZs2ddog1y9onlPaxq0Jt240oM,5460
+PyamilySeq/Group_Extractor.py,sha256=FSeCY2z01GTSd--uWZpNEmddaLZizDNrjvcOnicuB_4,4153
+PyamilySeq/Group_Sizes.py,sha256=VmJQ_DGJUO4fbrBGVq1eG6HypkjylVcwKvBB0w0CTTU,4075
+PyamilySeq/Group_Splitter.py,sha256=iA2-_GA_9_wgALe307xKphQJRQ34sepYjS_lESamtxM,30069
+PyamilySeq/Group_Summary.py,sha256=1CfzsmnVLLP1c8RGvfYprBFnMaAUqeUz6e-mEJ-P460,7529
+PyamilySeq/PyamilySeq.py,sha256=Odt5Qpz9jX_8-CsIs4vQlU8DyxM_Xhhjx68mOg0M9wE,19231
+PyamilySeq/PyamilySeq_Genus.py,sha256=5E3gDLp6lD8sSR8fepAVmxZJoP-dIeF0y9y7-gE24tM,12470
+PyamilySeq/PyamilySeq_Species.py,sha256=vkeIViMFSwjBdQ2fF_J9yP3M3Y4jc3k3jHp5gnsqt6c,22327
+PyamilySeq/Seq_Combiner.py,sha256=q6nU90oCdZdPaaPanPONvCiOg6RepUmZuPmFXld1aRs,10768
+PyamilySeq/Seq_Extractor.py,sha256=PWVYHC6pyAdd_1evkbOgGsEoOvV3bPYLDoYpwYTQUAs,4497
+PyamilySeq/Seq_Finder.py,sha256=IF4yuc3w2kpSZgaYDJJYODhIsEOND1IubsAxxdTTahk,3089
+PyamilySeq/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+PyamilySeq/clusterings.py,sha256=73k3Ffu3lVG0NTU2lqiTFU4L7TF3tipNK5P-q4XpkAY,22374
+PyamilySeq/constants.py,sha256=8DjqzKkB32OsgEjUrVbMzFMTlhJ8N8v0sZdoFMyCqyM,6470
+PyamilySeq/utils.py,sha256=woFCv9l93drNGOQ_Ekg7wiHoU2eHq4_9WWErmm76Szs,37104
+pyamilyseq-1.3.3.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+pyamilyseq-1.3.3.dist-info/METADATA,sha256=yEVExWk6mTp8etYfJtsFiJyXAM7Oh4chk6Xhifz8MME,58533
+pyamilyseq-1.3.3.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+pyamilyseq-1.3.3.dist-info/entry_points.txt,sha256=1P7oCXW1ONiy6LvGZ_Z6LPGDGcCIsZs7r0BIEtP_rmQ,830
+pyamilyseq-1.3.3.dist-info/top_level.txt,sha256=J6JhugUQTq4rq96yibAlQu3o4KCM9WuYfqr3w1r119M,11
+pyamilyseq-1.3.3.dist-info/RECORD,,

{pyamilyseq-1.3.1.dist-info → pyamilyseq-1.3.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{pyamilyseq-1.3.1.dist-info → pyamilyseq-1.3.3.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

pyamilyseq-1.3.1.dist-info/RECORD

@@ -1,22 +0,0 @@
-PyamilySeq/Cluster_Compare.py,sha256=2jRXBYN8T9TUDLV9bj3SWFQ2pBUH3BAKW1FYrDYSQBw,4421
-PyamilySeq/Cluster_Summary.py,sha256=efXMfGvATERCTxwaqbauhZwt_5Hrf9KpGKY3EgsHVDk,6720
-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/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
-PyamilySeq/Seq_Combiner.py,sha256=G49zthWtsTfqYX1tqc7op9a9cSia1IL0VTiAtwgdTwc,4746
-PyamilySeq/Seq_Extractor.py,sha256=IQk4Qn6LJkPXD1O4TQesneS3_ZN8hBsTVZQGlZ1c-Dk,3072
-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/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,,