PyamilySeq 0.7.0__tar.gz → 0.7.1__tar.gz

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Files changed (19) hide show
  1. {pyamilyseq-0.7.0/src/PyamilySeq.egg-info → pyamilyseq-0.7.1}/PKG-INFO +32 -33
  2. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/README.md +31 -32
  3. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/setup.cfg +1 -1
  4. pyamilyseq-0.7.1/src/PyamilySeq/Constants.py +2 -0
  5. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/src/PyamilySeq/PyamilySeq.py +13 -2
  6. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1/src/PyamilySeq.egg-info}/PKG-INFO +32 -33
  7. pyamilyseq-0.7.0/src/PyamilySeq/Constants.py +0 -2
  8. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/LICENSE +0 -0
  9. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/pyproject.toml +0 -0
  10. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/src/PyamilySeq/PyamilySeq_Genus.py +0 -0
  11. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/src/PyamilySeq/PyamilySeq_Species.py +0 -0
  12. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/src/PyamilySeq/Seq_Combiner.py +0 -0
  13. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/src/PyamilySeq/__init__.py +0 -0
  14. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/src/PyamilySeq/clusterings.py +0 -0
  15. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/src/PyamilySeq/utils.py +0 -0
  16. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/src/PyamilySeq.egg-info/SOURCES.txt +0 -0
  17. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/src/PyamilySeq.egg-info/dependency_links.txt +0 -0
  18. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/src/PyamilySeq.egg-info/entry_points.txt +0 -0
  19. {pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/src/PyamilySeq.egg-info/top_level.txt +0 -0
{pyamilyseq-0.7.0/src/PyamilySeq.egg-info → pyamilyseq-0.7.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: PyamilySeq
3
- Version: 0.7.0
3
+ Version: 0.7.1
4
4
  Summary: PyamilySeq - A a tool to look for sequence-based gene groups 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
@@ -58,7 +58,7 @@ Escherichia_coli_110957|ENSB:TIZS9kbTvShDvyX Escherichia_coli_110957|ENSB:TIZS9k
58
58
  ```
59
59
  ### Example output:
60
60
  ```
61
- Running PyamilySeq v0.7.0
61
+ Running PyamilySeq v0.7.1
62
62
  Calculating Groups
63
63
  Gene Groups:
64
64
  First_core_99: 2682
@@ -80,7 +80,7 @@ PyamilySeq -run_mode Partial -group_mode Genus -clustering_format CD-HIT -output
80
80
  -cluster_file .../test_data/genus/CD-HIT/combined_cds_cd-hit_80_60.clstr -gpa
81
81
  ```
82
82
  ```commandline
83
- Running PyamilySeq v0.7.0
83
+ Running PyamilySeq v0.7.1
84
84
  Calculating Groups
85
85
  Genus Groups:
86
86
  First_genera_1: 28549
@@ -98,37 +98,36 @@ Please report any issues to: https://github.com/NickJD/PyamilySeq/issues
98
98
  ### Reclustering can be used to see where additional sequences/genes lay in relation to a contemporary pangenome/gene grouping.
99
99
  ```
100
100
  PyamilySeq -run_mode Partial -group_mode Species -clustering_format CD-HIT -output_dir .../test_data/species/CD-HIT/testing
101
- -cluster_file .../test_data/species/CD-HIT/E-coli_extracted_cds_cd-hit_90_60.clstr -gpa
102
- -reclustered .../test_data/species/CD-HIT/E-coli_extracted_cds_cd-hit_90_60_And_StORFs_cds_90_60.clstr
101
+ -cluster_file .../test_data/species/CD-HIT/E-coli_extracted_cds_cd-hit_80_60.clstr -gpa
102
+ -reclustered .../test_data/species/CD-HIT/E-coli_extracted_cds_cd-hit_80_60_And_StORFs_cds_80_60.clstr
103
103
  ```
104
104
  #### As can be seen below, the additional sequences recovered by the StORF-Reporter annotation tool have 'extended' contemporary or created entirely new gene groups. 'First' corresponds to the groups identified from the first clustering round and 'Second' for the second. In 'reclustering' mode, First_core_# groups are unaffected thus retaining the initial grouping information.
105
105
  ```commandline
106
- Running PyamilySeq v0.7.0
107
106
  Calculating Groups
108
107
  Gene Groups:
109
- First_core_99: 69
110
- First_core_95: 1002
111
- First_core_15: 4716
112
- First_core_0: 37960
113
- extended_core_99: 6
114
- extended_core_95: 73
115
- extended_core_15: 331
116
- extended_core_0: 582
117
- combined_core_99: 4
118
- combined_core_95: 88
119
- combined_core_15: 455
120
- combined_core_0: 228
108
+ First_core_99: 587
109
+ First_core_95: 1529
110
+ First_core_15: 3708
111
+ First_core_0: 29992
112
+ extended_core_99: 29
113
+ extended_core_95: 67
114
+ extended_core_15: 431
115
+ extended_core_0: 1331
116
+ combined_core_99: 2
117
+ combined_core_95: 4
118
+ combined_core_15: 5
119
+ combined_core_0: 4
121
120
  Second_core_99: 0
122
- Second_core_95: 5
123
- Second_core_15: 254
124
- Second_core_0: 3714
125
- only_Second_core_99: 6
126
- only_Second_core_95: 364
127
- only_Second_core_15: 3950
128
- only_Second_core_0: 31269
129
- Total Number of First Gene Groups (Including Singletons): 43747
130
- Total Number of Second Gene Groups (Including Singletons): 66525
131
- Total Number of First Gene Groups That Had Additional Second Sequences But Not New Genomes: 9593
121
+ Second_core_95: 6
122
+ Second_core_15: 172
123
+ Second_core_0: 1825
124
+ only_Second_core_99: 53
125
+ only_Second_core_95: 493
126
+ only_Second_core_15: 3806
127
+ only_Second_core_0: 27569
128
+ Total Number of First Gene Groups (Including Singletons): 35816
129
+ Total Number of Second Gene Groups (Including Singletons): 67728
130
+ Total Number of First Gene Groups That Had Additional Second Sequences But Not New Genomes: 136
132
131
  Outputting gene_presence_absence file
133
132
  Thank you for using PyamilySeq -- A detailed user manual can be found at https://github.com/NickJD/PyamilySeq
134
133
  Please report any issues to: https://github.com/NickJD/PyamilySeq/issues
@@ -138,14 +137,14 @@ Please report any issues to: https://github.com/NickJD/PyamilySeq/issues
138
137
  ## PyamilySeq - Menu:
139
138
  ### PyamilySeq is separated into two main 'run modes', Full and Partial. They each have their own set of required and optional arguments.
140
139
  ```
141
- Running PyamilySeq v0.7.0
140
+ Running PyamilySeq v0.7.1
142
141
  usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus} -clustering_format {CD-HIT,TSV,CSV} -output_dir OUTPUT_DIR
143
142
  [-input_type {separate,combined}] [-input_dir INPUT_DIR] [-name_split NAME_SPLIT] [-sequence_type {AA,DNA}] [-gene_ident GENE_IDENT]
144
143
  [-pid PIDENT] [-len_diff LEN_DIFF] [-mem CLUSTERING_MEMORY] [-t CLUSTERING_THREADS] [-cluster_file CLUSTER_FILE]
145
144
  [-reclustered RECLUSTERED] [-seq_tag SEQUENCE_TAG] [-core_groups CORE_GROUPS] [-genus_groups GENUS_GROUPS] [-w WRITE_GROUPS] [-a]
146
145
  [-original_fasta ORIGINAL_FASTA] [-gpa] [-verbose] [-v]
147
146
 
148
- PyamilySeq v0.7.0: A tool that groups genes into unique clusters.
147
+ PyamilySeq v0.7.1: A tool that groups genes into unique clusters.
149
148
 
150
149
  options:
151
150
  -h, --help show this help message and exit
@@ -198,9 +197,9 @@ Output Parameters:
198
197
  -w WRITE_GROUPS Default - No output: Output sequences of identified groups (provide levels at which to output - Species "-w 99,95" Genus "-w 2,3" -
199
198
  Must provide FASTA file with -original_fasta if in Partial run mode.
200
199
  -a Default - No output: SLOW! (Only works for Species mode) Output aligned and concatinated sequences of identified groups -provide
201
- group levels at which to output "-w 99,95" - Must provide FASTA file with -original_fasta in Partialrun mode.
200
+ group levels at which to output "-w 99,95" - Must provide FASTA file with -original_fasta in Partial run mode.
202
201
  -original_fasta ORIGINAL_FASTA
203
- FASTA file to use in conjunction with "-w" or "-con" when running in Partial Mode.
202
+ FASTA file to use in conjunction with "-w" or "-a" when running in Partial Mode.
204
203
  -gpa Default - False: If selected, a Roary/Panaroo formatted gene_presence_absence.csv will be created - Required for Coinfinder and
205
204
  other downstream tools
206
205
 
@@ -222,7 +221,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split _combined.gff3 -output
222
221
  ```
223
222
  usage: Seq_Combiner.py [-h] -input_dir INPUT_DIR -input_type {separate,combined,fasta} -name_split NAME_SPLIT -output_dir OUTPUT_DIR -output_name OUTPUT_FILE [-gene_ident GENE_IDENT] [-translate] [-v]
224
223
 
225
- Seq-Combiner v0.7.0: A tool to extract sequences from GFF/FASTA files.
224
+ Seq-Combiner v0.7.1: A tool to extract sequences from GFF/FASTA files.
226
225
 
227
226
  options:
228
227
  -h, --help show this help message and exit
{pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/README.md RENAMED
@@ -43,7 +43,7 @@ Escherichia_coli_110957|ENSB:TIZS9kbTvShDvyX Escherichia_coli_110957|ENSB:TIZS9k
43
43
  ```
44
44
  ### Example output:
45
45
  ```
46
- Running PyamilySeq v0.7.0
46
+ Running PyamilySeq v0.7.1
47
47
  Calculating Groups
48
48
  Gene Groups:
49
49
  First_core_99: 2682
@@ -65,7 +65,7 @@ PyamilySeq -run_mode Partial -group_mode Genus -clustering_format CD-HIT -output
65
65
  -cluster_file .../test_data/genus/CD-HIT/combined_cds_cd-hit_80_60.clstr -gpa
66
66
  ```
67
67
  ```commandline
68
- Running PyamilySeq v0.7.0
68
+ Running PyamilySeq v0.7.1
69
69
  Calculating Groups
70
70
  Genus Groups:
71
71
  First_genera_1: 28549
@@ -83,37 +83,36 @@ Please report any issues to: https://github.com/NickJD/PyamilySeq/issues
83
83
  ### Reclustering can be used to see where additional sequences/genes lay in relation to a contemporary pangenome/gene grouping.
84
84
  ```
85
85
  PyamilySeq -run_mode Partial -group_mode Species -clustering_format CD-HIT -output_dir .../test_data/species/CD-HIT/testing
86
- -cluster_file .../test_data/species/CD-HIT/E-coli_extracted_cds_cd-hit_90_60.clstr -gpa
87
- -reclustered .../test_data/species/CD-HIT/E-coli_extracted_cds_cd-hit_90_60_And_StORFs_cds_90_60.clstr
86
+ -cluster_file .../test_data/species/CD-HIT/E-coli_extracted_cds_cd-hit_80_60.clstr -gpa
87
+ -reclustered .../test_data/species/CD-HIT/E-coli_extracted_cds_cd-hit_80_60_And_StORFs_cds_80_60.clstr
88
88
  ```
89
89
  #### As can be seen below, the additional sequences recovered by the StORF-Reporter annotation tool have 'extended' contemporary or created entirely new gene groups. 'First' corresponds to the groups identified from the first clustering round and 'Second' for the second. In 'reclustering' mode, First_core_# groups are unaffected thus retaining the initial grouping information.
90
90
  ```commandline
91
- Running PyamilySeq v0.7.0
92
91
  Calculating Groups
93
92
  Gene Groups:
94
- First_core_99: 69
95
- First_core_95: 1002
96
- First_core_15: 4716
97
- First_core_0: 37960
98
- extended_core_99: 6
99
- extended_core_95: 73
100
- extended_core_15: 331
101
- extended_core_0: 582
102
- combined_core_99: 4
103
- combined_core_95: 88
104
- combined_core_15: 455
105
- combined_core_0: 228
93
+ First_core_99: 587
94
+ First_core_95: 1529
95
+ First_core_15: 3708
96
+ First_core_0: 29992
97
+ extended_core_99: 29
98
+ extended_core_95: 67
99
+ extended_core_15: 431
100
+ extended_core_0: 1331
101
+ combined_core_99: 2
102
+ combined_core_95: 4
103
+ combined_core_15: 5
104
+ combined_core_0: 4
106
105
  Second_core_99: 0
107
- Second_core_95: 5
108
- Second_core_15: 254
109
- Second_core_0: 3714
110
- only_Second_core_99: 6
111
- only_Second_core_95: 364
112
- only_Second_core_15: 3950
113
- only_Second_core_0: 31269
114
- Total Number of First Gene Groups (Including Singletons): 43747
115
- Total Number of Second Gene Groups (Including Singletons): 66525
116
- Total Number of First Gene Groups That Had Additional Second Sequences But Not New Genomes: 9593
106
+ Second_core_95: 6
107
+ Second_core_15: 172
108
+ Second_core_0: 1825
109
+ only_Second_core_99: 53
110
+ only_Second_core_95: 493
111
+ only_Second_core_15: 3806
112
+ only_Second_core_0: 27569
113
+ Total Number of First Gene Groups (Including Singletons): 35816
114
+ Total Number of Second Gene Groups (Including Singletons): 67728
115
+ Total Number of First Gene Groups That Had Additional Second Sequences But Not New Genomes: 136
117
116
  Outputting gene_presence_absence file
118
117
  Thank you for using PyamilySeq -- A detailed user manual can be found at https://github.com/NickJD/PyamilySeq
119
118
  Please report any issues to: https://github.com/NickJD/PyamilySeq/issues
@@ -123,14 +122,14 @@ Please report any issues to: https://github.com/NickJD/PyamilySeq/issues
123
122
  ## PyamilySeq - Menu:
124
123
  ### PyamilySeq is separated into two main 'run modes', Full and Partial. They each have their own set of required and optional arguments.
125
124
  ```
126
- Running PyamilySeq v0.7.0
125
+ Running PyamilySeq v0.7.1
127
126
  usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus} -clustering_format {CD-HIT,TSV,CSV} -output_dir OUTPUT_DIR
128
127
  [-input_type {separate,combined}] [-input_dir INPUT_DIR] [-name_split NAME_SPLIT] [-sequence_type {AA,DNA}] [-gene_ident GENE_IDENT]
129
128
  [-pid PIDENT] [-len_diff LEN_DIFF] [-mem CLUSTERING_MEMORY] [-t CLUSTERING_THREADS] [-cluster_file CLUSTER_FILE]
130
129
  [-reclustered RECLUSTERED] [-seq_tag SEQUENCE_TAG] [-core_groups CORE_GROUPS] [-genus_groups GENUS_GROUPS] [-w WRITE_GROUPS] [-a]
131
130
  [-original_fasta ORIGINAL_FASTA] [-gpa] [-verbose] [-v]
132
131
 
133
- PyamilySeq v0.7.0: A tool that groups genes into unique clusters.
132
+ PyamilySeq v0.7.1: A tool that groups genes into unique clusters.
134
133
 
135
134
  options:
136
135
  -h, --help show this help message and exit
@@ -183,9 +182,9 @@ Output Parameters:
183
182
  -w WRITE_GROUPS Default - No output: Output sequences of identified groups (provide levels at which to output - Species "-w 99,95" Genus "-w 2,3" -
184
183
  Must provide FASTA file with -original_fasta if in Partial run mode.
185
184
  -a Default - No output: SLOW! (Only works for Species mode) Output aligned and concatinated sequences of identified groups -provide
186
- group levels at which to output "-w 99,95" - Must provide FASTA file with -original_fasta in Partialrun mode.
185
+ group levels at which to output "-w 99,95" - Must provide FASTA file with -original_fasta in Partial run mode.
187
186
  -original_fasta ORIGINAL_FASTA
188
- FASTA file to use in conjunction with "-w" or "-con" when running in Partial Mode.
187
+ FASTA file to use in conjunction with "-w" or "-a" when running in Partial Mode.
189
188
  -gpa Default - False: If selected, a Roary/Panaroo formatted gene_presence_absence.csv will be created - Required for Coinfinder and
190
189
  other downstream tools
191
190
 
@@ -207,7 +206,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split _combined.gff3 -output
207
206
  ```
208
207
  usage: Seq_Combiner.py [-h] -input_dir INPUT_DIR -input_type {separate,combined,fasta} -name_split NAME_SPLIT -output_dir OUTPUT_DIR -output_name OUTPUT_FILE [-gene_ident GENE_IDENT] [-translate] [-v]
209
208
 
210
- Seq-Combiner v0.7.0: A tool to extract sequences from GFF/FASTA files.
209
+ Seq-Combiner v0.7.1: A tool to extract sequences from GFF/FASTA files.
211
210
 
212
211
  options:
213
212
  -h, --help show this help message and exit
{pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/setup.cfg RENAMED
@@ -1,6 +1,6 @@
1
1
  [metadata]
2
2
  name = PyamilySeq
3
- version = v0.7.0
3
+ version = v0.7.1
4
4
  author = Nicholas Dimonaco
5
5
  author_email = nicholas@dimonaco.co.uk
6
6
  description = PyamilySeq - A a tool to look for sequence-based gene groups identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.
pyamilyseq-0.7.1/src/PyamilySeq/Constants.py ADDED
@@ -0,0 +1,2 @@
1
+ PyamilySeq_Version = 'v0.7.1'
2
+
{pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/src/PyamilySeq/PyamilySeq.py RENAMED
@@ -41,6 +41,7 @@ def run_cd_hit(options, input_file, clustering_output, clustering_mode):
41
41
 
42
42
  def main():
43
43
  parser = argparse.ArgumentParser(description='PyamilySeq ' + PyamilySeq_Version + ': A tool that groups genes into unique clusters.')
44
+ vparser = argparse.ArgumentParser()
44
45
  ### Required Arguments
45
46
  required = parser.add_argument_group('Required Arguments')
46
47
  required.add_argument('-run_mode', action='store', dest='run_mode', choices=['Full','Partial'],
@@ -132,10 +133,20 @@ def main():
132
133
  misc = parser.add_argument_group('Misc')
133
134
  misc.add_argument('-verbose', action='store_true', dest='verbose', default=None, help='Default - False: Print out runtime messages',
134
135
  required = False)
135
- misc.add_argument('-v', action='store_true', dest='version',
136
+
137
+ ### Version Arguments
138
+ version = vparser.add_argument_group('Version')
139
+ version.add_argument('-v', action='store_true', dest='version',
136
140
  help='Default - False: Print out version number and exit',
137
141
  required=False)
138
142
 
143
+
144
+
145
+ args, unknown = vparser.parse_known_args()
146
+
147
+ if args.version == True:
148
+ sys.exit("PyamilySeq version: "+PyamilySeq_Version)
149
+
139
150
  options = parser.parse_args()
140
151
 
141
152
  ### Checking all required parameters are provided by user #!!# Doesn't seem to work
@@ -288,5 +299,5 @@ def main():
288
299
  "Please report any issues to: https://github.com/NickJD/PyamilySeq/issues\n#####")
289
300
 
290
301
  if __name__ == "__main__":
291
- print("Running PyamilySeq "+PyamilySeq_Version)
302
+ #print("Running PyamilySeq "+PyamilySeq_Version)
292
303
  main()
{pyamilyseq-0.7.0 → pyamilyseq-0.7.1/src/PyamilySeq.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: PyamilySeq
3
- Version: 0.7.0
3
+ Version: 0.7.1
4
4
  Summary: PyamilySeq - A a tool to look for sequence-based gene groups 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
@@ -58,7 +58,7 @@ Escherichia_coli_110957|ENSB:TIZS9kbTvShDvyX Escherichia_coli_110957|ENSB:TIZS9k
58
58
  ```
59
59
  ### Example output:
60
60
  ```
61
- Running PyamilySeq v0.7.0
61
+ Running PyamilySeq v0.7.1
62
62
  Calculating Groups
63
63
  Gene Groups:
64
64
  First_core_99: 2682
@@ -80,7 +80,7 @@ PyamilySeq -run_mode Partial -group_mode Genus -clustering_format CD-HIT -output
80
80
  -cluster_file .../test_data/genus/CD-HIT/combined_cds_cd-hit_80_60.clstr -gpa
81
81
  ```
82
82
  ```commandline
83
- Running PyamilySeq v0.7.0
83
+ Running PyamilySeq v0.7.1
84
84
  Calculating Groups
85
85
  Genus Groups:
86
86
  First_genera_1: 28549
@@ -98,37 +98,36 @@ Please report any issues to: https://github.com/NickJD/PyamilySeq/issues
98
98
  ### Reclustering can be used to see where additional sequences/genes lay in relation to a contemporary pangenome/gene grouping.
99
99
  ```
100
100
  PyamilySeq -run_mode Partial -group_mode Species -clustering_format CD-HIT -output_dir .../test_data/species/CD-HIT/testing
101
- -cluster_file .../test_data/species/CD-HIT/E-coli_extracted_cds_cd-hit_90_60.clstr -gpa
102
- -reclustered .../test_data/species/CD-HIT/E-coli_extracted_cds_cd-hit_90_60_And_StORFs_cds_90_60.clstr
101
+ -cluster_file .../test_data/species/CD-HIT/E-coli_extracted_cds_cd-hit_80_60.clstr -gpa
102
+ -reclustered .../test_data/species/CD-HIT/E-coli_extracted_cds_cd-hit_80_60_And_StORFs_cds_80_60.clstr
103
103
  ```
104
104
  #### As can be seen below, the additional sequences recovered by the StORF-Reporter annotation tool have 'extended' contemporary or created entirely new gene groups. 'First' corresponds to the groups identified from the first clustering round and 'Second' for the second. In 'reclustering' mode, First_core_# groups are unaffected thus retaining the initial grouping information.
105
105
  ```commandline
106
- Running PyamilySeq v0.7.0
107
106
  Calculating Groups
108
107
  Gene Groups:
109
- First_core_99: 69
110
- First_core_95: 1002
111
- First_core_15: 4716
112
- First_core_0: 37960
113
- extended_core_99: 6
114
- extended_core_95: 73
115
- extended_core_15: 331
116
- extended_core_0: 582
117
- combined_core_99: 4
118
- combined_core_95: 88
119
- combined_core_15: 455
120
- combined_core_0: 228
108
+ First_core_99: 587
109
+ First_core_95: 1529
110
+ First_core_15: 3708
111
+ First_core_0: 29992
112
+ extended_core_99: 29
113
+ extended_core_95: 67
114
+ extended_core_15: 431
115
+ extended_core_0: 1331
116
+ combined_core_99: 2
117
+ combined_core_95: 4
118
+ combined_core_15: 5
119
+ combined_core_0: 4
121
120
  Second_core_99: 0
122
- Second_core_95: 5
123
- Second_core_15: 254
124
- Second_core_0: 3714
125
- only_Second_core_99: 6
126
- only_Second_core_95: 364
127
- only_Second_core_15: 3950
128
- only_Second_core_0: 31269
129
- Total Number of First Gene Groups (Including Singletons): 43747
130
- Total Number of Second Gene Groups (Including Singletons): 66525
131
- Total Number of First Gene Groups That Had Additional Second Sequences But Not New Genomes: 9593
121
+ Second_core_95: 6
122
+ Second_core_15: 172
123
+ Second_core_0: 1825
124
+ only_Second_core_99: 53
125
+ only_Second_core_95: 493
126
+ only_Second_core_15: 3806
127
+ only_Second_core_0: 27569
128
+ Total Number of First Gene Groups (Including Singletons): 35816
129
+ Total Number of Second Gene Groups (Including Singletons): 67728
130
+ Total Number of First Gene Groups That Had Additional Second Sequences But Not New Genomes: 136
132
131
  Outputting gene_presence_absence file
133
132
  Thank you for using PyamilySeq -- A detailed user manual can be found at https://github.com/NickJD/PyamilySeq
134
133
  Please report any issues to: https://github.com/NickJD/PyamilySeq/issues
@@ -138,14 +137,14 @@ Please report any issues to: https://github.com/NickJD/PyamilySeq/issues
138
137
  ## PyamilySeq - Menu:
139
138
  ### PyamilySeq is separated into two main 'run modes', Full and Partial. They each have their own set of required and optional arguments.
140
139
  ```
141
- Running PyamilySeq v0.7.0
140
+ Running PyamilySeq v0.7.1
142
141
  usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus} -clustering_format {CD-HIT,TSV,CSV} -output_dir OUTPUT_DIR
143
142
  [-input_type {separate,combined}] [-input_dir INPUT_DIR] [-name_split NAME_SPLIT] [-sequence_type {AA,DNA}] [-gene_ident GENE_IDENT]
144
143
  [-pid PIDENT] [-len_diff LEN_DIFF] [-mem CLUSTERING_MEMORY] [-t CLUSTERING_THREADS] [-cluster_file CLUSTER_FILE]
145
144
  [-reclustered RECLUSTERED] [-seq_tag SEQUENCE_TAG] [-core_groups CORE_GROUPS] [-genus_groups GENUS_GROUPS] [-w WRITE_GROUPS] [-a]
146
145
  [-original_fasta ORIGINAL_FASTA] [-gpa] [-verbose] [-v]
147
146
 
148
- PyamilySeq v0.7.0: A tool that groups genes into unique clusters.
147
+ PyamilySeq v0.7.1: A tool that groups genes into unique clusters.
149
148
 
150
149
  options:
151
150
  -h, --help show this help message and exit
@@ -198,9 +197,9 @@ Output Parameters:
198
197
  -w WRITE_GROUPS Default - No output: Output sequences of identified groups (provide levels at which to output - Species "-w 99,95" Genus "-w 2,3" -
199
198
  Must provide FASTA file with -original_fasta if in Partial run mode.
200
199
  -a Default - No output: SLOW! (Only works for Species mode) Output aligned and concatinated sequences of identified groups -provide
201
- group levels at which to output "-w 99,95" - Must provide FASTA file with -original_fasta in Partialrun mode.
200
+ group levels at which to output "-w 99,95" - Must provide FASTA file with -original_fasta in Partial run mode.
202
201
  -original_fasta ORIGINAL_FASTA
203
- FASTA file to use in conjunction with "-w" or "-con" when running in Partial Mode.
202
+ FASTA file to use in conjunction with "-w" or "-a" when running in Partial Mode.
204
203
  -gpa Default - False: If selected, a Roary/Panaroo formatted gene_presence_absence.csv will be created - Required for Coinfinder and
205
204
  other downstream tools
206
205
 
@@ -222,7 +221,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split _combined.gff3 -output
222
221
  ```
223
222
  usage: Seq_Combiner.py [-h] -input_dir INPUT_DIR -input_type {separate,combined,fasta} -name_split NAME_SPLIT -output_dir OUTPUT_DIR -output_name OUTPUT_FILE [-gene_ident GENE_IDENT] [-translate] [-v]
224
223
 
225
- Seq-Combiner v0.7.0: A tool to extract sequences from GFF/FASTA files.
224
+ Seq-Combiner v0.7.1: A tool to extract sequences from GFF/FASTA files.
226
225
 
227
226
  options:
228
227
  -h, --help show this help message and exit
pyamilyseq-0.7.0/src/PyamilySeq/Constants.py DELETED
@@ -1,2 +0,0 @@
1
- PyamilySeq_Version = 'v0.7.0'
2
-
{pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/LICENSE RENAMED
File without changes
{pyamilyseq-0.7.0 → pyamilyseq-0.7.1}/pyproject.toml RENAMED
File without changes