PyamilySeq 0.5.1__tar.gz → 0.5.2__tar.gz

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Files changed (19) hide show
  1. {pyamilyseq-0.5.1/src/PyamilySeq.egg-info → pyamilyseq-0.5.2}/PKG-INFO +46 -65
  2. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/README.md +45 -64
  3. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/setup.cfg +1 -1
  4. pyamilyseq-0.5.2/src/PyamilySeq/Constants.py +2 -0
  5. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/src/PyamilySeq/PyamilySeq.py +10 -2
  6. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2/src/PyamilySeq.egg-info}/PKG-INFO +46 -65
  7. pyamilyseq-0.5.1/src/PyamilySeq/Constants.py +0 -2
  8. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/LICENSE +0 -0
  9. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/pyproject.toml +0 -0
  10. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/src/PyamilySeq/CD-Hit_StORF-Reporter_Cross-Genera_Builder.py +0 -0
  11. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/src/PyamilySeq/PyamilySeq_Genus.py +0 -0
  12. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/src/PyamilySeq/PyamilySeq_Species.py +0 -0
  13. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/src/PyamilySeq/Seq_Combiner.py +0 -0
  14. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/src/PyamilySeq/__init__.py +0 -0
  15. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/src/PyamilySeq/utils.py +0 -0
  16. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/src/PyamilySeq.egg-info/SOURCES.txt +0 -0
  17. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/src/PyamilySeq.egg-info/dependency_links.txt +0 -0
  18. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/src/PyamilySeq.egg-info/entry_points.txt +0 -0
  19. {pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/src/PyamilySeq.egg-info/top_level.txt +0 -0
{pyamilyseq-0.5.1/src/PyamilySeq.egg-info → pyamilyseq-0.5.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: PyamilySeq
3
- Version: 0.5.1
3
+ Version: 0.5.2
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
@@ -34,107 +34,88 @@ PyamilySeq requires Python 3.6 or higher. Install using pip:
34
34
  pip install PyamilySeq
35
35
  ```
36
36
 
37
+ ### Examples: Below are two examples of running PyamilySeq in its two main modes.
38
+ #### 'Full Mode': Will conduct clustering of sequences as part of PyamilySeq run
39
+ ```bash
40
+ 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
41
+ ```
42
+ #### 'Partial Mode': Will take the output of a sequence clustering
43
+ ```bash
44
+ 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
45
+ ```
46
+
47
+ ```bash
48
+ Calculating Groups
49
+ Gene Groups:
50
+ first_core_99: 3103
51
+ first_core_95: 0
52
+ first_core_15: 3217
53
+ first_core_0: 4808
54
+ Total Number of Gene Groups (Including Singletons): 11128
55
+ ```
56
+
57
+
37
58
  ## Usage - Menu
38
59
  ```
39
- usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus}
40
- -clust_tool {CD-HIT} -output_dir OUTPUT_DIR
41
- [-input_type {separate,combined}] [-input_dir INPUT_DIR]
42
- [-name_split NAME_SPLIT] [-pid PIDENT]
43
- [-len_diff LEN_DIFF] [-cluster_file CLUSTER_FILE]
44
- [-reclustered RECLUSTERED] [-seq_tag SEQUENCE_TAG]
45
- [-groups CORE_GROUPS] [-w WRITE_FAMILIES] [-con CON_CORE]
46
- [-original_fasta ORIGINAL_FASTA]
47
- [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}]
48
- [-v]
49
-
50
- PyamilySeq v0.5.1: PyamilySeq Run Parameters.
60
+ usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species} -clust_tool {CD-HIT} -output_dir OUTPUT_DIR [-input_type {separate,combined}] [-input_dir INPUT_DIR] [-name_split NAME_SPLIT] [-pid PIDENT] [-len_diff LEN_DIFF] [-mem CLUSTERING_MEMORY] [-t CLUSTERING_THREADS] [-cluster_file CLUSTER_FILE]
61
+ [-reclustered RECLUSTERED] [-seq_tag SEQUENCE_TAG] [-groups CORE_GROUPS] [-w WRITE_FAMILIES] [-con CON_CORE] [-original_fasta ORIGINAL_FASTA] [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}] [-v]
62
+
63
+ PyamilySeq v0.5.2: PyamilySeq Run Parameters.
51
64
 
52
65
  options:
53
66
  -h, --help show this help message and exit
54
67
 
55
68
  Required Arguments:
56
69
  -run_mode {Full,Partial}
57
- Run Mode: Should PyamilySeq be run in "Full" or
58
- "Partial" mode?
70
+ Run Mode: Should PyamilySeq be run in "Full" or "Partial" mode?
59
71
  -group_mode {Species}
60
- Group Mode: Should PyamilySeq be run in "Species" or
61
- "Genus" mode? - Genus mode not currently functioning
62
- -clust_tool {CD-HIT} Clustering tool to use: CD-HIT, DIAMOND, BLAST or
63
- MMseqs2.
72
+ Group Mode: Should PyamilySeq be run in "Species" or "Genus" mode? - Genus mode not currently functioning
73
+ -clust_tool {CD-HIT} Clustering tool to use: CD-HIT, DIAMOND, BLAST or MMseqs2.
64
74
  -output_dir OUTPUT_DIR
65
75
  Directory for all output files.
66
76
 
67
77
  Full-Mode Arguments - Required when "-run_mode Full" is used:
68
78
  -input_type {separate,combined}
69
- Type of input files: 'separate' for separate FASTA and
70
- GFF files, 'combined' for GFF files with embedded
71
- FASTA sequences.
79
+ Type of input files: 'separate' for separate FASTA and GFF files, 'combined' for GFF files with embedded FASTA sequences.
72
80
  -input_dir INPUT_DIR Directory containing GFF/FASTA files.
73
81
  -name_split NAME_SPLIT
74
- substring used to split the filename and extract the
75
- genome name ('_combined.gff3' or '.gff').
82
+ substring used to split the filename and extract the genome name ('_combined.gff3' or '.gff').
76
83
  -pid PIDENT Default 0.95: Pident threshold for clustering.
77
- -len_diff LEN_DIFF Default 0.80: Minimum length difference between
78
- clustered sequences - (-s) threshold for CD-HIT
79
- clustering.
84
+ -len_diff LEN_DIFF Default 0.80: Minimum length difference between clustered sequences - (-s) threshold for CD-HIT clustering.
85
+
86
+ Clustering Runtime Arguments - Optional when "-run_mode Full" is used:
87
+ -mem CLUSTERING_MEMORY
88
+ Default 4000: Memory to be allocated for clustering (in MBs).
89
+ -t CLUSTERING_THREADS
90
+ Default 4: Threads to be allocated for clustering.
80
91
 
81
92
  Partial-Mode Arguments - Required when "-run_mode Partial" is used:
82
93
  -cluster_file CLUSTER_FILE
83
- Clustering output file containing CD-HIT, TSV or CSV
84
- Edge List
94
+ Clustering output file containing CD-HIT, TSV or CSV Edge List
85
95
 
86
96
  Grouping Arguments - Use to fine-tune grouping of genes after clustering:
87
97
  -reclustered RECLUSTERED
88
- Clustering output file from secondary round of
89
- clustering
98
+ Clustering output file from secondary round of clustering
90
99
  -seq_tag SEQUENCE_TAG
91
- Default - "StORF": Unique identifier to be used to
92
- distinguish the second of two rounds of clustered
93
- sequences
100
+ Default - "StORF": Unique identifier to be used to distinguish the second of two rounds of clustered sequences
94
101
  -groups CORE_GROUPS Default - ('99,95,15'): Gene family groups to use
95
102
 
96
103
  Output Parameters:
97
- -w WRITE_FAMILIES Default - No output: Output sequences of identified
98
- families (provide levels at which to output "-w 99,95"
99
- - Must provide FASTA file with -fasta
100
- -con CON_CORE Default - No output: Output aligned and concatinated
101
- sequences of identified families - used for MSA
102
- (provide levels at which to output "-w 99,95" - Must
103
- provide FASTA file with -fasta
104
+ -w WRITE_FAMILIES Default - No output: Output sequences of identified families (provide levels at which to output "-w 99,95" - Must provide FASTA file with -fasta
105
+ -con CON_CORE Default - No output: Output aligned and concatinated sequences of identified families - used for MSA (provide levels at which to output "-w 99,95" - Must provide FASTA file with -fasta
104
106
  -original_fasta ORIGINAL_FASTA
105
- FASTA file to use in conjunction with "-w" or "-con"
106
- when running in Partial Mode.
107
+ FASTA file to use in conjunction with "-w" or "-con" when running in Partial Mode.
107
108
  -gpa GENE_PRESENCE_ABSENCE_OUT
108
- Default - False: If selected, a Roary formatted
109
- gene_presence_absence.csv will be created - Required
110
- for Coinfinder and other downstream tools
109
+ Default - False: If selected, a Roary formatted gene_presence_absence.csv will be created - Required for Coinfinder and other downstream tools
111
110
 
112
111
  Misc:
113
112
  -verbose {True,False}
114
113
  Default - False: Print out runtime messages
115
114
  -v Default - False: Print out version number and exit
116
115
 
117
- ```
118
116
 
119
- ### Examples: Below are two examples of running PyamilySeq in its two main modes.
120
- #### 'Full Mode': Will conduct clustering of sequences as part of PyamilySeq run
121
- ```bash
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
- ```
124
- #### 'Partial Mode': Will take the output of a sequence clustering
125
- ```bash
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
117
  ```
128
118
 
129
- ```bash
130
- Calculating Groups
131
- Gene Groups:
132
- first_core_99: 3103
133
- first_core_95: 0
134
- first_core_15: 3217
135
- first_core_0: 4808
136
- Total Number of Gene Groups (Including Singletons): 11128
137
- ```
138
119
 
139
120
  ## Seq-Combiner: This tool is provided to enable the pre-processing of multiple GFF/FASTA files together ready to be clustered by the user
140
121
  ### Example:
@@ -145,7 +126,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split _combined.gff3 -output
145
126
  ```bash
146
127
  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
128
 
148
- Seq-Combiner v0.5.1: Seq-Combiner Run Parameters.
129
+ Seq-Combiner v0.5.2: Seq-Combiner Run Parameters.
149
130
 
150
131
  options:
151
132
  -h, --help show this help message and exit
{pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/README.md RENAMED
@@ -19,107 +19,88 @@ PyamilySeq requires Python 3.6 or higher. Install using pip:
19
19
  pip install PyamilySeq
20
20
  ```
21
21
 
22
+ ### Examples: Below are two examples of running PyamilySeq in its two main modes.
23
+ #### 'Full Mode': Will conduct clustering of sequences as part of PyamilySeq run
24
+ ```bash
25
+ 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
26
+ ```
27
+ #### 'Partial Mode': Will take the output of a sequence clustering
28
+ ```bash
29
+ 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
30
+ ```
31
+
32
+ ```bash
33
+ Calculating Groups
34
+ Gene Groups:
35
+ first_core_99: 3103
36
+ first_core_95: 0
37
+ first_core_15: 3217
38
+ first_core_0: 4808
39
+ Total Number of Gene Groups (Including Singletons): 11128
40
+ ```
41
+
42
+
22
43
  ## Usage - Menu
23
44
  ```
24
- usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus}
25
- -clust_tool {CD-HIT} -output_dir OUTPUT_DIR
26
- [-input_type {separate,combined}] [-input_dir INPUT_DIR]
27
- [-name_split NAME_SPLIT] [-pid PIDENT]
28
- [-len_diff LEN_DIFF] [-cluster_file CLUSTER_FILE]
29
- [-reclustered RECLUSTERED] [-seq_tag SEQUENCE_TAG]
30
- [-groups CORE_GROUPS] [-w WRITE_FAMILIES] [-con CON_CORE]
31
- [-original_fasta ORIGINAL_FASTA]
32
- [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}]
33
- [-v]
34
-
35
- PyamilySeq v0.5.1: PyamilySeq Run Parameters.
45
+ usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species} -clust_tool {CD-HIT} -output_dir OUTPUT_DIR [-input_type {separate,combined}] [-input_dir INPUT_DIR] [-name_split NAME_SPLIT] [-pid PIDENT] [-len_diff LEN_DIFF] [-mem CLUSTERING_MEMORY] [-t CLUSTERING_THREADS] [-cluster_file CLUSTER_FILE]
46
+ [-reclustered RECLUSTERED] [-seq_tag SEQUENCE_TAG] [-groups CORE_GROUPS] [-w WRITE_FAMILIES] [-con CON_CORE] [-original_fasta ORIGINAL_FASTA] [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}] [-v]
47
+
48
+ PyamilySeq v0.5.2: PyamilySeq Run Parameters.
36
49
 
37
50
  options:
38
51
  -h, --help show this help message and exit
39
52
 
40
53
  Required Arguments:
41
54
  -run_mode {Full,Partial}
42
- Run Mode: Should PyamilySeq be run in "Full" or
43
- "Partial" mode?
55
+ Run Mode: Should PyamilySeq be run in "Full" or "Partial" mode?
44
56
  -group_mode {Species}
45
- Group Mode: Should PyamilySeq be run in "Species" or
46
- "Genus" mode? - Genus mode not currently functioning
47
- -clust_tool {CD-HIT} Clustering tool to use: CD-HIT, DIAMOND, BLAST or
48
- MMseqs2.
57
+ Group Mode: Should PyamilySeq be run in "Species" or "Genus" mode? - Genus mode not currently functioning
58
+ -clust_tool {CD-HIT} Clustering tool to use: CD-HIT, DIAMOND, BLAST or MMseqs2.
49
59
  -output_dir OUTPUT_DIR
50
60
  Directory for all output files.
51
61
 
52
62
  Full-Mode Arguments - Required when "-run_mode Full" is used:
53
63
  -input_type {separate,combined}
54
- Type of input files: 'separate' for separate FASTA and
55
- GFF files, 'combined' for GFF files with embedded
56
- FASTA sequences.
64
+ Type of input files: 'separate' for separate FASTA and GFF files, 'combined' for GFF files with embedded FASTA sequences.
57
65
  -input_dir INPUT_DIR Directory containing GFF/FASTA files.
58
66
  -name_split NAME_SPLIT
59
- substring used to split the filename and extract the
60
- genome name ('_combined.gff3' or '.gff').
67
+ substring used to split the filename and extract the genome name ('_combined.gff3' or '.gff').
61
68
  -pid PIDENT Default 0.95: Pident threshold for clustering.
62
- -len_diff LEN_DIFF Default 0.80: Minimum length difference between
63
- clustered sequences - (-s) threshold for CD-HIT
64
- clustering.
69
+ -len_diff LEN_DIFF Default 0.80: Minimum length difference between clustered sequences - (-s) threshold for CD-HIT clustering.
70
+
71
+ Clustering Runtime Arguments - Optional when "-run_mode Full" is used:
72
+ -mem CLUSTERING_MEMORY
73
+ Default 4000: Memory to be allocated for clustering (in MBs).
74
+ -t CLUSTERING_THREADS
75
+ Default 4: Threads to be allocated for clustering.
65
76
 
66
77
  Partial-Mode Arguments - Required when "-run_mode Partial" is used:
67
78
  -cluster_file CLUSTER_FILE
68
- Clustering output file containing CD-HIT, TSV or CSV
69
- Edge List
79
+ Clustering output file containing CD-HIT, TSV or CSV Edge List
70
80
 
71
81
  Grouping Arguments - Use to fine-tune grouping of genes after clustering:
72
82
  -reclustered RECLUSTERED
73
- Clustering output file from secondary round of
74
- clustering
83
+ Clustering output file from secondary round of clustering
75
84
  -seq_tag SEQUENCE_TAG
76
- Default - "StORF": Unique identifier to be used to
77
- distinguish the second of two rounds of clustered
78
- sequences
85
+ Default - "StORF": Unique identifier to be used to distinguish the second of two rounds of clustered sequences
79
86
  -groups CORE_GROUPS Default - ('99,95,15'): Gene family groups to use
80
87
 
81
88
  Output Parameters:
82
- -w WRITE_FAMILIES Default - No output: Output sequences of identified
83
- families (provide levels at which to output "-w 99,95"
84
- - Must provide FASTA file with -fasta
85
- -con CON_CORE Default - No output: Output aligned and concatinated
86
- sequences of identified families - used for MSA
87
- (provide levels at which to output "-w 99,95" - Must
88
- provide FASTA file with -fasta
89
+ -w WRITE_FAMILIES Default - No output: Output sequences of identified families (provide levels at which to output "-w 99,95" - Must provide FASTA file with -fasta
90
+ -con CON_CORE Default - No output: Output aligned and concatinated sequences of identified families - used for MSA (provide levels at which to output "-w 99,95" - Must provide FASTA file with -fasta
89
91
  -original_fasta ORIGINAL_FASTA
90
- FASTA file to use in conjunction with "-w" or "-con"
91
- when running in Partial Mode.
92
+ FASTA file to use in conjunction with "-w" or "-con" when running in Partial Mode.
92
93
  -gpa GENE_PRESENCE_ABSENCE_OUT
93
- Default - False: If selected, a Roary formatted
94
- gene_presence_absence.csv will be created - Required
95
- for Coinfinder and other downstream tools
94
+ Default - False: If selected, a Roary formatted gene_presence_absence.csv will be created - Required for Coinfinder and other downstream tools
96
95
 
97
96
  Misc:
98
97
  -verbose {True,False}
99
98
  Default - False: Print out runtime messages
100
99
  -v Default - False: Print out version number and exit
101
100
 
102
- ```
103
101
 
104
- ### Examples: Below are two examples of running PyamilySeq in its two main modes.
105
- #### 'Full Mode': Will conduct clustering of sequences as part of PyamilySeq run
106
- ```bash
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
108
- ```
109
- #### 'Partial Mode': Will take the output of a sequence clustering
110
- ```bash
111
- 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
112
102
  ```
113
103
 
114
- ```bash
115
- Calculating Groups
116
- Gene Groups:
117
- first_core_99: 3103
118
- first_core_95: 0
119
- first_core_15: 3217
120
- first_core_0: 4808
121
- Total Number of Gene Groups (Including Singletons): 11128
122
- ```
123
104
 
124
105
  ## Seq-Combiner: This tool is provided to enable the pre-processing of multiple GFF/FASTA files together ready to be clustered by the user
125
106
  ### Example:
@@ -130,7 +111,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split _combined.gff3 -output
130
111
  ```bash
131
112
  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
132
113
 
133
- Seq-Combiner v0.5.1: Seq-Combiner Run Parameters.
114
+ Seq-Combiner v0.5.2: Seq-Combiner Run Parameters.
134
115
 
135
116
  options:
136
117
  -h, --help show this help message and exit
{pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/setup.cfg RENAMED
@@ -1,6 +1,6 @@
1
1
  [metadata]
2
2
  name = PyamilySeq
3
- version = v0.5.1
3
+ version = v0.5.2
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 families identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.
pyamilyseq-0.5.2/src/PyamilySeq/Constants.py ADDED
@@ -0,0 +1,2 @@
1
+ PyamilySeq_Version = 'v0.5.2'
2
+
{pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/src/PyamilySeq/PyamilySeq.py RENAMED
@@ -25,7 +25,8 @@ def run_cd_hit(input_file, clustering_output, options):
25
25
  '-o', clustering_output,
26
26
  '-c', str(options.pident),
27
27
  '-s', str(options.len_diff),
28
- '-T', "20",
28
+ '-T', str(options.clustering_threads),
29
+ '-M', str(options.clustering_memory),
29
30
  '-d', "0",
30
31
  '-sc', "1",
31
32
  '-sf', "1"
@@ -70,7 +71,14 @@ def main():
70
71
  full_mode_args.add_argument("-len_diff", action="store", dest="len_diff", type=float, default=0.80,
71
72
  help="Default 0.80: Minimum length difference between clustered sequences - (-s) threshold for CD-HIT clustering.",
72
73
  required=False)
73
-
74
+ ###Clustering Arguments
75
+ clustering_args = parser.add_argument_group('Clustering Runtime Arguments - Optional when "-run_mode Full" is used')
76
+ clustering_args.add_argument("-mem", action="store", dest="clustering_memory", type=int, default=4000,
77
+ help="Default 4000: Memory to be allocated for clustering (in MBs).",
78
+ required=False)
79
+ clustering_args.add_argument("-t", action="store", dest="clustering_threads", type=int, default=4,
80
+ help="Default 4: Threads to be allocated for clustering.",
81
+ required=False)
74
82
 
75
83
  ###Partial-Mode Arguments
76
84
  partial_mode_args = parser.add_argument_group('Partial-Mode Arguments - Required when "-run_mode Partial" is used')
{pyamilyseq-0.5.1 → pyamilyseq-0.5.2/src/PyamilySeq.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: PyamilySeq
3
- Version: 0.5.1
3
+ Version: 0.5.2
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
@@ -34,107 +34,88 @@ PyamilySeq requires Python 3.6 or higher. Install using pip:
34
34
  pip install PyamilySeq
35
35
  ```
36
36
 
37
+ ### Examples: Below are two examples of running PyamilySeq in its two main modes.
38
+ #### 'Full Mode': Will conduct clustering of sequences as part of PyamilySeq run
39
+ ```bash
40
+ 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
41
+ ```
42
+ #### 'Partial Mode': Will take the output of a sequence clustering
43
+ ```bash
44
+ 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
45
+ ```
46
+
47
+ ```bash
48
+ Calculating Groups
49
+ Gene Groups:
50
+ first_core_99: 3103
51
+ first_core_95: 0
52
+ first_core_15: 3217
53
+ first_core_0: 4808
54
+ Total Number of Gene Groups (Including Singletons): 11128
55
+ ```
56
+
57
+
37
58
  ## Usage - Menu
38
59
  ```
39
- usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus}
40
- -clust_tool {CD-HIT} -output_dir OUTPUT_DIR
41
- [-input_type {separate,combined}] [-input_dir INPUT_DIR]
42
- [-name_split NAME_SPLIT] [-pid PIDENT]
43
- [-len_diff LEN_DIFF] [-cluster_file CLUSTER_FILE]
44
- [-reclustered RECLUSTERED] [-seq_tag SEQUENCE_TAG]
45
- [-groups CORE_GROUPS] [-w WRITE_FAMILIES] [-con CON_CORE]
46
- [-original_fasta ORIGINAL_FASTA]
47
- [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}]
48
- [-v]
49
-
50
- PyamilySeq v0.5.1: PyamilySeq Run Parameters.
60
+ usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species} -clust_tool {CD-HIT} -output_dir OUTPUT_DIR [-input_type {separate,combined}] [-input_dir INPUT_DIR] [-name_split NAME_SPLIT] [-pid PIDENT] [-len_diff LEN_DIFF] [-mem CLUSTERING_MEMORY] [-t CLUSTERING_THREADS] [-cluster_file CLUSTER_FILE]
61
+ [-reclustered RECLUSTERED] [-seq_tag SEQUENCE_TAG] [-groups CORE_GROUPS] [-w WRITE_FAMILIES] [-con CON_CORE] [-original_fasta ORIGINAL_FASTA] [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}] [-v]
62
+
63
+ PyamilySeq v0.5.2: PyamilySeq Run Parameters.
51
64
 
52
65
  options:
53
66
  -h, --help show this help message and exit
54
67
 
55
68
  Required Arguments:
56
69
  -run_mode {Full,Partial}
57
- Run Mode: Should PyamilySeq be run in "Full" or
58
- "Partial" mode?
70
+ Run Mode: Should PyamilySeq be run in "Full" or "Partial" mode?
59
71
  -group_mode {Species}
60
- Group Mode: Should PyamilySeq be run in "Species" or
61
- "Genus" mode? - Genus mode not currently functioning
62
- -clust_tool {CD-HIT} Clustering tool to use: CD-HIT, DIAMOND, BLAST or
63
- MMseqs2.
72
+ Group Mode: Should PyamilySeq be run in "Species" or "Genus" mode? - Genus mode not currently functioning
73
+ -clust_tool {CD-HIT} Clustering tool to use: CD-HIT, DIAMOND, BLAST or MMseqs2.
64
74
  -output_dir OUTPUT_DIR
65
75
  Directory for all output files.
66
76
 
67
77
  Full-Mode Arguments - Required when "-run_mode Full" is used:
68
78
  -input_type {separate,combined}
69
- Type of input files: 'separate' for separate FASTA and
70
- GFF files, 'combined' for GFF files with embedded
71
- FASTA sequences.
79
+ Type of input files: 'separate' for separate FASTA and GFF files, 'combined' for GFF files with embedded FASTA sequences.
72
80
  -input_dir INPUT_DIR Directory containing GFF/FASTA files.
73
81
  -name_split NAME_SPLIT
74
- substring used to split the filename and extract the
75
- genome name ('_combined.gff3' or '.gff').
82
+ substring used to split the filename and extract the genome name ('_combined.gff3' or '.gff').
76
83
  -pid PIDENT Default 0.95: Pident threshold for clustering.
77
- -len_diff LEN_DIFF Default 0.80: Minimum length difference between
78
- clustered sequences - (-s) threshold for CD-HIT
79
- clustering.
84
+ -len_diff LEN_DIFF Default 0.80: Minimum length difference between clustered sequences - (-s) threshold for CD-HIT clustering.
85
+
86
+ Clustering Runtime Arguments - Optional when "-run_mode Full" is used:
87
+ -mem CLUSTERING_MEMORY
88
+ Default 4000: Memory to be allocated for clustering (in MBs).
89
+ -t CLUSTERING_THREADS
90
+ Default 4: Threads to be allocated for clustering.
80
91
 
81
92
  Partial-Mode Arguments - Required when "-run_mode Partial" is used:
82
93
  -cluster_file CLUSTER_FILE
83
- Clustering output file containing CD-HIT, TSV or CSV
84
- Edge List
94
+ Clustering output file containing CD-HIT, TSV or CSV Edge List
85
95
 
86
96
  Grouping Arguments - Use to fine-tune grouping of genes after clustering:
87
97
  -reclustered RECLUSTERED
88
- Clustering output file from secondary round of
89
- clustering
98
+ Clustering output file from secondary round of clustering
90
99
  -seq_tag SEQUENCE_TAG
91
- Default - "StORF": Unique identifier to be used to
92
- distinguish the second of two rounds of clustered
93
- sequences
100
+ Default - "StORF": Unique identifier to be used to distinguish the second of two rounds of clustered sequences
94
101
  -groups CORE_GROUPS Default - ('99,95,15'): Gene family groups to use
95
102
 
96
103
  Output Parameters:
97
- -w WRITE_FAMILIES Default - No output: Output sequences of identified
98
- families (provide levels at which to output "-w 99,95"
99
- - Must provide FASTA file with -fasta
100
- -con CON_CORE Default - No output: Output aligned and concatinated
101
- sequences of identified families - used for MSA
102
- (provide levels at which to output "-w 99,95" - Must
103
- provide FASTA file with -fasta
104
+ -w WRITE_FAMILIES Default - No output: Output sequences of identified families (provide levels at which to output "-w 99,95" - Must provide FASTA file with -fasta
105
+ -con CON_CORE Default - No output: Output aligned and concatinated sequences of identified families - used for MSA (provide levels at which to output "-w 99,95" - Must provide FASTA file with -fasta
104
106
  -original_fasta ORIGINAL_FASTA
105
- FASTA file to use in conjunction with "-w" or "-con"
106
- when running in Partial Mode.
107
+ FASTA file to use in conjunction with "-w" or "-con" when running in Partial Mode.
107
108
  -gpa GENE_PRESENCE_ABSENCE_OUT
108
- Default - False: If selected, a Roary formatted
109
- gene_presence_absence.csv will be created - Required
110
- for Coinfinder and other downstream tools
109
+ Default - False: If selected, a Roary formatted gene_presence_absence.csv will be created - Required for Coinfinder and other downstream tools
111
110
 
112
111
  Misc:
113
112
  -verbose {True,False}
114
113
  Default - False: Print out runtime messages
115
114
  -v Default - False: Print out version number and exit
116
115
 
117
- ```
118
116
 
119
- ### Examples: Below are two examples of running PyamilySeq in its two main modes.
120
- #### 'Full Mode': Will conduct clustering of sequences as part of PyamilySeq run
121
- ```bash
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
- ```
124
- #### 'Partial Mode': Will take the output of a sequence clustering
125
- ```bash
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
117
  ```
128
118
 
129
- ```bash
130
- Calculating Groups
131
- Gene Groups:
132
- first_core_99: 3103
133
- first_core_95: 0
134
- first_core_15: 3217
135
- first_core_0: 4808
136
- Total Number of Gene Groups (Including Singletons): 11128
137
- ```
138
119
 
139
120
  ## Seq-Combiner: This tool is provided to enable the pre-processing of multiple GFF/FASTA files together ready to be clustered by the user
140
121
  ### Example:
@@ -145,7 +126,7 @@ Seq-Combiner -input_dir .../test_data/genomes -name_split _combined.gff3 -output
145
126
  ```bash
146
127
  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
128
 
148
- Seq-Combiner v0.5.1: Seq-Combiner Run Parameters.
129
+ Seq-Combiner v0.5.2: Seq-Combiner Run Parameters.
149
130
 
150
131
  options:
151
132
  -h, --help show this help message and exit
pyamilyseq-0.5.1/src/PyamilySeq/Constants.py DELETED
@@ -1,2 +0,0 @@
1
- PyamilySeq_Version = 'v0.5.1'
2
-
{pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/LICENSE RENAMED
File without changes
{pyamilyseq-0.5.1 → pyamilyseq-0.5.2}/pyproject.toml RENAMED
File without changes