PyamilySeq 0.5.1__tar.gz → 0.6.0__tar.gz

{pyamilyseq-0.5.1/src/PyamilySeq.egg-info → pyamilyseq-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyamilySeq
-Version: 0.5.1
+Version: 0.6.0
 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
@@ -34,80 +34,83 @@ PyamilySeq requires Python 3.6 or higher. Install using pip:
 pip install PyamilySeq
 ```
 
+### 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 -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
+```
+
+```bash
+Calculating Groups
+Gene Groups:
+first_core_99: 3103
+first_core_95: 0
+first_core_15: 3217
+first_core_0: 4808
+Total Number of Gene Groups (Including Singletons): 11128
+```
+
+
 ## Usage - Menu
 ```
-usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus}
-                     -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] [-cluster_file CLUSTER_FILE]
-                     [-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]
-
-PyamilySeq v0.5.1: PyamilySeq Run Parameters.
+usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus} -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] [-reclustered RECLUSTERED] [-seq_tag SEQUENCE_TAG]
+                     [-core_groups CORE_GROUPS] [-genus_groups GENUS_GROUPS] [-w WRITE_FAMILIES] [-con CON_CORE] [-original_fasta ORIGINAL_FASTA] [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}] [-v]
+
+PyamilySeq v0.6.0: PyamilySeq Run Parameters.
 
 options:
   -h, --help            show this help message and exit
 
 Required Arguments:
   -run_mode {Full,Partial}
-                        Run Mode: Should PyamilySeq be run in "Full" or
-                        "Partial" mode?
-  -group_mode {Species}
-                        Group Mode: Should PyamilySeq be run in "Species" or
-                        "Genus" mode?  - Genus mode not currently functioning
-  -clust_tool {CD-HIT}  Clustering tool to use: CD-HIT, DIAMOND, BLAST or
-                        MMseqs2.
+                        Run Mode: Should PyamilySeq be run in "Full" or "Partial" mode?
+  -group_mode {Species,Genus}
+                        Group Mode: Should PyamilySeq be run in "Species" or "Genus" mode?
+  -clust_tool {CD-HIT}  Clustering tool to use: CD-HIT, DIAMOND, BLAST or MMseqs2.
   -output_dir OUTPUT_DIR
                         Directory for all output files.
 
 Full-Mode Arguments - Required when "-run_mode Full" is used:
   -input_type {separate,combined}
-                        Type of input files: 'separate' for separate FASTA and
-                        GFF files, 'combined' for GFF files with embedded
-                        FASTA sequences.
+                        Type of input files: 'separate' for separate FASTA and GFF files, 'combined' for GFF files with embedded FASTA sequences.
   -input_dir INPUT_DIR  Directory containing GFF/FASTA files.
   -name_split NAME_SPLIT
-                        substring used to split the filename and extract the
-                        genome name ('_combined.gff3' or '.gff').
+                        substring used to split the filename and extract the genome name ('_combined.gff3' or '.gff').
   -pid PIDENT           Default 0.95: Pident threshold for clustering.
-  -len_diff LEN_DIFF    Default 0.80: Minimum length difference between
-                        clustered sequences - (-s) threshold for CD-HIT
-                        clustering.
+  -len_diff LEN_DIFF    Default 0.80: Minimum length difference between clustered sequences - (-s) threshold for CD-HIT clustering.
+
+Clustering Runtime Arguments - Optional when "-run_mode Full" is used:
+  -mem CLUSTERING_MEMORY
+                        Default 4000: Memory to be allocated for clustering (in MBs).
+  -t CLUSTERING_THREADS
+                        Default 4: Threads to be allocated for clustering.
 
 Partial-Mode Arguments - Required when "-run_mode Partial" is used:
   -cluster_file CLUSTER_FILE
-                        Clustering output file containing CD-HIT, TSV or CSV
-                        Edge List
+                        Clustering output file containing CD-HIT, TSV or CSV Edge List
 
 Grouping Arguments - Use to fine-tune grouping of genes after clustering:
   -reclustered RECLUSTERED
-                        Clustering output file from secondary round of
-                        clustering
+                        Currently only works on Partial Mode: Clustering output file from secondary round of clustering.
   -seq_tag SEQUENCE_TAG
-                        Default - "StORF": Unique identifier to be used to
-                        distinguish the second of two rounds of clustered
-                        sequences
-  -groups CORE_GROUPS   Default - ('99,95,15'): Gene family groups to use
+                        Default - "StORF": Unique identifier to be used to distinguish the second of two rounds of clustered sequences
+  -core_groups CORE_GROUPS
+                        Default - ('99,95,15'): Gene family groups to use for "Species" mode
+  -genus_groups GENUS_GROUPS
+                        Default - ('1,2,3,4,5,6'): Gene family groups to use for "Genus" mode
 
 Output Parameters:
-  -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
-  -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
+  -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
+  -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
   -original_fasta ORIGINAL_FASTA
-                        FASTA file to use in conjunction with "-w" or "-con"
-                        when running in Partial Mode.
+                        FASTA file to use in conjunction with "-w" or "-con" when running in Partial Mode.
   -gpa GENE_PRESENCE_ABSENCE_OUT
-                        Default - False: If selected, a Roary formatted
-                        gene_presence_absence.csv will be created - Required
-                        for Coinfinder and other downstream tools
+                        Default - False: If selected, a Roary formatted gene_presence_absence.csv will be created - Required for Coinfinder and other downstream tools
 
 Misc:
   -verbose {True,False}
@@ -116,25 +119,6 @@ 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 -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
-```
-
-```bash
-Calculating Groups
-Gene Groups:
-first_core_99: 3103
-first_core_95: 0
-first_core_15: 3217
-first_core_0: 4808
-Total Number of Gene Groups (Including Singletons): 11128
-```
 
 ## Seq-Combiner: This tool is provided to enable the pre-processing of multiple GFF/FASTA files together ready to be clustered by the user
 ### Example:
@@ -145,7 +129,7 @@ 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 v0.5.1: Seq-Combiner Run Parameters.
+Seq-Combiner v0.6.0: Seq-Combiner Run Parameters.
 
 options:
   -h, --help            show this help message and exit

{pyamilyseq-0.5.1 → pyamilyseq-0.6.0}/README.md

@@ -19,80 +19,83 @@ PyamilySeq requires Python 3.6 or higher. Install using pip:
 pip install PyamilySeq
 ```
 
+### 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 -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
+```
+
+```bash
+Calculating Groups
+Gene Groups:
+first_core_99: 3103
+first_core_95: 0
+first_core_15: 3217
+first_core_0: 4808
+Total Number of Gene Groups (Including Singletons): 11128
+```
+
+
 ## Usage - Menu
 ```
-usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus}
-                     -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] [-cluster_file CLUSTER_FILE]
-                     [-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]
-
-PyamilySeq v0.5.1: PyamilySeq Run Parameters.
+usage: PyamilySeq.py [-h] -run_mode {Full,Partial} -group_mode {Species,Genus} -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] [-reclustered RECLUSTERED] [-seq_tag SEQUENCE_TAG]
+                     [-core_groups CORE_GROUPS] [-genus_groups GENUS_GROUPS] [-w WRITE_FAMILIES] [-con CON_CORE] [-original_fasta ORIGINAL_FASTA] [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}] [-v]
+
+PyamilySeq v0.6.0: PyamilySeq Run Parameters.
 
 options:
   -h, --help            show this help message and exit
 
 Required Arguments:
   -run_mode {Full,Partial}
-                        Run Mode: Should PyamilySeq be run in "Full" or
-                        "Partial" mode?
-  -group_mode {Species}
-                        Group Mode: Should PyamilySeq be run in "Species" or
-                        "Genus" mode?  - Genus mode not currently functioning
-  -clust_tool {CD-HIT}  Clustering tool to use: CD-HIT, DIAMOND, BLAST or
-                        MMseqs2.
+                        Run Mode: Should PyamilySeq be run in "Full" or "Partial" mode?
+  -group_mode {Species,Genus}
+                        Group Mode: Should PyamilySeq be run in "Species" or "Genus" mode?
+  -clust_tool {CD-HIT}  Clustering tool to use: CD-HIT, DIAMOND, BLAST or MMseqs2.
   -output_dir OUTPUT_DIR
                         Directory for all output files.
 
 Full-Mode Arguments - Required when "-run_mode Full" is used:
   -input_type {separate,combined}
-                        Type of input files: 'separate' for separate FASTA and
-                        GFF files, 'combined' for GFF files with embedded
-                        FASTA sequences.
+                        Type of input files: 'separate' for separate FASTA and GFF files, 'combined' for GFF files with embedded FASTA sequences.
   -input_dir INPUT_DIR  Directory containing GFF/FASTA files.
   -name_split NAME_SPLIT
-                        substring used to split the filename and extract the
-                        genome name ('_combined.gff3' or '.gff').
+                        substring used to split the filename and extract the genome name ('_combined.gff3' or '.gff').
   -pid PIDENT           Default 0.95: Pident threshold for clustering.
-  -len_diff LEN_DIFF    Default 0.80: Minimum length difference between
-                        clustered sequences - (-s) threshold for CD-HIT
-                        clustering.
+  -len_diff LEN_DIFF    Default 0.80: Minimum length difference between clustered sequences - (-s) threshold for CD-HIT clustering.
+
+Clustering Runtime Arguments - Optional when "-run_mode Full" is used:
+  -mem CLUSTERING_MEMORY
+                        Default 4000: Memory to be allocated for clustering (in MBs).
+  -t CLUSTERING_THREADS
+                        Default 4: Threads to be allocated for clustering.
 
 Partial-Mode Arguments - Required when "-run_mode Partial" is used:
   -cluster_file CLUSTER_FILE
-                        Clustering output file containing CD-HIT, TSV or CSV
-                        Edge List
+                        Clustering output file containing CD-HIT, TSV or CSV Edge List
 
 Grouping Arguments - Use to fine-tune grouping of genes after clustering:
   -reclustered RECLUSTERED
-                        Clustering output file from secondary round of
-                        clustering
+                        Currently only works on Partial Mode: Clustering output file from secondary round of clustering.
   -seq_tag SEQUENCE_TAG
-                        Default - "StORF": Unique identifier to be used to
-                        distinguish the second of two rounds of clustered
-                        sequences
-  -groups CORE_GROUPS   Default - ('99,95,15'): Gene family groups to use
+                        Default - "StORF": Unique identifier to be used to distinguish the second of two rounds of clustered sequences
+  -core_groups CORE_GROUPS
+                        Default - ('99,95,15'): Gene family groups to use for "Species" mode
+  -genus_groups GENUS_GROUPS
+                        Default - ('1,2,3,4,5,6'): Gene family groups to use for "Genus" mode
 
 Output Parameters:
-  -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
-  -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
+  -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
+  -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
   -original_fasta ORIGINAL_FASTA
-                        FASTA file to use in conjunction with "-w" or "-con"
-                        when running in Partial Mode.
+                        FASTA file to use in conjunction with "-w" or "-con" when running in Partial Mode.
   -gpa GENE_PRESENCE_ABSENCE_OUT
-                        Default - False: If selected, a Roary formatted
-                        gene_presence_absence.csv will be created - Required
-                        for Coinfinder and other downstream tools
+                        Default - False: If selected, a Roary formatted gene_presence_absence.csv will be created - Required for Coinfinder and other downstream tools
 
 Misc:
   -verbose {True,False}
@@ -101,25 +104,6 @@ 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 -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
-```
-
-```bash
-Calculating Groups
-Gene Groups:
-first_core_99: 3103
-first_core_95: 0
-first_core_15: 3217
-first_core_0: 4808
-Total Number of Gene Groups (Including Singletons): 11128
-```
 
 ## Seq-Combiner: This tool is provided to enable the pre-processing of multiple GFF/FASTA files together ready to be clustered by the user
 ### Example:
@@ -130,7 +114,7 @@ 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 v0.5.1: Seq-Combiner Run Parameters.
+Seq-Combiner v0.6.0: Seq-Combiner Run Parameters.
 
 options:
   -h, --help            show this help message and exit

{pyamilyseq-0.5.1 → pyamilyseq-0.6.0}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = PyamilySeq
-version = v0.5.1
+version = v0.6.0
 author = Nicholas Dimonaco
 author_email = nicholas@dimonaco.co.uk
 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-0.6.0/src/PyamilySeq/Constants.py

@@ -0,0 +1,2 @@
+PyamilySeq_Version = 'v0.6.0'
+

{pyamilyseq-0.5.1 → pyamilyseq-0.6.0}/src/PyamilySeq/PyamilySeq.py

@@ -7,11 +7,13 @@ import subprocess
 
 
 try:
-    from .PyamilySeq_Species import cluster
+    from .PyamilySeq_Species import cluster as species_cluster
+    from .PyamilySeq_Genus import cluster as genus_cluster
     from .Constants import *
     from .utils import *
 except (ModuleNotFoundError, ImportError, NameError, TypeError) as error:
-    from PyamilySeq_Species import cluster
+    from PyamilySeq_Species import cluster as species_cluster
+    from PyamilySeq_Genus import cluster as genus_cluster
     from Constants import *
     from utils import *
 
@@ -25,7 +27,8 @@ def run_cd_hit(input_file, clustering_output, options):
         '-o', clustering_output,
         '-c', str(options.pident),
         '-s', str(options.len_diff),
-        '-T', "20",
+        '-T', str(options.clustering_threads),
+        '-M', str(options.clustering_memory),
         '-d', "0",
         '-sc', "1",
         '-sf', "1"
@@ -43,8 +46,8 @@ 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'],
-                          help='Group Mode: Should PyamilySeq be run in "Species" or "Genus" mode? - Genus mode not currently functioning',
+    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=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.",
@@ -70,7 +73,14 @@ def main():
     full_mode_args.add_argument("-len_diff", action="store", dest="len_diff", type=float, default=0.80,
                           help="Default 0.80: Minimum length difference between clustered sequences - (-s) threshold for CD-HIT clustering.",
                           required=False)
-
+    ###Clustering Arguments
+    clustering_args = parser.add_argument_group('Clustering Runtime Arguments - Optional when "-run_mode Full" is used')
+    clustering_args.add_argument("-mem", action="store", dest="clustering_memory", type=int, default=4000,
+                          help="Default 4000: Memory to be allocated for clustering (in MBs).",
+                          required=False)
+    clustering_args.add_argument("-t", action="store", dest="clustering_threads", type=int, default=4,
+                          help="Default 4: Threads to be allocated for clustering.",
+                          required=False)
 
     ###Partial-Mode Arguments
     partial_mode_args = parser.add_argument_group('Partial-Mode Arguments - Required when "-run_mode Partial" is used')
@@ -80,13 +90,17 @@ def main():
 
     ###Grouping Arguments
     grouping_args = parser.add_argument_group('Grouping Arguments - Use to fine-tune grouping of genes after clustering')
-    grouping_args.add_argument('-reclustered', action='store', dest='reclustered', help='Clustering output file from secondary round of clustering',
+    grouping_args.add_argument('-reclustered', action='store', dest='reclustered',
+                        help='Currently only works on Partial Mode: Clustering output file from secondary round of clustering.',
                         required=False)
     grouping_args.add_argument('-seq_tag', action='store', dest='sequence_tag', default='StORF',
                         help='Default - "StORF": Unique identifier to be used to distinguish the second of two rounds of clustered sequences',
                         required=False)
-    grouping_args.add_argument('-groups', action="store", dest='core_groups', default="99,95,15",
-                        help='Default - (\'99,95,15\'): Gene family groups to use',
+    grouping_args.add_argument('-core_groups', action="store", dest='core_groups', default="99,95,15",
+                        help='Default - (\'99,95,15\'): Gene family groups to use for "Species" mode',
+                        required=False)
+    grouping_args.add_argument('-genus_groups', action="store", dest='genus_groups', default="1,2,3,4,5,6",
+                        help='Default - (\'1,2,3,4,5,6\'): Gene family groups to use for "Genus" mode',
                         required=False)
 
     ###Output Arguments
@@ -118,6 +132,8 @@ def main():
 
     ### Checking all required parameters are provided by user
     if options.run_mode == 'Full':
+        if options.reclustered != None:
+            sys.exit("Currently reclustering only works on Partial Mode.")
         required_full_mode = [options.input_type, options.input_dir, options.name_split, options.clust_tool,
                               options.pident, options.len_diff]
         if all(required_full_mode):
@@ -157,7 +173,7 @@ def main():
         else:
             exit("mafft is not installed. Please install mafft to proceed.")
     ##CD-HIT
-    if options.clust_tool == 'CD-HIT':
+    if options.clust_tool == 'CD-HIT' and options.run_mode == 'Full':
         if is_tool_installed('cd-hit'):
             if options.verbose == True:
                 print("cd-hit is installed. Proceeding with clustering.")
@@ -167,7 +183,7 @@ def main():
     if options.write_families != None and options.original_fasta == False:
         exit("-fasta must br provided if -w is used")
 
-    options.core_groups = options.core_groups + ',0'
+
 
 
     if options.cluster_file:
@@ -183,24 +199,30 @@ def main():
     combined_out_file = os.path.join(output_path, "combined_sequences.fasta")
     clustering_output = os.path.join(output_path, 'clustering_' + options.clust_tool)
 
-
-    if options.run_mode == 'Full':
-
+    if options.group_type == 'Species':
+        options.core_groups = options.core_groups + ',0'
+        groups_to_use = options.core_groups
+    else:
+        options.genus_groups = options.genus_groups + ',>'
+        groups_to_use = options.genus_groups
 
 
+    if options.run_mode == 'Full':
         if options.input_type == 'separate':
             read_separate_files(options.input_dir, options.name_split, combined_out_file)
         else:
             read_combined_files(options.input_dir, options.name_split, combined_out_file)
 
         run_cd_hit(combined_out_file, clustering_output, options)
+
         class clustering_options:
             def __init__(self):
                 self.cluster_format = options.clust_tool
                 self.reclustered = options.reclustered
                 self.sequence_tag = options.sequence_tag
-                self.core_groups = '99,95,15,0'
+                self.core_groups = groups_to_use
                 self.clusters = clustering_output + clust_affix
+                self.output_dir = options.output_dir
                 self.gene_presence_absence_out = options.gene_presence_absence_out
                 self.write_families = options.write_families
                 self.con_core = options.con_core
@@ -215,8 +237,9 @@ def main():
                 self.cluster_format = options.clust_tool
                 self.reclustered = options.reclustered
                 self.sequence_tag = options.sequence_tag
-                self.core_groups = '99,95,15,0'
+                self.core_groups = groups_to_use
                 self.clusters = options.cluster_file
+                self.output_dir = options.output_dir
                 self.gene_presence_absence_out = options.gene_presence_absence_out
                 self.write_families = options.write_families
                 self.con_core = options.con_core
@@ -226,9 +249,10 @@ def main():
         clustering_options = clustering_options()
 
 
-
-
-    cluster(clustering_options)
+    if options.group_type == 'Species':
+        species_cluster(clustering_options)
+    elif options.group_type == 'Genus':
+        genus_cluster((clustering_options))
 
     print("Thank you for using PyamilySeq -- A detailed user manual can be found at https://github.com/NickJD/PyamilySeq\n"
           "Please report any issues to: https://github.com/NickJD/PyamilySeq/issues\n#####")