PyamilySeq 0.3.0__tar.gz → 0.4.0__tar.gz

pyamilyseq-0.4.0/PKG-INFO

@@ -0,0 +1,92 @@
+Metadata-Version: 2.1
+Name: PyamilySeq
+Version: 0.4.0
+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
+Author-email: nicholas@dimonaco.co.uk
+Project-URL: Bug Tracker, https://github.com/NickJD/PyamilySeq/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# PyamilySeq - !BETA!
+**PyamilySeq** (Family Seek) is a Python tool for clustering gene sequences into families based on sequence similarity identified by tools such as CD-HIT, BLAST, DIAMOND or MMseqs2.
+This work is an extension of the gene family / pangenome tool developed for the StORF-Reporter publication in NAR (https://doi.org/10.1093/nar/gkad814).
+
+## Features
+- **End-to-End**: PyamilySeq can take a directory of GFF+FASTA files, run CD-HIT for clustering and process the results.
+- **Clustering**: Supports input from CD-HIT formatted files as well as CSV and TSV edge lists (-outfmt 6 from BLAST/DIAMOND).
+- **Reclustering**: Allows for the addition of new sequences post-initial clustering.
+- **Output**: Generates a gene 'Roary/Panaroo' formatted presence-absence CSV formatted file for downstream analysis.
+  - Align representative sequences using MAFFT.
+  - Output concatenated aligned sequences for downstream analysis.
+  - Optionally output sequences of identified families.
+
+
+### Installation
+PyamilySeq requires Python 3.6 or higher. Install using pip:
+
+```bash
+pip install PyamilySeq
+```
+
+## Usage - Menu
+```
+usage: PyamilySeq.py [-h] -id INPUT_DIR -od OUTPUT_DIR -it {separate,combined} -ns NAME_SPLIT -pid PIDENT -ld LEN_DIFF -co CLUSTERING_OUT -ct {CD-HIT,BLAST,DIAMOND,MMseqs2} [-w WRITE_FAMILIES] [-con CON_CORE] [-fasta FASTA] [-rc RECLUSTERED] [-st SEQUENCE_TAG] [-groups CORE_GROUPS]
+                     [-gpa GENE_PRESENCE_ABSENCE_OUT]
+                     ...
+
+PyamilySeq v0.4.0: PyamilySeq Run Parameters.
+
+positional arguments:
+  pyamilyseq_args       Additional arguments for PyamilySeq.
+
+options:
+  -h, --help            show this help message and exit
+
+Required Arguments:
+  -id INPUT_DIR         Directory containing GFF/FASTA files.
+  -od OUTPUT_DIR        Directory for all output files.
+  -it {separate,combined}
+                        Type of input files: 'separate' for separate FASTA and GFF files, 'combined' for GFF files with embedded FASTA sequences.
+  -ns NAME_SPLIT        Character used to split the filename and extract the genome name.
+  -pid PIDENT           Pident threshold for CD-HIT clustering.
+  -ld LEN_DIFF          Length difference (-s) threshold for CD-HIT clustering.
+  -co CLUSTERING_OUT    Output file for initial clustering.
+  -ct {CD-HIT,BLAST,DIAMOND,MMseqs2}
+                        Clustering format for PyamilySeq.
+
+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
+  -fasta FASTA          FASTA file to use in conjunction with "-w" or "-con"
+
+Optional Arguments:
+  -rc RECLUSTERED       Clustering output file from secondary round of clustering
+  -st 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
+  -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
+```
+
+### Example Run End-to-End - 'genomes' is a test-directory containing GFF files with ##FASTA at the bottom
+
+```bash
+PyamilySeq -id .../genomes -it combined -ns _combined.gff3 -pid 0.90 -ld 0.60 -co testing_cd-hit -ct CD-HIT -od .../testing
+```
+
+```Calculating Groups
+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
+```
+
+

pyamilyseq-0.4.0/README.md

@@ -0,0 +1,77 @@
+# PyamilySeq - !BETA!
+**PyamilySeq** (Family Seek) is a Python tool for clustering gene sequences into families based on sequence similarity identified by tools such as CD-HIT, BLAST, DIAMOND or MMseqs2.
+This work is an extension of the gene family / pangenome tool developed for the StORF-Reporter publication in NAR (https://doi.org/10.1093/nar/gkad814).
+
+## Features
+- **End-to-End**: PyamilySeq can take a directory of GFF+FASTA files, run CD-HIT for clustering and process the results.
+- **Clustering**: Supports input from CD-HIT formatted files as well as CSV and TSV edge lists (-outfmt 6 from BLAST/DIAMOND).
+- **Reclustering**: Allows for the addition of new sequences post-initial clustering.
+- **Output**: Generates a gene 'Roary/Panaroo' formatted presence-absence CSV formatted file for downstream analysis.
+  - Align representative sequences using MAFFT.
+  - Output concatenated aligned sequences for downstream analysis.
+  - Optionally output sequences of identified families.
+
+
+### Installation
+PyamilySeq requires Python 3.6 or higher. Install using pip:
+
+```bash
+pip install PyamilySeq
+```
+
+## Usage - Menu
+```
+usage: PyamilySeq.py [-h] -id INPUT_DIR -od OUTPUT_DIR -it {separate,combined} -ns NAME_SPLIT -pid PIDENT -ld LEN_DIFF -co CLUSTERING_OUT -ct {CD-HIT,BLAST,DIAMOND,MMseqs2} [-w WRITE_FAMILIES] [-con CON_CORE] [-fasta FASTA] [-rc RECLUSTERED] [-st SEQUENCE_TAG] [-groups CORE_GROUPS]
+                     [-gpa GENE_PRESENCE_ABSENCE_OUT]
+                     ...
+
+PyamilySeq v0.4.0: PyamilySeq Run Parameters.
+
+positional arguments:
+  pyamilyseq_args       Additional arguments for PyamilySeq.
+
+options:
+  -h, --help            show this help message and exit
+
+Required Arguments:
+  -id INPUT_DIR         Directory containing GFF/FASTA files.
+  -od OUTPUT_DIR        Directory for all output files.
+  -it {separate,combined}
+                        Type of input files: 'separate' for separate FASTA and GFF files, 'combined' for GFF files with embedded FASTA sequences.
+  -ns NAME_SPLIT        Character used to split the filename and extract the genome name.
+  -pid PIDENT           Pident threshold for CD-HIT clustering.
+  -ld LEN_DIFF          Length difference (-s) threshold for CD-HIT clustering.
+  -co CLUSTERING_OUT    Output file for initial clustering.
+  -ct {CD-HIT,BLAST,DIAMOND,MMseqs2}
+                        Clustering format for PyamilySeq.
+
+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
+  -fasta FASTA          FASTA file to use in conjunction with "-w" or "-con"
+
+Optional Arguments:
+  -rc RECLUSTERED       Clustering output file from secondary round of clustering
+  -st 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
+  -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
+```
+
+### Example Run End-to-End - 'genomes' is a test-directory containing GFF files with ##FASTA at the bottom
+
+```bash
+PyamilySeq -id .../genomes -it combined -ns _combined.gff3 -pid 0.90 -ld 0.60 -co testing_cd-hit -ct CD-HIT -od .../testing
+```
+
+```Calculating Groups
+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
+```
+
+

{pyamilyseq-0.3.0 → pyamilyseq-0.4.0}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = PyamilySeq
-version = v0.3.0
+version = v0.4.0
 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.
@@ -27,7 +27,7 @@ include = *
 
 [options.entry_points]
 console_scripts = 
-	PyamilySeq = PyamilySeq.PyamilySeq_Species:main
+	PyamilySeq = PyamilySeq.PyamilySeq:main
 
 [egg_info]
 tag_build = 

{pyamilyseq-0.3.0 → pyamilyseq-0.4.0}/src/PyamilySeq/Constants.py

@@ -1,6 +1,6 @@
 import subprocess
 
-PyamilySeq_Version = 'v0.3.0'
+PyamilySeq_Version = 'v0.4.0'
 
 
 

pyamilyseq-0.4.0/src/PyamilySeq/PyamilySeq.py

@@ -0,0 +1,186 @@
+import argparse
+import collections
+import os
+import glob
+import subprocess
+from PyamilySeq_Species import *
+
+
+try:
+    from .PyamilySeq_Species import cluster
+    from .Constants import *
+except (ModuleNotFoundError, ImportError, NameError, TypeError) as error:
+    from PyamilySeq_Species import cluster
+    from Constants import *
+
+def reverse_complement(seq):
+    complement = {'A': 'T', 'T': 'A', 'G': 'C', 'C': 'G', 'N': 'N'}
+    return ''.join(complement[base] for base in reversed(seq))
+
+
+def read_separate_files(input_dir, name_split, combined_out):
+    with open(combined_out, 'w') as combined_out_file:
+        for fasta_file in glob.glob(os.path.join(input_dir, '*' + name_split)):
+            genome_name = os.path.basename(fasta_file).split(name_split)[0]
+            corresponding_gff_file = fasta_file.replace('.fasta', '.gff')
+            if not os.path.exists(corresponding_gff_file):
+                continue
+            cds_sequences = extract_cds_from_gff(fasta_file, corresponding_gff_file)
+            for gene_name, seq in cds_sequences:
+                header = f">{genome_name}_{gene_name}\n"
+                combined_out_file.write(header)
+                combined_out_file.write(seq + '\n')
+
+def read_combined_files(input_dir, name_split, combined_out):
+    with open(combined_out, 'w') as combined_out_file:
+        for gff_file in glob.glob(os.path.join(input_dir, '*' + name_split)):
+            genome_name = os.path.basename(gff_file).split(name_split)[0]
+            fasta_dict = collections.defaultdict(str)
+            gff_features = []
+            with open(gff_file, 'r') as file:
+                lines = file.readlines()
+                fasta_section = False
+                for line in lines:
+                    if line.startswith('##FASTA'):
+                        fasta_section = True
+                        continue
+                    if fasta_section:
+                        if line.startswith('>'):
+                            current_contig = line[1:].split()[0]
+                            fasta_dict[current_contig] = []
+                        else:
+                            fasta_dict[current_contig].append(line.strip())
+                    else:
+                        line_data = line.split('\t')
+                        if len(line_data) == 9:
+                            if line_data[2] == 'CDS':
+                                contig = line_data[0]
+                                feature = line_data[2]
+                                start, end = int(line_data[3]), int(line_data[4])
+                                seq_id = line_data[8].split('ID=')[1].split(';')[0]
+                                gff_features.append((contig, start, end, seq_id))
+
+                if fasta_dict and gff_features:
+                    for contig, start, end, seq_id in gff_features:
+                        if contig in fasta_dict:
+                            full_sequence = ''.join(fasta_dict[contig])
+                            cds_sequence = full_sequence[start - 1:end]
+                            wrapped_sequence = '\n'.join([cds_sequence[i:i + 60] for i in range(0, len(cds_sequence), 60)])
+                            combined_out_file.write(f">{genome_name}|{seq_id}\n{wrapped_sequence}\n")
+
+
+def run_cd_hit(input_file, clustering_output, options):
+    cdhit_command = [
+        'cd-hit-est',
+        '-i', input_file,
+        '-o', clustering_output,
+        '-c', str(options.pident),
+        '-s', str(options.len_diff),
+        '-T', "20",
+        '-d', "0",
+        '-sc', "1",
+        '-sf', "1"
+    ]
+    subprocess.run(cdhit_command)
+
+
+
+
+
+
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description='PyamilySeq ' + PyamilySeq_Version + ': PyamilySeq Run Parameters.')
+    required = parser.add_argument_group('Required Arguments')
+    required.add_argument("-id", action="store", dest="input_dir",
+                          help="Directory containing GFF/FASTA files.",
+                          required=True)
+    required.add_argument("-od", action="store", dest="output_dir",
+                          help="Directory for all output files.",
+                          required=True)
+    required.add_argument("-it", action="store", dest="input_type", choices=['separate', 'combined'],
+                        help="Type of input files: 'separate' for separate FASTA and GFF files,"
+                             " 'combined' for GFF files with embedded FASTA sequences.",
+                          required=True)
+    required.add_argument("-ns", action="store", dest="name_split",
+                          help="Character used to split the filename and extract the genome name.",
+                          required=True)
+    required.add_argument("-pid", action="store", dest="pident", type=float,
+                          help="Pident threshold for CD-HIT clustering.",
+                          required=True)
+    required.add_argument("-ld", action="store", dest="len_diff", type=float,
+                          help="Length difference (-s) threshold for CD-HIT clustering.",
+                          required=True)
+    required.add_argument("-co", action="store", dest="clustering_out",
+                          help="Output file for initial clustering.",
+                          required=True)
+    required.add_argument("-ct", action="store", dest="clustering_type", choices=['CD-HIT', 'BLAST', 'DIAMOND', "MMseqs2"],
+                        help="Clustering format for PyamilySeq.",
+                          required=True)
+
+    output_args = parser.add_argument_group('Output Parameters')
+    output_args.add_argument('-w', action="store", dest='write_families', default=None,
+                          help='Default - No output: Output sequences of identified families (provide levels at which to output "-w 99,95"'
+                               ' - Must provide FASTA file with -fasta',
+                          required=False)
+    output_args.add_argument('-con', action="store", dest='con_core', default=None,
+                          help='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',
+                          required=False)
+    output_args.add_argument('-fasta', action='store', dest='fasta',
+                          help='FASTA file to use in conjunction with "-w" or "-con"',
+                          required=False)
+
+    optional = parser.add_argument_group('Optional Arguments')
+    optional.add_argument('-rc', action='store', dest='reclustered', help='Clustering output file from secondary round of clustering',
+                        required=False)
+    optional.add_argument('-st', action='store', dest='sequence_tag', help='Default - "StORF": Unique identifier to be used to distinguish the second of two rounds of clustered sequences',
+                        required=False)
+    optional.add_argument('-groups', action="store", dest='core_groups', default="99,95,15",
+                        help='Default - (\'99,95,15\'): Gene family groups to use')
+    optional.add_argument('-gpa', action='store', dest='gene_presence_absence_out', help='Default - False: If selected, a Roary formatted gene_presence_absence.csv will be created - Required for Coinfinder and other downstream tools',
+                        required=False)
+
+    parser.add_argument("pyamilyseq_args", nargs=argparse.REMAINDER, help="Additional arguments for PyamilySeq.")
+    options = parser.parse_args()
+
+
+
+    output_path = os.path.abspath(options.output_dir)
+    combined_out_file = os.path.join(output_path,"end_to_end_combined_sequences.fasta")
+    clustering_output = os.path.join(output_path,'clustering_'+options.clustering_type)
+
+
+
+    # Step 1: Read and rename sequences from files based on input type
+    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)
+
+    # Step 2: Run CD-HIT on the renamed sequences
+    run_cd_hit(combined_out_file, clustering_output, options)
+
+
+    class clustering_options:
+        def __init__(self):
+            self.format = 'CD-HIT'
+            self.reclustered = options.reclustered
+            self.sequence_tag = 'StORF'
+            self.core_groups = '99,95,15,0'
+            self.clusters = clustering_output+'.clstr'
+            self.gene_presence_absence_out = options.gene_presence_absence_out
+            self.write_families = options.write_families
+            self.con_core = options.con_core
+
+    clustering_options = clustering_options()
+
+    # Step 3: Run PyamilySeq with the CD-HIT output
+    cluster(clustering_options)
+    #run_pyamilyseq(options.clustering_out, options.clustering_type, combined_out_file, options.pyamilyseq_args)
+
+
+if __name__ == "__main__":
+    main()

{pyamilyseq-0.3.0 → pyamilyseq-0.4.0}/src/PyamilySeq/PyamilySeq_Species.py

@@ -722,22 +722,25 @@ def cluster(options):
 
 def main():
 
-    parser = argparse.ArgumentParser(description='PyamilySeq ' + PyamilySeq_Version + ': PyamilySeq Run Parameters.')
+    parser = argparse.ArgumentParser(description='PyamilySeq-Species ' + PyamilySeq_Version + ': PyamilySeq-Species Run Parameters.')
     parser._action_groups.pop()
 
     required = parser.add_argument_group('Required Arguments')
     required.add_argument('-c', action='store', dest='clusters', help='Clustering output file from CD-HIT, TSV or CSV Edge List',
                         required=True)
     required.add_argument('-f', action='store', dest='format', choices=['CD-HIT', 'CSV', 'TSV'],
-                        help='Which format to use (CD-HIT or  Comma/Tab Separated Edge-List (such as MMseqs2 tsv output))', required=True)
+                        help='Which format to use (CD-HIT or  Comma/Tab Separated Edge-List (such as MMseqs2 tsv output))',
+                        required=True)
 
     output_args = parser.add_argument_group('Output Parameters')
     output_args.add_argument('-w', action="store", dest='write_families', default=None,
                           help='Default - No output: Output sequences of identified families (provide levels at which to output "-w 99,95"'
-                               ' - Must provide FASTA file with -fasta')
+                               ' - Must provide FASTA file with -fasta',
+                          required=False)
     output_args.add_argument('-con', action="store", dest='con_core', default=None,
                           help='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')
+                               ' - Must provide FASTA file with -fasta',
+                          required=False)
     output_args.add_argument('-fasta', action='store', dest='fasta',
                           help='FASTA file to use in conjunction with "-w" or "-con"',
                           required=False)
@@ -754,9 +757,11 @@ def main():
 
     misc = parser.add_argument_group('Misc')
     misc.add_argument('-verbose', action='store', dest='verbose', default=False, type=eval, choices=[True, False],
-                        help='Default - False: Print out runtime messages')
+                        help='Default - False: Print out runtime messages',
+                        required = False)
     misc.add_argument('-v', action='store_true', dest='version',
-                        help='Default - False: Print out version number and exit')
+                        help='Default - False: Print out version number and exit',
+                        required=False)
 
 
     options = parser.parse_args()

pyamilyseq-0.4.0/src/PyamilySeq.egg-info/PKG-INFO

@@ -0,0 +1,92 @@
+Metadata-Version: 2.1
+Name: PyamilySeq
+Version: 0.4.0
+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
+Author-email: nicholas@dimonaco.co.uk
+Project-URL: Bug Tracker, https://github.com/NickJD/PyamilySeq/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# PyamilySeq - !BETA!
+**PyamilySeq** (Family Seek) is a Python tool for clustering gene sequences into families based on sequence similarity identified by tools such as CD-HIT, BLAST, DIAMOND or MMseqs2.
+This work is an extension of the gene family / pangenome tool developed for the StORF-Reporter publication in NAR (https://doi.org/10.1093/nar/gkad814).
+
+## Features
+- **End-to-End**: PyamilySeq can take a directory of GFF+FASTA files, run CD-HIT for clustering and process the results.
+- **Clustering**: Supports input from CD-HIT formatted files as well as CSV and TSV edge lists (-outfmt 6 from BLAST/DIAMOND).
+- **Reclustering**: Allows for the addition of new sequences post-initial clustering.
+- **Output**: Generates a gene 'Roary/Panaroo' formatted presence-absence CSV formatted file for downstream analysis.
+  - Align representative sequences using MAFFT.
+  - Output concatenated aligned sequences for downstream analysis.
+  - Optionally output sequences of identified families.
+
+
+### Installation
+PyamilySeq requires Python 3.6 or higher. Install using pip:
+
+```bash
+pip install PyamilySeq
+```
+
+## Usage - Menu
+```
+usage: PyamilySeq.py [-h] -id INPUT_DIR -od OUTPUT_DIR -it {separate,combined} -ns NAME_SPLIT -pid PIDENT -ld LEN_DIFF -co CLUSTERING_OUT -ct {CD-HIT,BLAST,DIAMOND,MMseqs2} [-w WRITE_FAMILIES] [-con CON_CORE] [-fasta FASTA] [-rc RECLUSTERED] [-st SEQUENCE_TAG] [-groups CORE_GROUPS]
+                     [-gpa GENE_PRESENCE_ABSENCE_OUT]
+                     ...
+
+PyamilySeq v0.4.0: PyamilySeq Run Parameters.
+
+positional arguments:
+  pyamilyseq_args       Additional arguments for PyamilySeq.
+
+options:
+  -h, --help            show this help message and exit
+
+Required Arguments:
+  -id INPUT_DIR         Directory containing GFF/FASTA files.
+  -od OUTPUT_DIR        Directory for all output files.
+  -it {separate,combined}
+                        Type of input files: 'separate' for separate FASTA and GFF files, 'combined' for GFF files with embedded FASTA sequences.
+  -ns NAME_SPLIT        Character used to split the filename and extract the genome name.
+  -pid PIDENT           Pident threshold for CD-HIT clustering.
+  -ld LEN_DIFF          Length difference (-s) threshold for CD-HIT clustering.
+  -co CLUSTERING_OUT    Output file for initial clustering.
+  -ct {CD-HIT,BLAST,DIAMOND,MMseqs2}
+                        Clustering format for PyamilySeq.
+
+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
+  -fasta FASTA          FASTA file to use in conjunction with "-w" or "-con"
+
+Optional Arguments:
+  -rc RECLUSTERED       Clustering output file from secondary round of clustering
+  -st 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
+  -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
+```
+
+### Example Run End-to-End - 'genomes' is a test-directory containing GFF files with ##FASTA at the bottom
+
+```bash
+PyamilySeq -id .../genomes -it combined -ns _combined.gff3 -pid 0.90 -ld 0.60 -co testing_cd-hit -ct CD-HIT -od .../testing
+```
+
+```Calculating Groups
+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
+```
+
+

{pyamilyseq-0.3.0 → pyamilyseq-0.4.0}/src/PyamilySeq.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ pyproject.toml
 setup.cfg
 src/PyamilySeq/CD-Hit_StORF-Reporter_Cross-Genera_Builder.py
 src/PyamilySeq/Constants.py
+src/PyamilySeq/PyamilySeq.py
 src/PyamilySeq/PyamilySeq_Species.py
 src/PyamilySeq/__init__.py
 src/PyamilySeq/combine_FASTA_with_genome_IDs.py

pyamilyseq-0.4.0/src/PyamilySeq.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+PyamilySeq = PyamilySeq.PyamilySeq:main

pyamilyseq-0.3.0/PKG-INFO

@@ -1,103 +0,0 @@
-Metadata-Version: 2.1
-Name: PyamilySeq
-Version: 0.3.0
-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
-Author-email: nicholas@dimonaco.co.uk
-Project-URL: Bug Tracker, https://github.com/NickJD/PyamilySeq/issues
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
-# PyamilySeq - !BETA!
-PyamilySeq (Family Seek) is a Python tool for clustering gene sequences into families based on sequence similarity identified by tools such as CD-HIT, DIAMOND or MMseqs2.
-This work is an extension of the gene family / pangenome tool developed for the StORF-Reporter publication in NAR (https://doi.org/10.1093/nar/gkad814).
-
-## Features
-
-- **Clustering**: Supports input from CD-HIT formatted files as well as TSV and CSV Edge List formats.
-- **Reclustering**: Allows for the addition of new sequences post-initial clustering.
-- **Output**: Generates a gene 'Roary' presence-absence CSV formatted file for downstream analysis.
-
-## Installation
-
-PyamilySeq requires Python 3.6 or higher. Install dependencies using pip:
-
-```bash
-pip install PyamilySeq
-```
-
-## Usage - Menu
-```
-usage: PyamilySeq_Species.py [-h] -c CLUSTERS -f {CD-HIT,CSV,TSV} [-w WRITE_FAMILIES] [-con CON_CORE] [-fasta FASTA] [-rc RECLUSTERED] [-st SEQUENCE_TAG]
-                             [-groups CORE_GROUPS] [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}] [-v]
-
-PyamilySeq v0.3.0: PyamilySeq Run Parameters.
-
-Required Arguments:
-  -c CLUSTERS           Clustering output file from CD-HIT, TSV or CSV Edge List
-  -f {CD-HIT,CSV,TSV}   Which format to use (CD-HIT or Comma/Tab Separated Edge-List (such as MMseqs2 tsv output))
-
-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
-  -fasta FASTA          FASTA file to use in conjunction with "-w" or "-con"
-
-Optional Arguments:
-  -rc RECLUSTERED       Clustering output file from secondary round of clustering
-  -st 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
-  -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
-
-Misc:
-  -verbose {True,False}
-                        Default - False: Print out runtime messages
-  -v                    Default - False: Print out version number and exit
-
-
-```
-
-### Clustering Analysis
-
-To perform clustering analysis:
-
-```bash
-python pyamilyseq.py -c clusters_file -f format
-```
-
-Replace `clusters_file` with the path to your clustering output file and `format` with one of: `CD-HIT`, `CSV`, or `TSV`.
-
-### Reclustering
-
-To add new sequences and recluster:
-
-```bash
-PyamilySeq -c clusters_file -f format --reclustered reclustered_file
-```
-
-Replace `reclustered_file` with the path to the file containing additional sequences.
-
-## Output
-
-PyamilySeq generates various outputs, including:
-
-- **Gene Presence-Absence File**: This CSV file details the presence and absence of genes across genomes.
-- **FASTA Files for Each Gene Family**:  
-
-## Gene Family Groups
-
-After analysis, PyamilySeq categorizes gene families into several groups:
-
-- **First Core**: Gene families present in all analysed genomes initially.
-- **Extended Core**: Gene families extended with additional sequences.
-- **Combined Core**: Gene families combined with both initial and additional sequences.
-- **Second Core**: Gene families identified only in the additional sequences.
-- **Only Second Core**: Gene families exclusively found in the additional sequences.

pyamilyseq-0.3.0/README.md

@@ -1,88 +0,0 @@
-# PyamilySeq - !BETA!
-PyamilySeq (Family Seek) is a Python tool for clustering gene sequences into families based on sequence similarity identified by tools such as CD-HIT, DIAMOND or MMseqs2.
-This work is an extension of the gene family / pangenome tool developed for the StORF-Reporter publication in NAR (https://doi.org/10.1093/nar/gkad814).
-
-## Features
-
-- **Clustering**: Supports input from CD-HIT formatted files as well as TSV and CSV Edge List formats.
-- **Reclustering**: Allows for the addition of new sequences post-initial clustering.
-- **Output**: Generates a gene 'Roary' presence-absence CSV formatted file for downstream analysis.
-
-## Installation
-
-PyamilySeq requires Python 3.6 or higher. Install dependencies using pip:
-
-```bash
-pip install PyamilySeq
-```
-
-## Usage - Menu
-```
-usage: PyamilySeq_Species.py [-h] -c CLUSTERS -f {CD-HIT,CSV,TSV} [-w WRITE_FAMILIES] [-con CON_CORE] [-fasta FASTA] [-rc RECLUSTERED] [-st SEQUENCE_TAG]
-                             [-groups CORE_GROUPS] [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}] [-v]
-
-PyamilySeq v0.3.0: PyamilySeq Run Parameters.
-
-Required Arguments:
-  -c CLUSTERS           Clustering output file from CD-HIT, TSV or CSV Edge List
-  -f {CD-HIT,CSV,TSV}   Which format to use (CD-HIT or Comma/Tab Separated Edge-List (such as MMseqs2 tsv output))
-
-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
-  -fasta FASTA          FASTA file to use in conjunction with "-w" or "-con"
-
-Optional Arguments:
-  -rc RECLUSTERED       Clustering output file from secondary round of clustering
-  -st 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
-  -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
-
-Misc:
-  -verbose {True,False}
-                        Default - False: Print out runtime messages
-  -v                    Default - False: Print out version number and exit
-
-
-```
-
-### Clustering Analysis
-
-To perform clustering analysis:
-
-```bash
-python pyamilyseq.py -c clusters_file -f format
-```
-
-Replace `clusters_file` with the path to your clustering output file and `format` with one of: `CD-HIT`, `CSV`, or `TSV`.
-
-### Reclustering
-
-To add new sequences and recluster:
-
-```bash
-PyamilySeq -c clusters_file -f format --reclustered reclustered_file
-```
-
-Replace `reclustered_file` with the path to the file containing additional sequences.
-
-## Output
-
-PyamilySeq generates various outputs, including:
-
-- **Gene Presence-Absence File**: This CSV file details the presence and absence of genes across genomes.
-- **FASTA Files for Each Gene Family**:  
-
-## Gene Family Groups
-
-After analysis, PyamilySeq categorizes gene families into several groups:
-
-- **First Core**: Gene families present in all analysed genomes initially.
-- **Extended Core**: Gene families extended with additional sequences.
-- **Combined Core**: Gene families combined with both initial and additional sequences.
-- **Second Core**: Gene families identified only in the additional sequences.
-- **Only Second Core**: Gene families exclusively found in the additional sequences.

pyamilyseq-0.3.0/src/PyamilySeq.egg-info/PKG-INFO

@@ -1,103 +0,0 @@
-Metadata-Version: 2.1
-Name: PyamilySeq
-Version: 0.3.0
-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
-Author-email: nicholas@dimonaco.co.uk
-Project-URL: Bug Tracker, https://github.com/NickJD/PyamilySeq/issues
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
-# PyamilySeq - !BETA!
-PyamilySeq (Family Seek) is a Python tool for clustering gene sequences into families based on sequence similarity identified by tools such as CD-HIT, DIAMOND or MMseqs2.
-This work is an extension of the gene family / pangenome tool developed for the StORF-Reporter publication in NAR (https://doi.org/10.1093/nar/gkad814).
-
-## Features
-
-- **Clustering**: Supports input from CD-HIT formatted files as well as TSV and CSV Edge List formats.
-- **Reclustering**: Allows for the addition of new sequences post-initial clustering.
-- **Output**: Generates a gene 'Roary' presence-absence CSV formatted file for downstream analysis.
-
-## Installation
-
-PyamilySeq requires Python 3.6 or higher. Install dependencies using pip:
-
-```bash
-pip install PyamilySeq
-```
-
-## Usage - Menu
-```
-usage: PyamilySeq_Species.py [-h] -c CLUSTERS -f {CD-HIT,CSV,TSV} [-w WRITE_FAMILIES] [-con CON_CORE] [-fasta FASTA] [-rc RECLUSTERED] [-st SEQUENCE_TAG]
-                             [-groups CORE_GROUPS] [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}] [-v]
-
-PyamilySeq v0.3.0: PyamilySeq Run Parameters.
-
-Required Arguments:
-  -c CLUSTERS           Clustering output file from CD-HIT, TSV or CSV Edge List
-  -f {CD-HIT,CSV,TSV}   Which format to use (CD-HIT or Comma/Tab Separated Edge-List (such as MMseqs2 tsv output))
-
-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
-  -fasta FASTA          FASTA file to use in conjunction with "-w" or "-con"
-
-Optional Arguments:
-  -rc RECLUSTERED       Clustering output file from secondary round of clustering
-  -st 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
-  -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
-
-Misc:
-  -verbose {True,False}
-                        Default - False: Print out runtime messages
-  -v                    Default - False: Print out version number and exit
-
-
-```
-
-### Clustering Analysis
-
-To perform clustering analysis:
-
-```bash
-python pyamilyseq.py -c clusters_file -f format
-```
-
-Replace `clusters_file` with the path to your clustering output file and `format` with one of: `CD-HIT`, `CSV`, or `TSV`.
-
-### Reclustering
-
-To add new sequences and recluster:
-
-```bash
-PyamilySeq -c clusters_file -f format --reclustered reclustered_file
-```
-
-Replace `reclustered_file` with the path to the file containing additional sequences.
-
-## Output
-
-PyamilySeq generates various outputs, including:
-
-- **Gene Presence-Absence File**: This CSV file details the presence and absence of genes across genomes.
-- **FASTA Files for Each Gene Family**:  
-
-## Gene Family Groups
-
-After analysis, PyamilySeq categorizes gene families into several groups:
-
-- **First Core**: Gene families present in all analysed genomes initially.
-- **Extended Core**: Gene families extended with additional sequences.
-- **Combined Core**: Gene families combined with both initial and additional sequences.
-- **Second Core**: Gene families identified only in the additional sequences.
-- **Only Second Core**: Gene families exclusively found in the additional sequences.

pyamilyseq-0.3.0/src/PyamilySeq.egg-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-PyamilySeq = PyamilySeq.PyamilySeq_Species:main