PyamilySeq 0.3.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

PyamilySeq/Constants.py

@@ -1,15 +1,2 @@
-import subprocess
+PyamilySeq_Version = 'v0.5.0'
 
-PyamilySeq_Version = 'v0.3.0'
-
-
-
-def is_tool_installed(tool_name):
-    """Check if a tool is installed and available in PATH."""
-    try:
-        subprocess.run([tool_name, '--version'], stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True)
-        return True
-    except subprocess.CalledProcessError:
-        return False
-    except FileNotFoundError:
-        return False

PyamilySeq/PyamilySeq.py

@@ -0,0 +1,237 @@
+import argparse
+import collections
+import os
+import glob
+import subprocess
+from PyamilySeq_Species import *
+
+
+try:
+    from .PyamilySeq_Species import cluster
+    from .Constants import *
+    from .utils import *
+except (ModuleNotFoundError, ImportError, NameError, TypeError) as error:
+    from PyamilySeq_Species import cluster
+    from Constants import *
+    from utils import *
+
+
+
+
+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"
+    ]
+    if options.verbose == True:
+        subprocess.run(cdhit_command)
+    else:
+        subprocess.run(cdhit_command, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+
+
+def main():
+    parser = argparse.ArgumentParser(description='PyamilySeq ' + PyamilySeq_Version + ': PyamilySeq Run Parameters.')
+    ### Required Arguments
+    required = parser.add_argument_group('Required Arguments')
+    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','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.",
+                          required=True)
+    required.add_argument("-output_dir", action="store", dest="output_dir",
+                          help="Directory for all output files.",
+                          required=True)
+    ### Full-Mode Arguments
+    full_mode_args = parser.add_argument_group('Full-Mode Arguments - Required when "-run_mode Full" is used')
+    full_mode_args.add_argument("-input_type", 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=False)
+    full_mode_args.add_argument("-input_dir", action="store", dest="input_dir",
+                          help="Directory containing GFF/FASTA files.",
+                          required=False)
+    full_mode_args.add_argument("-name_split", action="store", dest="name_split",
+                          help="substring used to split the filename and extract the genome name ('_combined.gff3' or '.gff').",
+                          required=False)
+    full_mode_args.add_argument("-pid", action="store", dest="pident", type=float, default=0.95,
+                          help="Default 0.95: Pident threshold for clustering.",
+                          required=False)
+    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)
+
+
+    ###Partial-Mode Arguments
+    partial_mode_args = parser.add_argument_group('Partial-Mode Arguments - Required when "-run_mode Partial" is used')
+    partial_mode_args.add_argument('-cluster_file', action='store', dest='cluster_file',
+                        help='Clustering output file containing CD-HIT, TSV or CSV Edge List',
+                        required=False)
+
+    ###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',
+                        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',
+                        required=False)
+
+    ###Output Arguments
+    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('-original_fasta', action='store', dest='original_fasta',
+                          help='FASTA file to use in conjunction with "-w" or "-con" when running in Partial Mode.',
+                          required=False)
+    output_args.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)
+
+    ### Misc Arguments
+    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',
+                        required = False)
+    misc.add_argument('-v', action='store_true', dest='version',
+                        help='Default - False: Print out version number and exit',
+                        required=False)
+
+    options = parser.parse_args()
+
+    ### Checking all required parameters are provided by user
+    if options.run_mode == 'Full':
+        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):
+            # Proceed with the Full mode
+            pass
+        else:
+            missing_options = [opt for opt in
+                               ['input_type', 'input_dir', 'name_split', 'clust_tool', 'pident', 'len_diff'] if
+                               not options.__dict__[opt]]
+            print(f"Missing required options for Full mode: {', '.join(missing_options)}")
+    elif options.run_mode == 'Partial':
+        required_partial_mode = [options.cluster_file, ]
+        if all(required_partial_mode):
+            # Proceed with the Partial mode
+            pass
+        else:
+            missing_options = [opt for opt in
+                               ['cluster_file',] if
+                               not options.__dict__[opt]]
+            print(f"Missing required options for Partial mode: {', '.join(missing_options)}")
+
+    if options.clust_tool == 'CD-HIT':
+        clust_affix = '.clstr'
+    elif options.clust_tool == 'TSV':
+        clust_affix = '.tsv'
+    elif options.clust_tool == 'CSV':
+        clust_affix = '.csv'
+
+
+
+    ###External tool checks:
+    ##MAFFT
+    if options.con_core == True:
+        if is_tool_installed('mafft'):
+            if options.verbose == True:
+                print("mafft is installed. Proceeding with alignment.")
+        else:
+            exit("mafft is not installed. Please install mafft to proceed.")
+    ##CD-HIT
+    if options.clust_tool == 'CD-HIT':
+        if is_tool_installed('cd-hit'):
+            if options.verbose == True:
+                print("cd-hit is installed. Proceeding with clustering.")
+        else:
+            exit("cd-hit is not installed. Please install cd-hit to proceed.")
+
+    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:
+        options.cluster_file = fix_path(options.cluster_file)
+    if options.reclustered:
+        options.reclustered = fix_path(options.reclustered)
+    if options.input_dir:
+        options.input_dir = fix_path(options.input_dir)
+    if options.output_dir:
+        options.output_dir = fix_path(options.output_dir)
+
+    output_path = os.path.abspath(options.output_dir)
+    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.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.clusters = clustering_output + clust_affix
+                self.gene_presence_absence_out = options.gene_presence_absence_out
+                self.write_families = options.write_families
+                self.con_core = options.con_core
+                self.fasta = combined_out_file
+                self.verbose = options.verbose
+
+        clustering_options = clustering_options()
+
+    elif options.run_mode == 'Partial':
+        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.clusters = options.cluster_file
+                self.gene_presence_absence_out = options.gene_presence_absence_out
+                self.write_families = options.write_families
+                self.con_core = options.con_core
+                self.fasta = options.original_fasta
+                self.verbose = options.verbose
+
+        clustering_options = clustering_options()
+
+
+
+
+    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#####")
+
+if __name__ == "__main__":
+    main()