PyamilySeq 1.0.0__py3-none-any.whl → 1.0.1__py3-none-any.whl

PyamilySeq/Cluster_Summary.py

@@ -0,0 +1,163 @@
+import argparse
+from collections import OrderedDict
+from collections import defaultdict
+
+try:
+    from .constants import *
+    from .utils import *
+except (ModuleNotFoundError, ImportError, NameError, TypeError) as error:
+    from constants import *
+    from utils import *
+
+
+def categorise_percentage(percent):
+    """Categorise the percentage of genomes with multicopy genes."""
+    if 20 <= percent < 40:
+        return "20-40%"
+    elif 40 <= percent < 60:
+        return "40-60%"
+    elif 60 <= percent < 80:
+        return "60-80%"
+    elif 80 <= percent < 95:
+        return "80-95%"
+    elif 95 <= percent < 99:
+        return "95-99%"
+    elif 99 <= percent <= 100:
+        return "99-100%"
+    return None
+
+# Read cd-hit .clstr file and extract information
+def read_cd_hit_output(clustering_output):
+    clusters = OrderedDict()
+
+    with open(clustering_output, 'r') as f:
+        current_cluster_id = None
+
+        for line in f:
+            line = line.strip()
+            if line.startswith(">Cluster"):
+                current_cluster_id = line.split(' ')[1]
+                clusters[current_cluster_id] = []
+            elif line and current_cluster_id is not None:
+                parts = line.split('\t')
+                if len(parts) > 1:
+                    clustered_info = parts[1]
+                    length = clustered_info.split(',')[0]
+                    length = int(''.join(c for c in length if c.isdigit()))
+                    clustered_header = clustered_info.split('>')[1].split('...')[0]
+                    clustered_header = '>' + clustered_header
+
+                    if 'at ' in clustered_info and '%' in clustered_info.split('at ')[-1]:
+                        percent_identity = extract_identity(clustered_info)
+                    elif line.endswith('*'):
+                        percent_identity = 100.0
+                    else:
+                        raise ValueError("Percent identity not found in the string.")
+
+                    clusters[current_cluster_id].append({
+                        'header': clustered_header,
+                        'length': length,
+                        'percent_identity': percent_identity
+                    })
+
+    return clusters
+
+
+# Summarise the information for each cluster
+def summarise_clusters(options,clusters, output):
+    multicopy_groups = defaultdict(int)  # Counter for groups with multicopy genes
+
+    with open(output, 'w') as out_f:
+        out_f.write("Cluster_ID\tNum_Sequences\tAvg_Length\tLength_Range\tAvg_Identity\tIdentity_Range\n")
+
+        for cluster_id, seqs in clusters.items():
+            num_seqs = len(seqs)
+            lengths = [seq['length'] for seq in seqs]
+            identities = [seq['percent_identity'] for seq in seqs]
+
+            avg_length = sum(lengths) / num_seqs if num_seqs > 0 else 0
+            length_range = f"{min(lengths)}-{max(lengths)}" if num_seqs > 0 else "N/A"
+
+            avg_identity = sum(identities) / num_seqs if num_seqs > 0 else 0
+            identity_range = f"{min(identities):.2f}-{max(identities):.2f}" if num_seqs > 0 else "N/A"
+
+            out_f.write(
+                f"{cluster_id}\t{num_seqs}\t{avg_length:.2f}\t{length_range}\t{avg_identity:.2f}\t{identity_range}\n")
+
+            # Count genomes with more than one gene
+            genome_to_gene_count = defaultdict(int)
+            for seq in seqs:
+                genome = seq['header'].split('|')[0].replace('>','')
+                genome_to_gene_count[genome] += 1
+
+            num_genomes_with_multiple_genes = sum(1 for count in genome_to_gene_count.values() if count > 1)
+
+            # Calculate the percentage of genomes with multicopy genes
+
+            multicopy_percentage = (num_genomes_with_multiple_genes / options.genome_num) * 100
+            category = categorise_percentage(multicopy_percentage)
+            if category:
+                multicopy_groups[category] += 1
+
+        # Define the order of categories for printout
+        category_order = ["20-40%", "40-60%", "60-80%", "80-95%", "95-99%", "99-100%"]
+
+        # Print the number of clusters with multicopy genes in each percentage range, in the correct order
+        for category in category_order:
+            print(f"Number of clusters with multicopy genes in {category} range: {multicopy_groups[category]}")
+
+
+# Main function to parse arguments and run the analysis
+def main():
+    parser = argparse.ArgumentParser(description='PyamilySeq ' + PyamilySeq_Version + ': Cluster-Summary - A tool to summarise CD-HIT clustering files.')
+    ### Required Arguments
+    required = parser.add_argument_group('Required Parameters')
+    required.add_argument('-input_clstr', action="store", dest="input_clstr",
+                          help='Input CD-HIT .clstr file',
+                          required=True)
+    required.add_argument('-output', action="store", dest="output",
+                          help="Output TSV file to store cluster summaries - Will add '.tsv' if not provided by user",
+                          required=True)
+    required.add_argument('-genome_num', action='store', dest='genome_num', type=int,
+                          help='The total number of genomes must be provide',
+                          required=True)
+    #required.add_argument("-clustering_format", action="store", dest="clustering_format", choices=['CD-HIT','TSV','CSV'],
+    #                      help="Clustering format to use: CD-HIT or TSV (MMseqs2, BLAST, DIAMOND) / CSV edge-list file (Node1\tNode2).",
+    #                      required=True)
+
+    optional = parser.add_argument_group('Optional Arguments')
+    optional.add_argument('-output_dir', action="store", dest="output_dir",
+                          help='Default: Same as input file',
+                          required=False)
+
+    misc = parser.add_argument_group("Misc Parameters")
+    misc.add_argument("-verbose", action="store_true", dest="verbose",
+                      help="Print verbose output.",
+                      required=False)
+    misc.add_argument("-v", "--version", action="version",
+                      version=f"PyamilySeq: Group-Summary version {PyamilySeq_Version} - Exiting",
+                      help="Print out version number and exit")
+
+
+    options = parser.parse_args()
+    print("Running PyamilySeq " + PyamilySeq_Version+ ": Group-Summary ")
+
+    ### File handling
+    options.input_clstr = fix_path(options.input_clstr)
+    if options.output_dir is None:
+        options.output_dir = os.path.dirname(os.path.abspath(options.input_clstr))
+    output_path = os.path.abspath(options.output_dir)
+    if not os.path.exists(output_path):
+        os.makedirs(output_path)
+    output_name = options.output
+    if not output_name.endswith('.tsv'):
+        output_name += '.tsv'
+    output_file_path = os.path.join(output_path, output_name)
+    ###
+
+    clusters = read_cd_hit_output(options.input_clstr)
+    summarise_clusters(options,clusters, output_file_path)
+
+
+if __name__ == "__main__":
+    main()