added cpu support for renaming fasta entries

docs/usage/index.rst

@@ -489,7 +489,8 @@ doi: 10.1093/gbe/evw179 and Steenwyk et al., PLOS Biology
 	phykit parsimony_informative_sites <alignment>
 
 Options: |br|
-*<alignment>*: first argument after function name should be an alignment file
+*<alignment>*: first argument after function name should be an alignment file |br|
+*\\-\\-cpu*: CPUs to use to accelerate calculation
 
 |
 
@@ -549,7 +550,8 @@ and Evolution (2003), doi: 10.1016/S1055-7903(03)00057-5.
 	phykit relative_composition_variability <alignment>
 
 Options: |br|
-*<alignment>*: first argument after function name should be an alignment file
+*<alignment>*: first argument after function name should be an alignment file |br|
+*\\-\\-cpu*: CPUs to use to accelerate calculation
 
 |
 

phykit/phykit.py

@@ -466,7 +466,7 @@ def alignment_length_no_gaps(argv):
             ),
         )
         parser.add_argument("alignment", type=str, help=SUPPRESS)
-        parser.add_argument("--cpu", type=str, help=SUPPRESS)
+        parser.add_argument("--cpu", type=int, help=SUPPRESS)
         args = parser.parse_args(argv)
         AlignmentLengthNoGaps(args).run()
 
@@ -606,7 +606,7 @@ def alignment_recoding(argv):
 
         parser.add_argument("alignment", type=str, help=SUPPRESS)
         parser.add_argument("-c", "--code", type=str, help=SUPPRESS)
-        parser.add_argument("--cpu", type=str, help=SUPPRESS)
+        parser.add_argument("--cpu", type=int, help=SUPPRESS)
         args = parser.parse_args(argv)
         AlignmentRecoding(args).run()
 
@@ -883,7 +883,7 @@ def pairwise_identity(argv):
         parser.add_argument(
             "-e", "--exclude_gaps", action="store_true", required=False, help=SUPPRESS
         )
-        parser.add_argument("--cpu", type=str, help=SUPPRESS)
+        parser.add_argument("--cpu", type=int, help=SUPPRESS)
         args = parser.parse_args(argv)
         PairwiseIdentity(args).run()
 
@@ -920,17 +920,21 @@ def parsimony_informative_sites(argv):
                   pk_parsimony_informative_sites, pk_pis
 
                 Usage:
-                phykit parsimony_informative_sites <alignment>
+                phykit parsimony_informative_sites <alignment> [--cpu <cpu>]
 
                 Options
                 =====================================================
                 <alignment>                 first argument after 
                                             function name should be
-                                            an alignment file          
+                                            an alignment file
+
+                --cpu                       CPUs to use to
+                                            accelerate calculation
                 """
             ),
         )
         parser.add_argument("alignment", type=str, help=SUPPRESS)
+        parser.add_argument("--cpu", type=int, help=SUPPRESS)
         args = parser.parse_args(argv)
         ParsimonyInformative(args).run()
 
@@ -953,23 +957,27 @@ def rcv(argv):
                 RCV is calculated following Phillips and Penny, Molecular Phylogenetics
                 and Evolution (2003), doi: 10.1016/S1055-7903(03)00057-5.
 
-                Aliases: 
+                Aliases:
                   relative_composition_variability, rel_comp_var, rcv
                 Command line interfaces:
                   pk_relative_composition_variability, pk_rel_comp_var, pk_rcv
 
                 Usage:
-                phykit relative_composition_variability <alignment>
+                phykit relative_composition_variability <alignment> [--cpu <cpu>]
 
                 Options
                 =====================================================
-                <alignment>                 first argument after 
+                <alignment>                 first argument after
                                             function name should be
-                                            an alignment file          
+                                            an alignment file
+
+                --cpu                       CPUs to use to
+                                            accelerate calculation
                 """
             ),
         )
         parser.add_argument("alignment", type=str, help=SUPPRESS)
+        parser.add_argument("--cpu", type=int, help=SUPPRESS)
         args = parser.parse_args(argv)
         RelativeCompositionVariability(args).run()
 
@@ -996,17 +1004,21 @@ def rcvt(argv):
                   pk_relative_composition_variability_taxon, pk_rel_comp_var_taxon, pk_rcvt
 
                 Usage:
-                phykit relative_composition_variability_taxon <alignment>
+                phykit relative_composition_variability_taxon <alignment> [--cpu <cpu>]
 
                 Options
                 =====================================================
                 <alignment>                 first argument after 
                                             function name should be
-                                            an alignment file          
+                                            an alignment file 
+
+                --cpu                       CPUs to use to
+                                            accelerate calculation
                 """
             ),
         )
         parser.add_argument("alignment", type=str, help=SUPPRESS)
+        parser.add_argument("--cpu", type=int, help=SUPPRESS)
         args = parser.parse_args(argv)
         RelativeCompositionVariabilityTaxon(args).run()
 
@@ -1034,7 +1046,7 @@ def rename_fasta_entries(argv):
 
                 Usage:
                 phykit rename_fasta_entries <fasta> -i/--idmap <idmap>
-                    [-o/--output <output_file>]
+                    [-o/--output <output_file> --cpu <cpu>]
 
                 Options
                 =====================================================
@@ -1052,12 +1064,16 @@ def rename_fasta_entries(argv):
                                             name as the input file with
                                             the suffix ".renamed.fa" added
                                             to it.
+                
+                --cpu                       CPUs to use to
+                                            accelerate calculation
                 """
             ),
         )
         parser.add_argument("fasta", type=str, help=SUPPRESS)
         parser.add_argument("-i", "--idmap", type=str, help=SUPPRESS)
         parser.add_argument("-o", "--output", type=str, required=False, help=SUPPRESS)
+        parser.add_argument("--cpu", type=int, help=SUPPRESS)
         args = parser.parse_args(argv)
         RenameFastaEntries(args).run()
 

phykit/services/alignment/base.py

@@ -1,8 +1,10 @@
 from collections import Counter
-import multiprocessing
+from multiprocessing import cpu_count
+from multiprocessing import Pool
 import sys
+from typing import Dict, List
 
-from typing import List
+from Bio.Seq import Seq
 
 from ..base import BaseService
 from ...helpers.files import (
@@ -45,9 +47,6 @@ def __init__(
         self.exclude_gaps = exclude_gaps
 
     def get_alignment_and_format(self):
-        """
-        automatic file type determination
-        """
         try:
             return get_alignment_and_format_helper(self.alignment_file_path)
         except FileNotFoundError:
@@ -58,43 +57,55 @@ def get_alignment_and_format(self):
     def calculate_rcv(self) -> float:
         alignment, _, _ = self.get_alignment_and_format()
         aln_len = alignment.get_alignment_length()
-
-        concat_seq = []
         num_records = len(alignment)
 
         concat_seq = "".join(str(record.seq) for record in alignment)
-
         total_counts = Counter(concat_seq)
 
         average_d = {
             seq: total_counts[seq] / num_records for seq in total_counts
         }
 
-        indiv_rcv_values = []
+        cpu = self.set_cpu()
 
-        for record in alignment:
-            record_counts = Counter(record.seq)
-            temp_rcv = sum(
-                abs(
-                    record_counts[seq_letter] - average_d[seq_letter]
-                ) for seq_letter in total_counts
+        with Pool(cpu) as pool:
+            indiv_rcv_values = pool.starmap(
+                self.calculate_indiv_rcv,
+                [
+                    (record.seq, average_d, total_counts, aln_len, num_records)
+                    for record in alignment
+                ]
             )
-            indiv_rcv_values.append(temp_rcv / (num_records * aln_len))
 
         relative_composition_variability = sum(indiv_rcv_values)
 
         return relative_composition_variability
 
+    def calculate_indiv_rcv(
+        self,
+        seq: Seq,
+        average_d: Dict[str, float],
+        total_counts: Counter,
+        aln_len: int,
+        num_records: int,
+    ) -> float:
+        record_counts = Counter(seq)
+        temp_rcv = sum(
+            abs(record_counts[seq_letter] - average_d[seq_letter])
+            for seq_letter in total_counts
+        )
+        return temp_rcv / (num_records * aln_len)
+
     def get_gap_chars(is_protein: bool) -> List[str]:
         if is_protein:
             return ["-", "?", "*", "X", "x"]
         else:
             return ["-", "?", "*", "X", "x", "N", "n"]
 
     def set_cpu(self) -> int:
-        cpu_available = multiprocessing.cpu_count()
+        cpu_available = cpu_count()
 
-        cpu = int(self.cpu[0]) if self.cpu[0] else multiprocessing.cpu_count()
+        cpu = int(self.cpu[0]) if self.cpu[0] else cpu_count()
 
         if cpu > cpu_available:
             return cpu_available

phykit/services/alignment/compositional_bias_per_site.py

@@ -45,28 +45,24 @@ def calculate_compositional_bias_per_site(
         List[Power_divergenceResult],
         List[Union[float, str]],
     ]:
-        # get aln length
         aln_len = alignment.get_alignment_length()
 
         stat_res = []
         p_vals = []
         nan_idx = []
 
         for idx in range(aln_len):
-            # Count occurrences of each character at site idx
-            num_occurrences = self.get_number_of_occurrences_per_character(alignment, idx)
+            num_occurrences = \
+                self.get_number_of_occurrences_per_character(alignment, idx)
 
-            # Perform chi-square test on the counts
             chisquare_res = chisquare(num_occurrences)
             stat_res.append(chisquare_res)
 
-            # Collect p-values and track NaN values
             if str(chisquare_res.pvalue) != "nan":
                 p_vals.append(chisquare_res.pvalue)
             else:
                 nan_idx.append(idx)
 
-        # Correct p-values using false discovery control
         p_vals_corrected = list(false_discovery_control(p_vals))
 
         # Reinsert "nan" values at the appropriate positions

phykit/services/alignment/create_concatenation_matrix.py

@@ -1,6 +1,7 @@
 import sys
 from textwrap import dedent
 from typing import Dict, List, Tuple
+
 from Bio import SeqIO
 from Bio.SeqRecord import SeqRecord
 

phykit/services/alignment/dna_threader.py

@@ -1,7 +1,9 @@
 import sys
 from typing import Dict, List
+
 from Bio import SeqIO
 from Bio.Seq import Seq
+
 from .base import Alignment
 
 

phykit/services/alignment/evolutionary_rate_per_site.py

@@ -54,7 +54,6 @@ def calculate_evolutionary_rate_per_site(
 
         gap_chars = self.get_gap_chars()
 
-        # calculate PIC for each site in the alignment
         for idx in range(aln_len):
             num_occurrences = self.get_number_of_occurrences_per_character(
                 alignment, idx, gap_chars

phykit/services/alignment/parsimony_informative_sites.py

@@ -1,4 +1,5 @@
 from collections import Counter
+from multiprocessing import Pool
 from typing import Dict, Tuple
 
 from Bio.Align import MultipleSeqAlignment
@@ -12,9 +13,8 @@ def __init__(self, args) -> None:
 
     def run(self):
         alignment, _, _ = self.get_alignment_and_format()
-        pi_sites, aln_len, pi_sites_per = self.calculate_parsimony_informative_sites(
-            alignment
-        )
+        pi_sites, aln_len, pi_sites_per = \
+            self.calculate_parsimony_informative_sites(alignment)
 
         print(f"{pi_sites}\t{aln_len}\t{round(pi_sites_per, 4)}")
 
@@ -36,21 +36,34 @@ def is_parsimony_informative(
         self,
         num_occurrences: Counter,
     ) -> bool:
-        informative_char_count = sum(1 for count in num_occurrences.values() if count >= 2)
+        informative_char_count = sum(
+            1 for count in num_occurrences.values() if count >= 2
+        )
         return informative_char_count >= 2
 
     def calculate_parsimony_informative_sites(
         self,
         alignment: MultipleSeqAlignment,
     ) -> Tuple[int, int, float]:
+        cpu = self.set_cpu()
+
         aln_len = alignment.get_alignment_length()
-        pi_sites = 0
 
-        for idx in range(aln_len):
-            num_occurrences = self.get_number_of_occurrences_per_character(alignment, idx)
-            if self.is_parsimony_informative(num_occurrences):
-                pi_sites += 1
+        with Pool(cpu) as pool:
+            results = pool.map(
+                self.check_site_parsimony_informative,
+                [(alignment, idx) for idx in range(aln_len)]
+            )
 
+        pi_sites = sum(results)
         pi_sites_per = (pi_sites / aln_len) * 100
 
         return pi_sites, aln_len, pi_sites_per
+
+    def check_site_parsimony_informative(
+        self,
+        args: Tuple[MultipleSeqAlignment, int]
+    ) -> int:
+        alignment, idx = args
+        num_occurrences = self.get_number_of_occurrences_per_character(alignment, idx)
+        return 1 if self.is_parsimony_informative(num_occurrences) else 0

phykit/services/alignment/rcv.py

@@ -11,4 +11,4 @@ def run(self):
         print(round(relative_composition_variability, 4))
 
     def process_args(self, args):
-        return dict(alignment_file_path=args.alignment)
+        return dict(alignment_file_path=args.alignment, cpu=args.cpu)