happy pylint

extend.py

@@ -2,23 +2,14 @@
 from Bio.Seq import Seq
 from Bio.SeqIO import SeqRecord
 from Bio.Align import MultipleSeqAlignment
-from glob import glob
 import logging
-import tempfile
 from pathlib import Path
 import re
-import subprocess
 from collections import namedtuple, defaultdict, Counter
 import bisect
-import os
-from Bio.Align import substitution_matrices
-from itertools import product, combinations
 import numpy as np
-from Bio.AlignIO.MafIO import MafWriter, MafIterator
-from Bio.AlignIO.MauveIO import MauveWriter, MauveIterator
-from logger import logger, TqdmToLogger, MIN_TQDM_INTERVAL
 from tqdm import tqdm
-import time
+from logger import logger, TqdmToLogger, MIN_TQDM_INTERVAL
 import spoa
 #%%
 

parsnp

@@ -5,19 +5,16 @@
 
 '''
 
-import os, sys, string, getopt, random,subprocess, time,operator, math, datetime,numpy #pysam
+import os, sys, string, random, subprocess, time, operator, math, datetime, numpy #pysam
 from collections import defaultdict
-import csv
 import shutil
 import shlex
 from tempfile import TemporaryDirectory
 import re
 import logging
 from logger import logger, TqdmToLogger, MIN_TQDM_INTERVAL
-import multiprocessing
 import argparse
 import signal
-import inspect
 from multiprocessing import Pool
 from Bio import SeqIO
 from glob import glob
@@ -149,7 +146,7 @@ def run_phipack(query,seqlen,workingdir):
     currdir = os.getcwd()
     os.chdir(workingdir)
     command = "Profile -o -v -n %d -w 100 -m 100 -f %s > %s.out"%(seqlen,query,query)
-    run_command(command,1, prepend_time=True)
+    run_command(command, 1)
     os.chdir(currdir)
 
 def run_fasttree(query,workingdir,recombination_sites):

partition.py

@@ -729,69 +729,3 @@ def merge_xmfas(
                     xmfa_out_handle.write(tx.read())
 
 
-if __name__ == "__main__":
-    args = parse_args()
-    os.makedirs(args.output_dir, exist_ok=True)
-
-    query_files = list()
-    for arg_path in args.sequences:
-        if arg_path.endswith(".txt"):
-            with open(arg_path) as input_list_handle:
-                for line in input_list_handle:
-                    query_files.append(line.strip())
-        elif any(arg_path.endswith(suff) for suff in FASTA_SUFFIX_LIST):
-            query_files.append(arg_path)
-        elif os.path.isdir(arg_path):
-            for f in os.listdir(arg_path): 
-                if any(f.endswith(suff) for suff in FASTA_SUFFIX_LIST):
-                    query_files.append(f"{arg_path}/{f}")
-
-    full_query_list_path = f"{args.output_dir}/input-list.txt"
-    with open(full_query_list_path, 'w') as input_list_handle:
-        for qf in query_files:
-            input_list_handle.write(qf + "\n")
-
-    partition_output_dir = f"{args.output_dir}/partition"
-    partition_list_dir = f"{partition_output_dir}/input-lists"
-    os.makedirs(partition_list_dir, exist_ok=True)
-    run_command(f"split -l {args.partition_size} -a 5 --additional-suffix '.txt' {full_query_list_path} {partition_list_dir}/{CHUNK_PREFIX}-")
-
-    chunk_label_parser = re.compile(f'{CHUNK_PREFIX}-(.*).txt')
-    chunk_labels = []
-    for partition_list_file in os.listdir(partition_list_dir):
-        chunk_labels.append(chunk_label_parser.search(partition_list_file).groups()[0])
-
-    parsnp_commands = []
-    for cl in chunk_labels:
-        chunk_output_dir = f"{partition_output_dir}/{CHUNK_PREFIX}-{cl}-out"
-        os.makedirs(chunk_output_dir, exist_ok=True)
-        chunk_command = f"./parsnp -d {partition_list_dir}/{CHUNK_PREFIX}-{cl}.txt -r {args.reference} -o {chunk_output_dir} "
-        chunk_command += args.parsnp_flags
-        chunk_command += f" > {chunk_output_dir}/parsnp.stdout 2> {chunk_output_dir}/parsnp.stderr"
-        parsnp_commands.append(chunk_command)
-
-    good_chunks = set(chunk_labels)
-    run_command_nocheck = partial(run_command, check=False)
-    with Pool(args.threads) as pool:
-        return_codes = tqdm(pool.imap(run_command_nocheck, parsnp_commands, chunksize=1), total=len(parsnp_commands))
-        for cl, rc in zip(chunk_labels, return_codes):
-            if rc != 0:
-                logger.error("Partition {cl} failed...")
-                good_chunks.remove(cl)
-
-    chunk_labels = list(good_chunks)
-
-    logger.info("Computing intersection of all partition LCBs...")
-    chunk_to_intvervaldict = get_chunked_intervals(partition_output_dir, chunk_labels)
-    intersected_interval_dict = get_intersected_intervals(chunk_to_intvervaldict)
-
-    logger.info("Trimming partitioned XMFAs back to intersected intervals...")
-    num_clusters = trim_xmfas(partition_output_dir, chunk_labels, intersected_interval_dict, args.threads)
-
-    os.makedirs(f"{args.output_dir}/merged-out/", exist_ok=True)
-    xmfa_out_f =  f"{args.output_dir}/merged-out/parsnp.xmfa"
-
-    logger.info(f"Merging trimmed XMFA files into a single XMFA at {xmfa_out_f}")
-    merge_xmfas(partition_output_dir, chunk_labels, xmfa_out_f, num_clusters, args.threads)
-
-