add a script to run linux cmd order using output as new input with multiple rounds

Author: Runsheng

runiter.py

@@ -0,0 +1,132 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# @Time    : 10/20/2020 4:02 PM
+# @Author  : Runsheng     
+# @File    : runiter.py
+
+"""
+A general runner for the functions require multiple rounds of iteration, like genome polishing
+"""
+
+from __future__ import print_function
+import os
+import argparse
+import subprocess
+import logging
+import sys
+import signal
+from glob import glob
+import re
+
+
+def myexe(cmd, timeout=0):
+    """
+    a simple wrap of the shell
+    mainly used to run the bwa mem mapping and samtool orders
+    """
+    def setupAlarm():
+        signal.signal(signal.SIGALRM, alarmHandler)
+        signal.alarm(timeout)
+
+    def alarmHandler(signum, frame):
+        sys.exit(1)
+
+    proc=subprocess.Popen(cmd, shell=True, preexec_fn=setupAlarm,
+                 stdout=subprocess.PIPE, stderr=subprocess.PIPE,cwd=os.getcwd())
+    out, err=proc.communicate()
+    print(err)
+    return out, err, proc.returncode
+
+def mylogger():
+    ###############
+    # create logger
+    logger = logging.getLogger('')
+    logger.setLevel(logging.INFO)
+    # create console handler and set level to debug
+    ch = logging.StreamHandler()
+    ch.setLevel(logging.INFO)
+    # create formatter
+    formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+    # add formatter to ch
+    ch.setFormatter(formatter)
+    # add ch to logger
+    logger.addHandler(ch)
+    # 'application' code
+    ###############
+    return logger
+
+
+def get_file_round(wkdir=None, key1="round1"):
+    if wkdir is None:
+        wkdir=os.getcwd()
+    os.chdir(wkdir)
+    key=key1.replace("1", "")
+
+    file_name_l=glob("*"+key+"*")
+    print(file_name_l)
+    if file_name_l>1:
+        num_l=[]
+        for filename in file_name_l:
+            x=re.findall(key+"[0-9]", filename)
+            for i in x:
+                num_x=int(i.replace(key, ""))
+                num_l.append(num_x)
+        return max(num_l)
+    else:
+        return 0
+
+def generate_one(cmd, round, key0="round0", key1="round1"):
+    """
+    place the cmd, and replace "_round1" with the current round "_roundn"
+    replace "_round0" to "_round(n-1)"
+    :param key0, the key has a 0 inside the string, indicate the iter1 input
+    :param key1, the key has a 1 inside the string, to indicate the iter1 output/ inter2 input
+    """
+    if key0 in cmd and key1 in cmd:
+        key=key1.replace("1", "")
+        key_new0=key+str(round-1)
+        key_new1=key+str(round)
+
+        cmd1 = cmd.replace(key1, key_new1)
+        cmd2 = cmd1.replace(key0, key_new0)
+        return cmd2
+
+    else:
+        raise KeyError("Keys used to indicate round do not fit the round0/round1 format")
+        return None
+
+if __name__=="__main__":
+
+    example_text = '''example:
+    ### example to run the runiter with 4 times
+    runiter.py -r 4 -0 round0 -1 round1 -c "minimap2 -ax asm20 -t 48 ref_round0.fa ../polish/slr/merge.fq > aln_round1.sam && racon -u -t 48 ../polish/slr/merge.fq  aln_round1.sam ref_round0.fa > ref_round1.fa"
+    
+    '''
+    parser = argparse.ArgumentParser(prog='runiter',
+                                     description='runiter',
+                                     epilog=example_text,
+                                     formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    parser.add_argument("-r", "--round", type=int, default=5, help="how many round will this cmd runs")
+    parser.add_argument("-c", "--cmd", default="echo test round0 round1", help="the cmd line to be run, with round0 and round1 indicating the iter items")
+    parser.add_argument("-0", "--key0", default="round0", help="the indicator of the key for iter0, need to have a 0 inside")
+    parser.add_argument("-1", "--key1", default="round1", help="the indicator of the key for iter1, need to have a 1 inside")
+    parser.add_argument("--resume", default="no", help="try to resume the former run by find the max round")
+
+    args = parser.parse_args()
+
+    logger=mylogger()
+
+    start_round=1
+
+    if args.resume=="yes":
+        n=get_file_round()
+        start_round=n+1
+        logger.info("found round{} output, start from round{}".format(n, start_round))
+
+    for i in range(start_round, args.round+1):
+        cmd_one=generate_one(args.cmd, i, key0=args.key0, key1=args.key1)
+        logger.info("running round {}".format(i))
+        logger.info("running {}".format(cmd_one))
+        myexe(cmd_one)
+        logger.info("##########finished round {} ##########".format(i))