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combine_modules.py
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combine_modules.py
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import logging
import sys
import os
import re
from copy import deepcopy
from pandas.io.json._normalize import nested_to_record
import yaml
from TDAS.Intermedia import Intermedia
#from TDAS.functions import *
from TDAS.stats_functions import BlockStat
from TDAS.working_functions import BlockWork
from TDAS.spfunctions import SPfucntions,mkdirs
# METHOD={
# "trim":trim,
# "STAR":star,
# "featureCounts":featureCounts,
# "format":format,
# "redistribute":redistribute,
# "other":self_func
# }
def determine_bg(cmd):
if "&" not in cmd:
return 0
if re.search("[^&]&[^&\d]",cmd) and cmd[0] != "#":
return 1
else:
return 0
last_cmd=cmd.split("&&")[-1]
return determine_bg(last_cmd)
def out_bash_cmd(cmds,threads=2):
for name in cmds:
if os.path.exists(name):
os.remove(name)
count=0
for name,cmd in cmds.items():
mkdirs(os.path.split(name)[0])
with open(name,'a ') as f:
for i in cmd:
f.write(i "\n")
count =determine_bg(i)
if count>=threads:
f.write("wait\n")
count=0
return True
def out_intermedia_new(config):
def out_intermedia(name):
with open (name,'w') as f:
f.write(Intermedia.dumps())
return True
for i in Intermedia.get_next_to_process(config):
project,configid=i
name=os.path.join(config[configid]["outdir"],config[configid]["data_name"])
out_intermedia(name)
return True
def process(config:dict,root_out_dir="",stat=True,threads=8,mode=0,**kwargs):
project_num=0
for i in Intermedia.get_next_to_process(config):
project,configid=i
project_num =1
if configid in config:
this_config=config[configid]
this_config["__source"] = configid
else:
this_config = deepcopy(config["DEFAULT"])
config[configid] = this_config
this_config["__source"] = "DEFAULT"
logging.warning("config_id: {} do not exist in config file, using DEFAULT config instead!".format(configid))
for attr in ["cmd_name","outdir","data_name","cmd_fusion_order","order","order_stat","workflow","stat"]:
if attr not in this_config:
this_config[attr]=config["DEFAULT"][attr]
if len(root_out_dir)==0:
outdir=os.path.join(os.getcwd(),this_config["outdir"])
else:
outdir=os.path.abspath(root_out_dir)
mkdirs(outdir)
if "order" in this_config:
orders=this_config["order"]
elif "order" in config["DEFAULT"]:
orders=config["DEFAULT"]
else:
logging.error('you config file is broken! "order" term is needed! ')
#start to itereach part
for part in orders:
partname=part.strip().split("/")[0]
if partname in SPfucntions: ## determine whether to process by pre-defined functions
func=SPfucntions[partname]
else:
func=SPfucntions["other"]
if "workflow" in this_config and part in this_config["workflow"]: ## using part defined in the config
func_config=this_config["workflow"][part]
elif part in config["DEFAULT"]["workflow"]: ## using part defined in DEFAULT config
func_config=config["DEFAULT"]["workflow"][part]
else:
logging.error(f"the part : {part} do not exist in config: {configid} and DEFAULT! ")
sys.exit(1)
#func(func_config,outdir,project,part)
BlockWork(name=part,outdir=outdir,project=project,params=func_config,config_id=configid,func=func,**kwargs)
if len(root_out_dir)==0:
outdir=""
else:
outdir=os.path.abspath(root_out_dir)
threads=min(threads,project_num)
out_intermedia_new(config)
if stat:
stat_process(config=config,root_out_dir=root_out_dir,threads=threads,mode=mode,**kwargs)
else:
out_bash_cmd(Intermedia.get_cmd_out(config,root_out_dir=outdir,mode=mode),threads=threads)
return True
def stat_process(config:dict,root_out_dir="",threads=8,mode=0,**kwargs):
for config_id in config.get("config_ids",["DEFAULT"]):
if config_id in config:
this_config=config[config_id]
# this_config["__source"] = config_id # assigned from above process function
print("config_id: {} exist in config file!".format(config_id) )
else:
this_config = deepcopy(config["DEFAULT"])
this_config["__source"] = "DEFAULT"
config[config_id] = this_config
logging.warning("config_id: {} do not exist in config file, using DEFAULT config instead!".format(config_id))
for attr in ["cmd_name","outdir","data_name","cmd_fusion_order","order","order_stat","workflow","stat"]:
if attr not in this_config:
this_config[attr]=config["DEFAULT"][attr]
if len(root_out_dir)==0:
outdir=os.path.join(os.getcwd(),this_config["outdir"])
else:
outdir=os.path.abspath(root_out_dir)
mkdirs(outdir)
stat_order=this_config["order_stat"]
if "order" in this_config:
stat_order=this_config["order_stat"]
elif "order" in config["DEFAULT"]:
stat_order=config["DEFAULT"]["order_stat"]
else:
logging.error('you config file is broken! "order" term is needed! ')
for part in stat_order:
if "stat" in this_config and part in this_config["stat"]:
func_config=this_config["stat"][part]
func_config["__source"] = this_config["__source"]
elif part in config["DEFAULT"]["stat"]:
func_config=config["DEFAULT"]["stat"][part]
func_config["__source"] = "DEFAULT"
else:
logging.error(f"the part : {part} do not exist in config: {config_id} and DEFAULT! ")
sys.exit(1)
BlockStat(name=part,outdir=outdir,project="STAT",params=func_config,config_id=config_id, select_source_id = func_config["__source"],**kwargs)
#out_bash_cmd(Intermedia.get_cmd_out(config,root_out_dir=outdir),threads=threads)
if len(root_out_dir)==0:
outdir=""
else:
outdir=os.path.abspath(root_out_dir)
out_bash_cmd(Intermedia.get_cmd_out(config,root_out_dir=outdir,mode=mode),threads=threads)
out_intermedia_new(config)
return True