Delete multi_config.smk

workflow/rules/ini/multi_config.smk

-import os
-import sys
-import shutil
-import gzip
-#import json
-import yaml
-import bz2
-import re
-from copy import deepcopy
-import subprocess
-import pandas as pd
-import fnmatch
-
-
-
-# default configuration file
-configfile:
-    srcdir("../../../config/config.multi.yaml")
-
-
-# default executable for snakmake
-shell.executable("bash")
-
-
-# some parameters
-SRCDIR = srcdir("../../scripts")
-BINDIR = srcdir("../../bin")
-ENVDIR = srcdir("../../envs")
-
-# get parameters from the command line
-# output
-OUTPUTDIR = config['outputdir']
-
-MULTI_STEPS = sorted(config['steps'].split())
-
-try:
-    samples = pd.read_csv(os.path.expandvars(config['sample_table']),sep="\t")
-except:
-    print("Sample table was not found. Please enter the absolute path and file name in the config file.")
-    raise
-if samples[['sample']].duplicated().any():
-    raise Exception('sample names should be unique.')
-samples = samples.set_index(["sample"],drop=False)
-samples['sample'] = samples['sample'].astype(str)
-for sam in samples['sample']:
-    if not re.match(r"[0-9a-zA-Z]",sam):
-        raise Exception('please start library names with a letter or number')
-samples['sample'] = samples['sample'].str.replace('[;|.-]','_')
-samples['sample'] = samples['sample'].str.replace('_+','_')
-if not 'path' in samples.columns:
-    raise Exception("You haven't supplied the paths to the data.")
-if samples['path'].duplicated().any():
-    raise Exception('paths should be unique.')
-if any([not os.path.isdir(path) for path in samples['path'].tolist()]):
-    raise Exception('Not all input directories could be found.')
-    
-multi_config = {}
-for sam in samples['sample']:
-    spath = samples.loc[samples['sample']==sam, "path"].iat[0] + "/sample.config.yaml"
-    if os.path.exists(spath):
-#        print("reading configuration from "+ spath)
-        with open(spath, 'r') as rhandle:
-            multi_config[sam] = yaml.load(rhandle,Loader=yaml.SafeLoader)
-    
-samples = samples.assign(mg=[1 if (multi_config[sam]['raws']['Metagenomics'].split() or multi_config[sam]['raws']['Alignment_metagenomics'].split() ) else 0 for sam in samples['sample']])
-samples = samples.assign(mt=[1 if (multi_config[sam]['raws']['Metatranscriptomics'].split() or multi_config[sam]['raws']['Alignment_metatranscriptomics'].split()) else 0 for sam in samples['sample']])
-if "collate" in MULTI_STEPS:
-    COLL_STEPS = sorted(config['collection']['results'].split())
-    samples = samples.assign(taxonomy=[1 if "taxonomy" in multi_config[sam]['steps'].split() and (multi_config[sam]['raws']['Metagenomics'].split() or multi_config[sam]['raws']['Metatranscriptomics'].split()) else 0 for sam in samples['sample']])
-    samples = samples.assign(EukDetect=[1 if "taxonomy" in multi_config[sam]['steps'].split() and (multi_config[sam]['raws']['Metagenomics'].split() or multi_config[sam]['raws']['Metatranscriptomics'].split()) and 'eukdetect' in multi_config[sam] and multi_config[sam]['eukdetect']['run_eukdetect'] else 0 for sam in samples['sample']])
-    samples = samples.assign(stats=[1 if "summary" in multi_config[sam]['steps'].split() and "stats" in multi_config[sam]['summary_steps'].split() else 0 for sam in samples['sample']])
-    for db in config['hmm_DBs'].split():        
-        samples[db] = 0
-        samples[db] = [1 if "analysis" in multi_config[sam]['steps'].split() and db in multi_config[sam]['hmm_DBs'].split() else 0 for sam in samples['sample']]
-if "catalogue" in MULTI_STEPS:
-    samples = samples.assign(genes=[1 if "analysis" in multi_config[sam]['steps'].split() else 0 for sam in samples['sample']])
-    samples["prokka_prefix"] = ""
-    for sam in samples['sample']:
-        if samples.genes[sam] == 1:
-            if os.path.isfile(samples.path[sam] + "/Analysis/annotation/prokka.faa"):
-                with open(samples.path[sam] + "/Analysis/annotation/prokka.faa",'r') as f:
-                    line = f.readline()
-                    samples.prokka_prefix[sam] = line.split("_")[0][1:]
-if "dereplicate" in MULTI_STEPS:
-    samples = samples.assign(bins=[1 if "binning" in multi_config[sam]['steps'].split() else 0 for sam in samples['sample']])
-    samples = samples.assign(ass=[1 if ("assembly" in multi_config[sam]['steps'].split() or multi_config[sam]['raws']['Contigs'].split()) else 0 for sam in samples['sample']])
-    samples["assembly_type"] = ""
-    for sam in samples['sample']:
-        if samples.ass[sam] == 1:
-            samples.assembly_type[sam] = [f.replace(".assembly.merged.fa","") for f in os.listdir(samples.path[sam] + "/Assembly/") if fnmatch.fnmatch(f,"m*.assembly.merged.fa")][0]
-    if config['dereplication']['cross_mapping_rebinning']['do']:
-        if not 'rebinning' in samples.columns:
-            samples['rebinning'] = "yes"
-
-#print(samples.EukDetect)
-
-TYPES=config['omes'].split()
-
-yaml.add_representer(OrderedDict, lambda dumper, data: dumper.represent_mapping('tag:yaml.org,2002:map', data.items()))
-yaml.add_representer(tuple, lambda dumper, data: dumper.represent_sequence('tag:yaml.org,2002:seq', data))
-
-# temporary directory will be stored inside the OUTPUTDIR directory
-# unless an absolute path is set
-TMPDIR = os.path.expandvars(config['tmp_dir'])
-if not os.path.isabs(TMPDIR):
-    TMPDIR = os.path.join(OUTPUTDIR, TMPDIR)
-if not os.path.exists(TMPDIR):
-    os.makedirs(TMPDIR)
-
-DBPATH = os.path.expandvars(config['db_path'])
-
-# hardware parameters
-BIGCORENO = config['mem']['big_mem_cores']
-BIGMEMTOTAL = config['mem']['big_mem_total_gb']
-MEMCORE = str(config['mem']['normal_mem_per_core_gb']) + "G"
-BIGMEMCORE = str(config['mem']['big_mem_per_core_gb']) + "G"
-
-SAMTOOLS_MEM = str(round(float(BIGMEMCORE[:-1]) * 0.75 - 0.5)) + "G"
-