def cleanup():
'''
Removes "nucmer.error" file (Mac only).
nucmer or mummer, which is run as part of quast, creates an error file
in the Py_code folder that will be deleted if present.
That seems to be a problem only for the Mac, not Linux
'''
PY_dir = config.get_DO_PATHS()['PY_dir'] + 'nucmer.error'
if os.path.exists(BASE_PATH + PY_dir + 'nucmer.error'):
os.remove(BASE_PATH + PY_dir + 'nucmer.error')
Created on Thu Jul 5 16:07:55 2018
@authors:
Wolfgang Haas, Pascal Lapierre, and Kimberlee A. Musser
Wadsworth Center, New York State Department of Health
120 New Scotland Ave., Albany, New York 12208
[email protected]
last update: 24 September 2020
"""
import pydot
from heapq import heappop, heappush
import config
BASE_PATH = config.get_DO_PATHS()['BASE_PATH']
TEMP_dir = config.get_DO_PATHS()['TEMP_dir']
##### generate the minimum spanning tree from distance data ###################
def make_graph(lo_concat_pairwise_diffs):
'''
Turns a list of [(G1, G2, V1),(G2, G1, V1),...] tuples into a graph, which
is in this case a dictionary of dictionaries. G1 and G2 are the Genomes
(isolates), V1 (Value) is the number of either SNPs or mutation events.
param: list lo_concat_pairwise_diffs = list of (G1, G2, V1) and its
inverse, (G2, G1, V1), which are both needed by prim_mst()
return: a graph (a dict of dict), input for prim_mst()
'''
@authors:
Wolfgang Haas, Pascal Lapierre, and Kimberlee A. Musser
Wadsworth Center, New York State Department of Health
120 New Scotland Ave., Albany, New York 12208
[email protected]
last update: 24 September 2020
"""
import os
import shutil
import re
import config
import toolshed
BASE_PATH = config.get_DO_PATHS()['BASE_PATH']
TEMP_dir = config.get_DO_PATHS()['TEMP_dir']
OUTPUT_dir = config.get_DO_PATHS()['OUTPUT_dir']
GENOMES_dir = config.get_DO_PATHS()['GENOMES_dir']
Parsnp_image, Parsnp_WorkingDir = config.get_DO_IMAGES()['Parsnp']
NU_image, NU_WorkingDir = config.get_DO_IMAGES()['Newick_utils']
##### housekeeping ############################################################
def sort_input(lo_phylo_tree_data):
'''
Converts a list of (sp_abbr, isolate, work_dir, ref_name), collected by
pipeline_master.py, into a dict of pipeline/ref/ : [(work_dir, isolate)]
items.
@authors:
Wolfgang Haas, Pascal Lapierre, and Kimberlee A. Musser
Wadsworth Center, New York State Department of Health
120 New Scotland Ave., Albany, New York 12208
[email protected]
last update: 24 September 2020
"""
import numpy as np
import config
import toolshed
BASE_PATH = config.get_DO_PATHS()['BASE_PATH']
OUTPUT_dir = config.get_DO_PATHS()['OUTPUT_dir']
Kraken_image, Kraken_WorkingDir = config.get_DO_IMAGES()['Kraken']
##### running Kraken ##########################################################
def run_Kraken(work_dir):
'''
Runs Minikraken to classify contigs by species. Output is a number for the
classification and kmer counts, which needs to translated into human-
readable form.
param: str work_dir = isolate-specific folder, e.g.: 'WH200812_001259/'
return: ReturnCode, StdOut, StdErr
output: 'kraken_out.txt' file
@authors:
Wolfgang Haas, Pascal Lapierre, and Kimberlee A. Musser
Wadsworth Center, New York State Department of Health
120 New Scotland Ave., Albany, New York 12208
[email protected]
last update: 24 September 2020
"""
import LegioCluster_main
import config
import os
import sys
# set the paths to various folders
BASE_PATH = config.get_DO_PATHS()['BASE_PATH']
INPUT_dir = config.get_DO_PATHS()['INPUT_dir']
VCF_dir = config.get_DO_PATHS()['VCF_dir']
GENOMES_dir = config.get_DO_PATHS()['GENOMES_dir']
READS_dir = config.get_DO_PATHS()['READS_dir']
TEMP_dir = config.get_DO_PATHS()['TEMP_dir']
OUTPUT_dir = config.get_DO_PATHS()['OUTPUT_dir']
REF_dir = config.get_DO_PATHS()['REF_dir']
##### various checks ##########################################################
# this is purely a check to see that these modules are available
import matplotlib
import numpy
import pydot
(also <reference_SNP_cons.txt> if not already present)
@authors:
Wolfgang Haas, Pascal Lapierre, and Kimberlee A. Musser
Wadsworth Center, New York State Department of Health
120 New Scotland Ave., Albany, New York 12208
[email protected]
last update: 24 September 2020
"""
import csv
import os
import config
BASE_PATH = config.get_DO_PATHS()['BASE_PATH']
TEMP_dir = config.get_DO_PATHS()['TEMP_dir']
REF_dir = config.get_DO_PATHS()['REF_dir']
VCF_dir = config.get_DO_PATHS()['VCF_dir']
##### reading the reference fasta file ########################################
def read_ref_file(SS_dir, ref_fa_file):
'''
Reads a fasta file with the sequence of the reference genome (consisting
of one or more contigs) and returns a list of headers and sequences.
param: str SS_dir = species-specific directory, e.g.: 'Lpn/'
param: str ref_fa_file = name of a reference strain's FASTA file
return: list lo_contigs = list of headers and sequences, e.g.:
[[NODE_1_length_6526_cov_26.4, 'ACTTGTACTAATTGGCTGATTGTTGACATAA...'],
import stat from numpy import median # dict of abbreviations : [species name, genome length] DO_SPECIES = config.get_DO_SPECIES() # list of species set up to run the pipeline LO_PIPELINES = config.get_LO_SP_ABBR() # folder where all files are located #BASE_PATH = config.get_DO_PATHS()['BASE_PATH'] #BASE_PATH = os.path.dirname(os.getcwd()) # parent folder to current folder BASE_PATH = os.getcwd() + '/' # current folder GENOMES_dir = config.get_DO_PATHS()['GENOMES_dir'] # 'Genomes/', PY_dir = config.get_DO_PATHS()['PY_dir'] # 'Py_code/', REF_dir = config.get_DO_PATHS()['REF_dir'] # 'References/', VCF_dir = config.get_DO_PATHS()['VCF_dir'] # 'VCF_files/', READS_dir = config.get_DO_PATHS()['READS_dir'] # 'reads/' ##### 1. user input ########################################################### def get_species_name():