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stringMLST.py
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stringMLST.py
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#!/usr/bin/env python
import getopt
import sys
import logging
import os
import time
import ast
import gzip
import re
import tempfile
import shutil
import xml.etree.ElementTree as ET
try:
from urllib.request import urlopen, urlretrieve
except ImportError:
from urllib import urlopen, urlretrieve
import argparse
version = """ stringMLST v0.6.3 (updated : September 02, 2020) """
"""
stringMLST free for academic users and requires permission before any commercial
use for any version of this code/algorithm. If you are a commercial user, please
contact king.jordan@biology.gatech.edu for permissions
LICENSE TERMS FOR stringMLST
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Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public
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bound by the terms and conditions of this Creative Commons Attribution-
NonCommercial-ShareAlike 4.0 International Public License ("Public License"). To
the extent this Public License may be interpreted as a contract, You are granted
the Licensed Rights in consideration of Your acceptance of these terms and
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jurisdiction or authority.
The program has 3 basic modes :
mainTool: for single sample (both single and paired end)
batchTool: for multiple samples stored at a common location (both single and paired end samples)
listTool: for multiple samples with location information stored in a list (both single and paired end samples)
predict part starts here
"""
#############################################################
# Function : get_links
# Input : speciesName and schemes dict
# Output : Dict containing links to alleles and profile
# Description: Gets the URLs from pubMLST for the required
# files (alleles, profile)
#############################################################
def get_links(xmlData, savePath, speciesName):
lociList = {}
profileURL = None
for species in xmlData:
if re.search(re.escape(speciesName), species.text, re.IGNORECASE, ):
for mlst in species:
for database in mlst:
for child in database:
if child.tag == "profiles":
profileURL = child[0].text
if child.tag == "loci":
for locus in child:
lociList[locus.text.rstrip()] = locus[0].text
if profileURL is None:
profileError = "Parsing failed: could not find profiles file"
print(profileError)
print("This usually means the provided species, '{}', does not exist on PubMLST".format(speciesName))
print("Use `{} --getMLST --species list` to list available species".format(sys.argv[0]))
print("Or visit PubMLST for more information:\nhttps://pubmlst.org/data/")
logging.debug(profileError)
sys.exit(1)
elif lociList == {}:
lociError = "Parsing failed: could not find allele sequences"
logging.debug(lociError)
print(lociError)
sys.exit(1)
else:
return profileURL, lociList
#############################################################
# Function : get_files
# Input : URLs from get_links
# Output : Downloads files and builds database
#############################################################
def get_files(filePrefix, loci, profileURL, speciesName):
with open(config, "w") as configFile:
configFile.write("[loci]\n")
for file in loci:
localFile = filePrefix + "_" + file + ".tfa"
try:
localFile, headers = urlretrieve(loci[file], localFile)
except:
print('\033[91m' + "There was an error downloading " + file + '\033[0m')
pass
configFile.write(file + "\t" + filePrefix + "_" + file + ".tfa\n")
localFile = filePrefix + "_profile.txt"
localFile, headers = urlretrieve(profileURL, localFile)
configFile.write("[profile]\n")
configFile.write("profile\t" + filePrefix + "_profile.txt\n")
configFile.close()
try:
makeCustomDB(config, k, filePrefix)
except:
print('\033[91m' + "Failed to create database " + speciesName + '\033[0m')
pass
else:
print("\t" + '\033[92m' + "Database ready for " + speciesName + '\033[0m')
print("\t" + filePrefix)
############################################################
# Function : batchTool
# Input : Directory name, paired or single, k value
# Output : STs and allelic profiles for each FASTQ file
# Description: Processes all FASTQ files present in the input
# directory
#############################################################
def batchTool(fdir, paired, k):
fileList = []
if not dir.endswith('/'):
fdir += '/'
for inputFile in os.listdir(fdir):
if paired is True:
if inputFile.endswith('1.fastq') or inputFile.endswith('1.fq') or inputFile.endswith('1.fq.gz') or inputFile.endswith('1.fastq.gz'):
fastq1 = fdir+inputFile
fastq2 = fdir+inputFile.replace('1.', '2.')
fileList.append((fastq1, fastq2))
else:
if inputFile.endswith('.fastq') or inputFile.endswith('.fq') or inputFile.endswith('.fq.gz') or inputFile.endswith('.fastq.gz'):
fastq1 = fdir + inputFile
fileList.append(fastq1)
results = multiSampleTool(fileList, paired, k)
return results
#############################################################
# Function : listTool
# Input : List file, paired or single, k value
# Output : STs and allelic profiles for each FASTQ file
# Description: Processes all FASTQ files present in the input
# list file
#############################################################
def listTool(fList, paired, k):
fileList = []
listf = open(fList, 'r')
samples = listf.readlines()
for sample in samples:
if paired is True:
s = sample.strip().split()
fastq1 = s[0]
try:
fastq2 = s[1]
except IndexError:
print("Error: Paired end files should be whitespace/tab seperated")
exit(0)
fileList.append((fastq1, fastq2))
else:
fastq1 = sample.rstrip()
fileList.append(fastq1)
results = multiSampleTool(fileList, paired, k)
return results
#############################################################
# Function : multiSampleTool
# Input : List of files to process, paired or single, k value
# Output : STs and allelic profiles for each FASTQ file
# Description: Processes all FASTQ files present in the input list
#############################################################
def multiSampleTool(fileList, paired, k):
results = {}
for sample in fileList:
if paired is True:
fastq1 = sample[0]
fastq2 = sample[1]
else:
fastq1 = sample
fastq2 = None
results = singleSampleTool(fastq1, fastq2, paired, k, results)
return results
#############################################################
# Function : singleSampleTool
# Input : fastq file 1 and 2, paired or single, k value, output dictionary
# Output : STs and allelic profiles for each FASTQ file
# Description: Processes both FASTQ files passed to the function
#############################################################
def singleSampleTool(fastq1, fastq2, paired, k, results):
if paired is True:
fileName = fastq1.split('/')[-1].split('.')[0][:-1]
else:
fileName = fastq1.split('/')[-1].split('.')[0]
if reads is True:
readFileName = fileName + '_reads.fq'
global readFile
readFile = open(readFileName, 'w+')
if paired is True:
msg = "singleSampleTool : " + fastq1 + ' and ' + fastq2
else:
msg = "singleSampleTool : " + fastq1
logging.debug(msg)
global alleleCount
alleleCount = {}
t1 = time.time()
if paired is True:
logging.debug("singleSampleTool : paired True")
logging.debug("singleSampleTool : fastq1 start")
singleFileTool(fastq1, k)
logging.debug("singleSampleTool : fastq1 done")
logging.debug("singleSampleTool : fastq2 start")
singleFileTool(fastq2, k)
logging.debug("singleSampleTool : fastq2 done")
if alleleCount == {}:
string = "No k-mer matches were found for the sample " + fastq1 + " and "+ fastq2 + ". Probable cause of the error: low quality data/too many N's in the data"
logging.error("singleSampleTool : " + string)
print(string)
# exit(0)
profileCount = alleleCount
else:
logging.debug("singleSampleTool : paired False")
logging.debug("singleSampleTool : fastq start")
singleFileTool(fastq1, k)
profileCount = alleleCount
logging.debug("singleSampleTool : fastq done")
if alleleCount == 0:
string = "No k-mer matches were found for the sample " + fastq1 + ". Probable cause of the error: low quality data/too many N's in the data"
logging.error("singleSampleTool : " + string)
print(string)
logging.debug("singleSampleTool : weightedProfile start")
weightedProfile = weightedProf(profileCount, weightDict)
logging.debug("singleSampleTool : weightedProfile finished")
logging.debug("singleSampleTool : getMaxCount start")
finalProfile = getMaxCount(weightedProfile, fileName)
logging.debug("singleSampleTool : getMaxCount end")
st = 0
if profileFile != '':
logging.debug("singleSampleTool : findST start")
st = findST(finalProfile, stProfile)
logging.debug("singleSampleTool : findST end")
if reads is True:
readFile.close()
t3 = time.time()
finalProfile['ST'] = st
finalProfile['t'] = t3-t1
results[fileName] = finalProfile
return results
#############################################################
# Function : singleFileTool
# Input : fastq file, k value
# Output : Edits a global dictionary - results
# Description: Processes the single fastq file
#############################################################
def singleFileTool(fastq, k):
msg = "singleFileTool :" + fastq
logging.debug(msg)
if os.path.isfile(fastq):
logging.debug("singleFileTool : fastq")
non_overlapping_window = 1
finalProfile = {}
t1 = time.time()
fileExplorer(fastq, k, non_overlapping_window)
t3 = time.time()
else:
msg = "File does not exist: " + fastq
logging.error("singleFileTool : msg")
print(msg)
def fileExplorer(file, k, non_overlapping_window):
if file.endswith('.gz'):
if sys.version_info[0] == 3:
f = gzip.open(file, 'rt')
else:
f = gzip.open(file, 'rb')
else:
f = open(file)
msg = "fileExplorer :" + file
logging.debug(msg)
lines = f.readlines()
i = 1
n_reads = 0
try:
if len(lines[1]) < k:
m1 = "Read length " + len(lines[1])+" for file " + file + " smaller than " + k
print(m1)
print("Skipping to next file.")
logging.debug(m1)
return 0
except Exception:
m2 = "Check fastq file " + file
print(m2)
logging.debug(m2)
return 0
start = int((len(lines[1])-k)//2)
end = int((len(lines[1])-k)//2)
yesRead = False
for line in lines:
if i % 4 == 0 and yesRead:
readFile.write(line)
if i % 4 != 3:
yesRead = False
if i%4 == 1:
head = line
if i%4 == 2:
s1 = str(line[start:k+start])
sn_1 = str(line[-k-end:-end]).rstrip()
if s1 in kmerDict[k]:
n_reads += 1
goodReads(line, k, non_overlapping_window)
if reads is True:
readFile.write(head)
readFile.write(line)
readFile.write('+\n')
yesRead = True
i += 1
#############################################################
# Function : goodReads
# Input : sequence read, k, step size
# Output : Edits the count of global variable alleleCount
# Description: Increment the count for each k-mer match
#############################################################
def goodReads(read, k, non_overlapping_window):
n = 0
line = read.rstrip()
while n+k <= len(line):
s = str(line[n:n+k])
if s in kmerDict[k]:
for probLoc in kmerDict[k][s]:
if probLoc not in alleleCount:
alleleCount[probLoc] = {}
a = kmerDict[k][s][probLoc]
for allele in a:
allele = allele.rstrip()
if allele in alleleCount[probLoc]:
alleleCount[probLoc][allele] += 1
else:
alleleCount[probLoc][allele] = 1
n += non_overlapping_window
#############################################################
# Function : weightedProf
# Input : allele count global var, weight factors
# Output/Desc: Normalizes alleleCount by weight factor
#############################################################
def weightedProf(alleleCount, weightDict):
logging.debug("weightedProf")
weightedDict = {}
for loc in alleleCount:
weightedDict[loc] = {}
for allele in alleleCount[loc]:
if loc in weightDict:
if allele in weightDict[loc]:
weightedDict[loc][allele] = (alleleCount[loc][allele] / weightDict[loc][allele])
else:
weightedDict[loc][allele] = alleleCount[loc][allele]
else:
weightedDict[loc][allele] = alleleCount[loc][allele]
return weightedDict
#############################################################
# Function : getMaxCount
# Input : allele counts
# Output : allelic profile and ST
# Description: Finds the alleles with maximum counts and
# generates the allelic profile and ST
#############################################################
def getMaxCount(alleleCount, fileName):
logging.debug("getMaxCount")
max_n = {}
secondMax = {}
maxSupport = {}
secondSupport = {}
finalProfileCount = {}
for locus in alleleNames:
finalProfileCount[locus] = {}
num = ''
for loc in alleleCount:
n = 0
m = 0
for num in alleleCount[loc]:
if alleleCount[loc][num] >= n:
m = n
n = alleleCount[loc][num]
if n-m < fuzzy:
try:
alleleCount[loc][num]
except:
pass
else:
alleleCount[loc][num] = str(alleleCount[loc][num])+'*'
max_n[loc] = str(n)+'*'
else:
max_n[loc] = n
secondMax[loc] = m
for loc in alleleCount:
try:
max_n[loc]
except:
pass
else:
maxSupport[loc] = {}
secondSupport[loc] = {}
num_max = []
num_max2 = []
compare = float(re.sub("\*$", "", str(max_n[loc])))
for num in alleleCount[loc]:
if float(re.sub("\*$", "", str(alleleCount[loc][num]))) == compare:
if "\*" in str(max_n[loc]):
insert = num + '*'
num_max.append(insert)
else:
num_max.append(num)
maxSupport[loc][num] = max_n[loc]
if alleleCount[loc][num] == secondMax[loc]:
num_max2.append(num)
secondSupport[loc][num] = secondMax[loc]
try:
finalProfileCount[loc] = num_max[0]
except LookupError:
finalProfileCount[loc] = 'NA'
msgs = "Max Support :" + fileName + " : " + str(maxSupport)
logging.debug(msgs)
msgs = "Second Max Support :" + fileName + " : " + str(secondSupport)
logging.debug(msgs)
return finalProfileCount
#############################################################
# Function : findST
# Input : allelic profile for one sample and profiles for all STs
# Output : ST number, or 0 if no ST match was found
# Description: Finds the ST number which best matches the given sample profile.
#############################################################
def findST(finalProfile, stProfile):
if not stProfile:
return 0
oneProfile = next(iter(stProfile.values()))
# The gene names in finalProfile may not exactly match those in stProfile. To deal with this,
# each finalProfile gene is associated with the best matching gene in the ST profiles.
finalGeneToSTGene = {}
profileGenes = list(oneProfile.keys())
for finalGene in list(finalProfile.keys()):
if finalGene in profileGenes: # exact match is preferable
finalGeneToSTGene[finalGene] = finalGene
else: # failing an exact match, look for a case-sensitive containment
for profileGene in profileGenes:
if finalGene in profileGene:
finalGeneToSTGene[finalGene] = profileGene
break
if finalGene not in finalGeneToSTGene: # if there's still no match, try a case-insensitive containment
for profileGene in profileGenes:
if finalGene.lower() in profileGene.lower():
finalGeneToSTGene[finalGene] = profileGene
break
if finalGene not in finalGeneToSTGene:
print("ERROR: gene names in config file do not match gene names in profile file")
exit(0)
transformedFinalProfile = {}
for gene, allele in finalProfile.items():
if allele:
allele = re.sub("\*", "", allele)
transformedFinalProfile[finalGeneToSTGene[gene]] = allele
# Check to see if the dictionary is empty, if so then means no allele were found at all
if bool(transformedFinalProfile) is False:
return 0
# Find the best matching ST, considering only the genes in the sample's profile. This is to
# allow for superfluous columns in the ST profile.
logging.debug("findST")
for stNum, profile in stProfile.items():
if all(x in list(profile.items()) for x in list(transformedFinalProfile.items())):
return stNum
return 0
#############################################################
# Function : loadModule
# Input : k value and prefix of the DB file
# Output : Updates the DB dictionary variables
# Description: Used in loading the DB as set of variables
# by calling other functions
#############################################################
def loadModule(k, dbPrefix):
global dbFile
dbFile = dbPrefix+'_'+str(k)+'.txt'
global weightFile
weightFile = dbPrefix+'_weight.txt'
global profileFile
profileFile = dbPrefix+'_profile.txt'
global kmerDict
kmerDict = {}
kmerDict[k] = loadKmerDict(dbFile)
global weightDict
weightDict = loadWeightDict(weightFile)
global stProfile
stProfile = loadSTfromFile(profileFile)
#############################################################
# Function : loadSTfromFile
# Input : profile definition file
# Output : Updates the DB dictionary variables
# Description: Used in loading the DB as set of variables
#############################################################
def loadSTfromFile(profileF):
with open(profileF, 'r') as definitionFile:
st = {}
index = {}
lines = definitionFile.readlines()
heads = lines[0].rstrip().split('\t')
for locus in heads:
index[locus] = heads.index(locus)
for line in lines:
pro = line.rstrip().split('\t')
l = {}
for locus in heads[1:]:
try:
l[locus] = pro[index[locus]]
except LookupError:
logging.debug("ERROR while loading ST")
pass
st[pro[0]] = l
return st
#############################################################
# Function : loadKmerDict
# Input : DB prefix
# Output : Updates the DB dictionary variables
# Description: Used in loading the DB as set of variables
#############################################################
def loadKmerDict(dbFile):
kmerTableDict = {}
with open(dbFile, 'r') as kmerTableFile:
lines = kmerTableFile.readlines()
global alleleNames
alleleNames = set()
for line in lines:
array = line.rstrip().rsplit('\t')
kmerTableDict[array[0]] = {}
kmerTableDict[array[0]][array[1]] = array[2][1:-1].rsplit(',')
alleleNames.add(array[1])
return kmerTableDict
#############################################################
# Function : loadWeightDict
# Input : Weight file prefix
# Output : Updates the DB dictionary variables
# Description: Used in loading the DB as set of variables
#############################################################
def loadWeightDict(weightFile):
weightDict = {}
with open(weightFile, 'r') as weightTableFile:
lines = weightTableFile.readlines()
for line in lines:
array = line.rstrip().rsplit('\t')
try:
(loc, allele) = array[0].replace('-', '_').rsplit('_', 1)
except ValueError:
print("Error : Allele name in locus file should be seperated by '_' or '-'")
exit(0)
if loc not in weightDict:
weightDict[loc] = {}
weightDict[loc][allele] = float(array[1])
return weightDict
#############################################################
# Function : loadConfig
# Input : config file path from getopts
# Output : Updates configDict
# Description: Used to find allele fasta files for getCoverage
#############################################################
def loadConfig(config):
global configDict
configDict = {}
with open(config) as configFile:
lines = configFile.readlines()
head = ''
for line in lines:
if line.rstrip() == '':
continue
if line.rstrip() == '[loci]':
head = 'loci'
configDict[head] = {}
elif line.rstrip() == '[profile]':
head = 'profile'
configDict[head] = {}
else:
arr = line.strip().split()
configDict[head][arr[0]] = arr[1]
for head in configDict:
for element in configDict[head]:
if not os.path.isfile(configDict[head][element]):
print("ERROR: %s file does not exist at %s" % (element, configDict[head][element]))
exit(0)
return configDict
#############################################################
# Function : getCoverage
# Input : results dictionary
# Output : Updates results to include coverage info
#############################################################
def getCoverage(results):
tmpdir = tempfile.mkdtemp()
for sample in results:
file = tmpdir +'/'+ sample + '.fasta'
bed = tmpdir +'/'+ sample + '.bed'
sortedFile = tmpdir +'/'+ sample + '.sorted'
covOut = tmpdir +'/'+ sample + '.out'
with open(file, 'w') as tmpFasta:
with open(bed, 'w') as bedFile:
for gene in configDict['loci']:
genes = Fasta(configDict['loci'][gene])
allele = gene+'_'+re.sub('\*', "", str(results[sample][gene]))
tmpFasta.write('>'+gene+'\n')
bedFile.write(gene+'\t0\t'+str(len(genes[allele]))+'\n')
for line in genes[allele]:
tmpFasta.write(str(line)+'\n')
cmdIndex = "bwa index %s 2>/dev/null"%(file)
os.system(cmdIndex)
readBWA = sample+'_reads.fq'
cmdBwaMem = "bwa mem %s %s 2>/dev/null| samtools view -uS - | samtools sort - -o %s"%(file, readBWA, sortedFile)
os.system(cmdBwaMem)
cmdCov = "bedtools coverage -a %s -b %s > %s"%(bed, sortedFile, covOut)
os.system(cmdCov)
with open(covOut, 'r') as cov:
for line in cov.readlines():
records = line.rstrip().rsplit('\t')
gene = records[0]
geneCov = float(records[6]) * 100
results[sample][gene] = results[sample][gene] + " (" + str("%.2f" % geneCov) + ")"
shutil.rmtree(tmpdir)
"""Prints the results in the format asked by the user."""
#############################################################
# Function : printResults
# Input : results, output file, overwrite?
# Output : Prints on the screen or in a file
# Description: Prints the results in the format asked by the user
#############################################################
def printResults(results, output_filename, overwrite, timeDisp):
if output_filename != None:
if overwrite is False:
outfile = open(output_filename, "a")
else:
outfile = open(output_filename, "w")
heading = "Sample"
for head in sorted(results[list(results.keys())[0]]):
if head == 'ST' or head == 't':
continue
heading += '\t' + head
heading += '\tST'
if timeDisp is True:
heading += '\tTime'
if output_filename != None:
outfile.write(heading)
outfile.write('\n')
else:
print(heading)
for s in results:
sample = s.split("_")[0]
for l in sorted(results[s]):
if l == 'ST' or l == 't':
continue
if results[s][l]:
sample += '\t'+results[s][l]
else:
sample += '\tNA'
if timeDisp is True:
sample += '\t' + str(results[s]['ST']) + '\t%.2f ' %results[s]['t']
else:
sample += '\t' + str(results[s]['ST'])
if output_filename != None:
outfile.write(sample)
outfile.write('\n')
else:
print(sample)
"""Predict part ends here"""
"""Build DB part starts"""
"""Returns the reverse complement of the sequence"""
def reverseComplement(seq):
seqU = seq.upper()
seq_dict = {'A':'T', 'T':'A', 'G':'C', 'C':'G', 'Y':'R', 'R':'Y', 'S':'S', 'W':'W', 'K':'M', 'M':'K', 'N':'N'}
try:
return "".join([seq_dict[base] for base in reversed(seqU)])
except Exception:
strn = "Reverse Complement Error:" + seqU
logging.debug(strn)
pass
#############################################################
# Function : getFastaDict
# Input : locus file name
# Output : dictionary with all the allele sequences
# Description: Stores each allele sequence in a dictionary
#############################################################
def getFastaDict(fullLocusFile):
logging.debug("Create Fasta Dict")
logging.debug(fullLocusFile)
fastaFile = open(fullLocusFile, 'r').read()
entries = [x for x in fastaFile.split('>') if len(x) != 0]
fastaDict = {}
for entry in entries:
key = [x for x in entry.split('\n')[0].split() if len(x) != 0][0]
sequence = ''.join(entry.split('\n')[1:]).rstrip()
fastaDict[key] = {'sequence':sequence}
return fastaDict
#############################################################
# Function : formKmerDB
# Input : configuration file, k value, output prefix
# Output : stringMLST DB
# Description: Constructs the k-mer DB in both strand orientation
#############################################################
def formKmerDB(configDict, k, output_filename):
dbFileName = output_filename+'_'+str(k)+'.txt'
weightFileName = output_filename+'_weight.txt'
kmerDict = {}
mean = {}
for locus in configDict['loci']:
msgs = "formKmerDB :" +locus
logging.debug(msgs)
fastaDict = getFastaDict(configDict['loci'][locus])
sum = 0
n = 0
for allele in list(fastaDict.keys()):
seq = fastaDict[allele]['sequence'].strip()
l = len(seq)
sum += l
n += 1
try:
(loc, num) = allele.replace('-', '_').rsplit('_', 1)
except ValueError:
print("Error : Allele name in locus file should be seperated by '_' or '-'")
exit(0)
splitId = allele.replace('-', '_').rsplit('_', 1)
i = 0
while i+k <= l:
kmer = seq[i:i+k]
revCompKmer = reverseComplement(kmer)
if kmer not in kmerDict:
kmerDict[kmer] = {}
kmerDict[kmer][splitId[0]] = []
kmerDict[kmer][splitId[0]].append(int(splitId[1]))
else:
if splitId[0] not in kmerDict[kmer]:
kmerDict[kmer][splitId[0]] = []
kmerDict[kmer][splitId[0]].append(int(splitId[1]))
else:
kmerDict[kmer][splitId[0]].append(int(splitId[1]))
if revCompKmer not in kmerDict:
kmerDict[revCompKmer] = {}
kmerDict[revCompKmer][splitId[0]] = []
kmerDict[revCompKmer][splitId[0]].append(int(splitId[1]))
else:
if splitId[0] not in kmerDict[revCompKmer]:
kmerDict[revCompKmer][splitId[0]] = []
kmerDict[revCompKmer][splitId[0]].append(int(splitId[1]))
else:
kmerDict[revCompKmer][splitId[0]].append(int(splitId[1]))
i += 1
mean[locus] = sum/n*1.0
with open(dbFileName, 'w') as kfile:
for key in kmerDict:
for key1 in kmerDict[key]:
string = key+'\t'+key1+'\t'+str(kmerDict[key][key1]).replace(" ", "")+'\n'
kfile.write(string)
with open(weightFileName, 'w') as wfile:
for locus in configDict['loci']:
fastaDict = getFastaDict(configDict['loci'][locus])
for allele in list(fastaDict.keys()):
splitId = allele.split('_')
seq = fastaDict[allele]['sequence']
l = len(seq)
fac = (l/mean[locus])
s = allele + '\t' + str(fac) + '\n'
if fac > 1.05 or fac < 0.95:
wfile.write(s)
"""Copies the profile definition file as a new file"""
def copyProfileFile(profileDict, output_filename):
profileFileName = output_filename+'_profile.txt'
with open(profileDict['profile']) as f:
lines = f.readlines()
with open(profileFileName, "w") as f1:
f1.writelines(lines)
#############################################################
# Function : makeCustomDB
# Input : configuration file, k value, output prefix
# Output : None
# Description: Processes the config file and calls the relevant
# function
#############################################################
def makeCustomDB(config, k, output_filename):
configDict = {}
if output_filename == None:
output_filename = 'kmerDB'
with open(config, 'r') as configFile:
lines = configFile.readlines()
head = ''
for line in lines:
if line.rstrip() == '':
continue
if line.rstrip() == '[loci]':
head = 'loci'
configDict[head] = {}
elif line.rstrip() == '[profile]':
head = 'profile'
configDict[head] = {}
else:
arr = line.strip().split()
configDict[head][arr[0]] = arr[1]
for head in configDict:
for element in configDict[head]:
if not os.path.isfile(configDict[head][element]):
print("ERROR: %s file does not exist at %s" % (element, configDict[head][element]))
exit(0)
formKmerDB(configDict, k, output_filename)
copyProfileFile(configDict['profile'], output_filename)