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Formatting fixes (#46)
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@ar0ch
ar0ch committed Mar 5, 2019
1 parent f9dc4b0 commit 479b0cb
Showing 1 changed file with 30 additions and 27 deletions.
57 changes: 30 additions & 27 deletions stringMLST.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
try:
from urllib.request import urlopen, urlretrieve
except ImportError:
from urllib import urlopen, urlretrieve
from urllib import urlopen, urlretrieve
import argparse
version = """ stringMLST v0.5.2 (updated : January, 7 2018) """
"""
Expand Down Expand Up @@ -259,11 +259,13 @@
def get_links(xmlData, savePath, speciesName):
lociList = {}
for species in xmlData:
if re.search(speciesName, species.text,re.IGNORECASE):
if re.search(speciesName, species.text, re.IGNORECASE):
for mlst in species:
for database in mlst:
for child in database:
print(child.text)
if child.tag == "profiles":
print(child[1].text)
profileURL = child[1].text
if child.tag == "loci":
for locus in child:
Expand All @@ -280,24 +282,24 @@ def get_files(filePrefix, loci, profileURL, speciesName):
for file in loci:
localFile = filePrefix + "_" + file + ".tfa"
try:
localFile, headers = urlretrieve(loci[file],localFile)
localFile, headers = urlretrieve(loci[file], localFile)
except:
print( '\033[91m' + "There was an error downloading " + file + '\033[0m')
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)
localFile, headers = urlretrieve(profileURL, localFile)
configFile.write("[profile]\n")
configFile.write("profile\t" + filePrefix + "_profile.txt\n")
configFile.close()
try:
makeCustomDB(config,k,filePrefix)
makeCustomDB(config, k, filePrefix)
except:
print( '\033[91m' + "Failed to create database " + speciesName + '\033[0m' )
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)
print("\t" + filePrefix)
############################################################
# Function : batchTool
# Input : Directory name, paired or single, k value
Expand Down Expand Up @@ -727,7 +729,7 @@ def loadWeightDict(weightFile):
for line in lines:
array = line.rstrip().rsplit('\t')
try:
(loc, allele) = array[0].replace('-','_').rsplit('_',1)
(loc, allele) = array[0].replace('-', '_').rsplit('_', 1)
except ValueError:
print("Error : Allele name in locus file should be seperated by '_' or '-'")
exit(0)
Expand Down Expand Up @@ -896,11 +898,11 @@ def formKmerDB(configDict, k, output_filename):
sum += l
n += 1
try:
(loc, num) = allele.replace('-','_').rsplit('_',1)
(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)
splitId = allele.replace('-', '_').rsplit('_', 1)
i = 0
while i+k <= l:
kmer = seq[i:i+k]
Expand Down Expand Up @@ -1351,7 +1353,7 @@ def checkParams(buildDB, predict, config, k, listMode, list, batch, dir, fastq1,
k = 35
fuzzy = 300
coverage = False
#print 'ARGV :', sys.argv[1:]
#print'ARGV :', sys.argv[1:]
#exit(0)
"""Input arguments"""
options, remainder = getopt.getopt(sys.argv[1:], 'o:x1:2:k:l:bd:pshP:c:trva:z:C', [
Expand Down Expand Up @@ -1432,7 +1434,7 @@ def checkParams(buildDB, predict, config, k, listMode, list, batch, dir, fastq1,
print("You provided '" + arg + "' for your fuzziness threshold, which is not an integer value")
exit(0)
elif opt in '--schemes':
print (", ".join(sorted(schemes.keys())))
print(", ".join(sorted(schemes.keys())))
exit(0)
elif opt in '--getMLST':
downloadDB = True
Expand Down Expand Up @@ -1481,17 +1483,17 @@ def checkParams(buildDB, predict, config, k, listMode, list, batch, dir, fastq1,
getCoverage(results)
printResults(results, output_filename, overwrite, timeDisp)
elif downloadDB is True:
dbURL="http://pubmlst.org/data/dbases.xml"
dbURL = "http://pubmlst.org/data/dbases.xml"
databaseXML = urlopen(dbURL)
dbTree = ET.parse(databaseXML)
dbRoot = dbTree.getroot()
if species is None:
print ("Please refer to --help to more information")
print("Please refer to --help to more information")
print()
print ("Expected command format:")
print("Expected command format:")
print("stringMLST.py --getMLST --species= <species> [-k kmer length] [-P DB prefix]")
print ()
print("To print available MLST Schemes use:")
print()
print("To printavailable MLST Schemes use:")
print("stringMLST.py --getMLST --species show")
exit(0)
elif species == "show":
Expand All @@ -1501,14 +1503,14 @@ def checkParams(buildDB, predict, config, k, listMode, list, batch, dir, fastq1,
print("Using a kmer size of " + str(k) + " for all databases.")
for species in dbRoot:
speciesName = species.text.rstrip()
print ('\033[1m' + "Preparing: " + speciesName + '\033[0m')
print('\033[1m' + "Preparing: " + speciesName + '\033[0m')
if re.search('[/#. ()]', speciesName):
normSpeciesName = re.sub('[/# ]', "_", speciesName)
normSpeciesName = re.sub('[.()]', "", normSpeciesName)
print( '\t\033[33m' + "INFO: normalizing name to: " + normSpeciesName + '\033[0m' )
print('\t\033[33m' + "INFO: normalizing name to: " + normSpeciesName + '\033[0m')
else:
normSpeciesName = species
filePrefix = str(dbPrefix.rsplit("/",1)[0]) + "/" + normSpeciesName
filePrefix = str(dbPrefix.rsplit("/", 1)[0]) + "/" + normSpeciesName
# Move the rest of this informational message into the download handler
# + " ( " + filePrefix + "/" + key + "_" +str(k) + " )")
try:
Expand All @@ -1521,28 +1523,29 @@ def checkParams(buildDB, predict, config, k, listMode, list, batch, dir, fastq1,
get_files(filePrefix, loci, profileURL, speciesName)
else:
print('\033[1m' + "Preparing: " + species + '\033[0m')
if re.search('[/#. ()]', speciesName):
normSpeciesName = re.sub('[/# ]', "_", speciesName)
if re.search('[/#. ()]', species):
normSpeciesName = re.sub('[/# ]', "_", species)
normSpeciesName = re.sub('[.()]', "", normSpeciesName)
print( '\t\033[33m' + "INFO: normalizing name to: " + normSpeciesName + '\033[0m' )
print('\t\033[33m' + "INFO: normalizing name to: " + normSpeciesName + '\033[0m')
else:
normSpeciesName = species
try:
os.makedirs(dbPrefix.rsplit("/",1)[0])
os.makedirs(dbPrefix.rsplit("/", 1)[0])
except OSError:
pass
if len(re.findall("/", dbPrefix)) == 0:
filePrefix = dbPrefix + "/" + normSpeciesName
elif len(re.findall("/", dbPrefix)) == 1 and len(dbPrefix.rsplit("/",1)[1]) > 0:
elif len(re.findall("/", dbPrefix)) == 1 and len(dbPrefix.rsplit("/", 1)[1]) > 0:
filePrefix = dbPrefix
elif len(re.findall("/", dbPrefix)) == 1 and len(dbPrefix.rsplit("/",1)[1]) == 0:
elif len(re.findall("/", dbPrefix)) == 1 and len(dbPrefix.rsplit("/", 1)[1]) == 0:
filePrefix = dbPrefix + normSpeciesName
elif len(re.findall("/", dbPrefix)) > 1:
if dbPrefix.endswith('/'):
filePrefix = dbPrefix + normSpeciesName
else:
filePrefix = dbPrefix
config = filePrefix + "_config.txt"
print("Get URLs")
profileURL, loci = get_links(dbRoot, filePrefix, species)
get_files(filePrefix, loci, profileURL, species)

Expand Down

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