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Better handling of errors while building from pubMLST #31

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May 17, 2017
Merged

Better handling of errors while building from pubMLST #31

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4 changes: 2 additions & 2 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,13 @@
from os import path
here = path.abspath(path.dirname(__file__))
long_description="Fast k-mer based tool for alignment and assembly-free multi locus sequence typing (MLST) directly from genome sequencing reads."
with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
with open(path.join(here, 'README.rst')) as f:
long_description = f.read()

setup(
name = 'stringMLST',
scripts = ['stringMLST.py'],
version = '0.3.6.3',
version = '0.4',
description = 'Fast k-mer based tool for alignment and assembly-free multi locus sequence typing (MLST) directly from genome sequencing reads.',
long_description=long_description,
author = 'Jordan Lab',
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32 changes: 22 additions & 10 deletions stringMLST.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
except ImportError:
from urllib import urlopen, urlretrieve
import argparse
version = """ stringMLST v0.3.6.3 (updated : April 18, 2017) """
version = """ stringMLST v0.4 (updated : May 17, 2017) """
"""

stringMLST free for academic users and requires permission before any commercial
Expand Down Expand Up @@ -281,19 +281,30 @@ def get_links(speciesName,schemes):
# Input : URLs from get_links
# Output : Downloads files and builds database
#############################################################
def get_files(profileURL):
def get_files(profileURL,species):
with open(config, "w") as configFile:
configFile.write("[loci]\n")
for file in loci:
localFile = filePrefix + "_" + file + ".tfa"
localFfile, headers = urlretrieve(loci[file],localFile)
try:
localFfile, 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()
makeCustomDB(config,k,filePrefix)
try:
makeCustomDB(config,k,filePrefix)
except:
print( '\033[91m' + "Failed to create database " + schemes[species] + '\033[0m' )
pass
else:
print("\t" + '\033[92m' + "Database ready for " + schemes[species] + '\033[0m')
print( "\t" + filePrefix)
############################################################
# Function : batchTool
# Input : Directory name, paired or single, k value
Expand Down Expand Up @@ -1382,7 +1393,7 @@ def checkParams(buildDB, predict, config, k, listMode, list, batch, dir, fastq1,
"orientia-tsutsugamushi" : "Orientia tsutsugamushi",
"ornithobacterium-rhinotracheale" : "Ornithobacterium rhinotracheale",
"paenibacillus-larvae" : "Paenibacillus larvae",
#"pasteurella-multocida1" : "Pasteurella multocida#1",
"pasteurella-multocida1" : "Pasteurella multocida#1",
"pasteurella-multocida2" : "Pasteurella multocida#2",
"pediococcus-pentosaceus" : "Pediococcus pentosaceus",
"photobacterium-damselae" : "Photobacterium damselae",
Expand Down Expand Up @@ -1594,15 +1605,17 @@ def checkParams(buildDB, predict, config, k, listMode, list, batch, dir, fastq1,
print("Using a kmer size of " + str(k) + " for all databases.")
for key in sorted(schemes.keys()):
filePrefix = str(dbPrefix.rsplit("/",1)[0]) + "/" + key
print ("Preparing: " + schemes[key] + " ( " + filePrefix + "/" + key + "_" +str(k) + " )")
print ('\033[1m' + "Preparing: " + schemes[key] + '\033[0m')
# Move the rest of this informational message into the download handler
# + " ( " + filePrefix + "/" + key + "_" +str(k) + " )")
try:
os.makedirs(filePrefix)
except OSError:
pass
filePrefix = filePrefix + "/" + key
config = filePrefix + "_config.txt"
profileURL = get_links(key,schemes)
get_files(profileURL)
get_files(profileURL,key)
else:
try:
os.makedirs(dbPrefix.rsplit("/",1)[0])
Expand All @@ -1621,9 +1634,8 @@ def checkParams(buildDB, predict, config, k, listMode, list, batch, dir, fastq1,
filePrefix = dbPrefix
config = filePrefix + "_config.txt"
profileURL = get_links(species,schemes)
get_files(profileURL)
print("Database ready for " + schemes[species])
print( filePrefix)
get_files(profileURL,species)

else:
print(helpTextSmall)
print("Error: Please select the mode: buildDB (for database building) or predict (for ST discovery) module")
Expand Down