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Fix coverage error #44

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merged 2 commits into from
Jan 7, 2019
Merged

Fix coverage error #44

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33bc3a7
Fix a pesky typo
ar0ch Jan 7, 2019
d66a31a
bump version
ar0ch Jan 7, 2019
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2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
setup(
name = 'stringMLST',
scripts = ['stringMLST.py'],
version = '0.5.1.2',
version = '0.5.2',
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',
Expand Down
26 changes: 13 additions & 13 deletions stringMLST.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,11 +15,11 @@
except ImportError:
from urllib import urlopen, urlretrieve
import argparse
version = """ stringMLST v0.5.1.2 (updated : July 26, 2018) """
version = """ stringMLST v0.5.2 (updated : January, 7 2018) """
"""

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
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 [email protected] for permissions

LICENSE TERMS FOR stringMLST
Expand Down Expand Up @@ -273,7 +273,7 @@ def get_links(speciesName,schemes):
if child.tag == "loci":
for locus in child:
loci[locus.text.rstrip()] = locus[0].text

return profileURL
#############################################################
# Function : get_files
Expand All @@ -289,7 +289,7 @@ def get_files(profileURL,species):
localFfile, headers = urlretrieve(loci[file],localFile)
except:
print( '\033[91m' + "There was an error downloading " + file + '\033[0m')
pass
pass
configFile.write(file + "\t" + filePrefix + "_" + file + ".tfa\n")
localFile = filePrefix + "_profile.txt"
localFile, headers = urlretrieve(profileURL,localFile)
Expand Down Expand Up @@ -736,7 +736,7 @@ def loadWeightDict(weightFile):
(loc, allele) = array[0].replace('-','_').rsplit('_',1)
except ValueError:
print("Error : Allele name in locus file should be seperated by '_' or '-'")
exit(0)
exit(0)
if loc not in weightDict:
weightDict[loc] = {}
weightDict[loc][allele] = float(array[1])
Expand Down Expand Up @@ -787,7 +787,7 @@ def getCoverage(results):
with open(bed, 'w') as bedFile:
for gene in configDict['loci']:
genes = Fasta(configDict['loci'][gene])
allele = gene+'_'+re.sub("*", "", str(results[sample][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]:
Expand Down Expand Up @@ -905,7 +905,7 @@ def formKmerDB(configDict, k, output_filename):
(loc, num) = allele.replace('-','_').rsplit('_',1)
except ValueError:
print("Error : Allele name in locus file should be seperated by '_' or '-'")
exit(0)
exit(0)
splitId = allele.replace('-','_').rsplit('_',1)
i = 0
while i+k <= l:
Expand Down Expand Up @@ -1178,7 +1178,7 @@ def checkParams(buildDB, predict, config, k, listMode, list, batch, dir, fastq1,
Identifier for getMLST module
--species= <species name>
Species name from the pubMLST schemes (use --schemes to get list of available schemes)
"all" will download and build all
"all" will download and build all
Optional arguments
-k = <kmer length>
Kmer size for which the db has to be formed(Default k = 35). Note the tool works best with kmer length in between 35 and 66
Expand Down Expand Up @@ -1317,7 +1317,7 @@ def checkParams(buildDB, predict, config, k, listMode, list, batch, dir, fastq1,
Identifier for getMLST module
--species= <species name>
Species name from the pubMLST schemes (use --schemes to get list of available schemes)
"all" will download and build all
"all" will download and build all
Optional arguments
-k = <kmer length>
Kmer size for which the db has to be formed(Default k = 35). Note the tool works best with kmer length in between 35 and 66
Expand Down Expand Up @@ -1627,15 +1627,15 @@ 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 ('\033[1m' + "Preparing: " + schemes[key] + '\033[0m')
# Move the rest of this informational message into the download handler
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"
config = filePrefix + "_config.txt"
profileURL = get_links(key,schemes)
get_files(profileURL,key)
else:
Expand Down