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Meera make python3 compatible #108

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Meera make python3 compatible #108

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0883fbe
Made Python 3 compatible
Jul 11, 2018
217dc1c
made python 3 compatible, updated samtools and bowtie2 versions
Jul 12, 2018
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54 changes: 28 additions & 26 deletions scripts/srst2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -305,8 +305,8 @@ def parse_fai(fai_file,db_type,delimiter):
gene_clusters.append(gene_cluster)

if len(delimiter_check) > 0:
print "Warning! MLST delimiter is " + delimiter + " but these genes may violate the pattern and cause problems:"
print ",".join(delimiter_check)
print("Warning! MLST delimiter is " + delimiter + " but these genes may violate the pattern and cause problems:")
print(",".join(delimiter_check))

return size, gene_clusters, unique_gene_symbols, unique_allele_symbols, gene_cluster_symbols

Expand Down Expand Up @@ -613,11 +613,11 @@ def check_command_version(command_list, version_identifier, command_name, requir
# allow multiple specific versions that have been specifically tested
def check_bowtie_version():
return check_command_versions([get_bowtie_execs()[0], '--version'], 'version ', 'bowtie',
['2.1.0','2.2.3','2.2.4','2.2.5','2.2.6','2.2.7','2.2.8','2.2.9'])
['2.1.0','2.2.3','2.2.4','2.2.5','2.2.6','2.2.7','2.2.8','2.2.9','2.3.2'])

def check_samtools_version():
return check_command_versions([get_samtools_exec()], 'Version: ', 'samtools',
['0.1.18','0.1.19','1.0','1.1','1.2','1.3','(0.1.18 is '
['1.5', '0.1.18','0.1.19','1.0','1.1','1.2','1.3','(0.1.18 is '
'recommended)'])

def check_command_versions(command_list, version_prefix, command_name, required_versions):
Expand All @@ -635,7 +635,9 @@ def check_command_versions(command_list, version_prefix, command_name, required_
command_stdout = e.output

for v in required_versions:
if version_prefix + v in command_stdout:
logging.error("COMMAND_STDOUT:")
logging.error(command_stdout)
if (str(version_prefix) + str(v)).encode() in command_stdout:
return v

logging.error("Incorrect version of {} installed.".format(command_name))
Expand Down Expand Up @@ -697,7 +699,7 @@ def run_bowtie(mapping_files_pre,sample_name,fastqs,args,db_name,db_full_path):
try:
command += ['-u',str(int(args.stop_after))]
except ValueError:
print "WARNING. You asked to stop after mapping '" + args.stop_after + "' reads. I don't understand this, and will map all reads. Please speficy an integer with --stop_after or leave this as default to map 1 million reads."
print("WARNING. You asked to stop after mapping '" + args.stop_after + "' reads. I don't understand this, and will map all reads. Please speficy an integer with --stop_after or leave this as default to map 1 million reads.")

if args.other:
x = args.other
Expand Down Expand Up @@ -805,12 +807,12 @@ def calculate_ST(allele_scores, ST_db, gene_names, sample_name, mlst_delimiter,
try:
clean_st = ST_db[allele_string]
except KeyError:
print "This combination of alleles was not found in the sequence type database:",
print sample_name,
print("This combination of alleles was not found in the sequence type database:",)
print(sample_name,)
for gene in allele_scores:
(allele,diffs,depth_problems,divergence) = allele_scores[gene]
print allele,
print
print(allele,)
print()
clean_st = "NF"
else:
clean_st = "ND"
Expand Down Expand Up @@ -847,7 +849,7 @@ def parse_ST_database(ST_filename,gene_names_from_fai):
ST_db = {} # key = allele string, value = ST
gene_names = []
num_gene_cols_expected = len(gene_names_from_fai)
print "Attempting to read " + str(num_gene_cols_expected) + " loci from ST database " + ST_filename
print("Attempting to read " + str(num_gene_cols_expected) + " loci from ST database " + ST_filename)
with open(ST_filename) as f:
count = 0
for line in f:
Expand All @@ -857,23 +859,23 @@ def parse_ST_database(ST_filename,gene_names_from_fai):
gene_names = line_split[1:min(num_gene_cols_expected+1,len(line_split))]
for g in gene_names_from_fai:
if g not in gene_names:
print "Warning: gene " + g + " in database file isn't among the columns in the ST definitions: " + ",".join(gene_names)
print " Any sequences with this gene identifer from the database will not be included in typing."
print("Warning: gene " + g + " in database file isn't among the columns in the ST definitions: " + ",".join(gene_names))
print(" Any sequences with this gene identifer from the database will not be included in typing.")
if len(line_split) == num_gene_cols_expected+1:
gene_names.pop() # we read too many columns
num_gene_cols_expected -= 1
for g in gene_names:
if g not in gene_names_from_fai:
print "Warning: gene " + g + " in ST definitions file isn't among those in the database " + ",".join(gene_names_from_fai)
print " This will result in all STs being called as unknown (but allele calls will be accurate for other loci)."
print("Warning: gene " + g + " in ST definitions file isn't among those in the database " + ",".join(gene_names_from_fai))
print(" This will result in all STs being called as unknown (but allele calls will be accurate for other loci).")
else:
ST = line_split[0]
if ST not in ST_db.values():
ST_string = " ".join(line_split[1:num_gene_cols_expected+1])
ST_db[ST_string] = ST
else:
print "Warning: this ST is not unique in the ST definitions file: " + ST
print "Read ST database " + ST_filename + " successfully"
print("Warning: this ST is not unique in the ST definitions file: " + ST)
print("Read ST database " + ST_filename + " successfully")
return (ST_db, gene_names)

def get_allele_name_from_db(allele,run_type,args,unique_allele_symbols=False,unique_cluster_symbols=False):
Expand Down Expand Up @@ -956,7 +958,7 @@ def parse_scores(run_type,args,scores, hash_edge_depth,
for gene in scores_by_gene:

gene_hash = scores_by_gene[gene]
scores_sorted = sorted(gene_hash.iteritems(),key=operator.itemgetter(1)) # sort by score
scores_sorted = sorted(gene_hash.items(),key=operator.itemgetter(1)) # sort by score
(top_allele,top_score) = scores_sorted[0]

# check if depth is adequate for confident call
Expand Down Expand Up @@ -1279,7 +1281,7 @@ def process_fasta_db(args, fileSets, run_type, db_reports, db_results_list, fast
db_path, db_name = os.path.split(fasta) # database
(db_name,db_ext) = os.path.splitext(db_name)
db_results = "__".join([args.output,run_type,db_name,"results.txt"])
db_report = file(db_results,"w")
db_report = open(db_results, "w") # file(db_results,"w")
db_reports.append(db_results)

# Get sequence lengths and gene names
Expand Down Expand Up @@ -1475,9 +1477,9 @@ def map_fileSet_to_db(args, sample_name, fastq_inputs, db_name, fasta, size, gen
full_results = "__".join([args.output,"fullgenes",db_name,"results.txt"])
logging.info("Printing verbose gene detection results to " + full_results)
if os.path.exists(full_results):
f = file(full_results,"a")
f = open(full_results,"a")
else:
f = file(full_results,"w") # create and write header
f = open(full_results,"w") # create and write header
f.write("\t".join(["Sample","DB","gene","allele","coverage","depth","diffs","uncertainty","divergence","length", "maxMAF","clusterid","seqid","annotation"])+"\n")
for gene in allele_scores:
(allele,diffs,depth_problem,divergence) = allele_scores[gene] # gene = top scoring alleles for each cluster
Expand Down Expand Up @@ -1655,9 +1657,9 @@ def main():
if not os.path.exists(output_dir):
try:
os.makedirs(output_dir)
print "Created directory " + output_dir + " for output"
print("Created directory " + output_dir + " for output")
except:
print "Error. Specified output as " + args.output + " however the directory " + output_dir + " does not exist and our attempt to create one failed."
print("Error. Specified output as " + args.output + " however the directory " + output_dir + " does not exist and our attempt to create one failed.")

if args.log is True:
logfile = args.output + ".log"
Expand Down Expand Up @@ -1702,9 +1704,9 @@ def main():
if not args.mlst_definitions:

# print warning to screen to alert user, may want to stop and restart
print "Warning, MLST allele sequences were provided without ST definitions:"
print " allele sequences: " + str(args.mlst_db)
print " these will be mapped and scored, but STs can not be calculated"
print("Warning, MLST allele sequences were provided without ST definitions:")
print(" allele sequences: " + str(args.mlst_db))
print(" these will be mapped and scored, but STs can not be calculated")

# log
logging.info("Warning, MLST allele sequences were provided without ST definitions:")
Expand Down