diff --git a/rules/Analysis/MGMT.rules b/rules/Analysis/MGMT.rules
index 47a5d0a0578146d596c59c26f14b949051c7eaab..3f79c90f035ff5618be7b1b60b04a8e0eac62f12 100644
--- a/rules/Analysis/MGMT.rules
+++ b/rules/Analysis/MGMT.rules
@@ -28,7 +28,7 @@ rule ANALYSIS_ANNOTATE:
cd $CUR
fi
- prokka --force --outdir {AN_OUT}/annotation --cpus {THREADS} --metagenome --norrna {input[0]} --fast >> {log} 2>&1
+ prokka --force --outdir {AN_OUT}/annotation --cpus {THREADS} --metagenome --norrna {input[0]} >> {log} 2>&1
# Prokka gives a weird gff file with all the sequences. We need to write some small code to produce a file that
# cleans up the output
diff --git a/src/genes.to.kronaTable.py b/src/genes.to.kronaTable.py
index 147dfe7b7810f49d7ab0c3fa3d1267ce5428dfec..7598f51d15f3d7e5bfe09473f3fd41f148b0d311 100755
--- a/src/genes.to.kronaTable.py
+++ b/src/genes.to.kronaTable.py
@@ -14,6 +14,11 @@
###################################
from argparse import ArgumentParser
+import sys
+import csv
+import numpy as np
+
+
parser = ArgumentParser()
parser.add_argument(
"-i", "--infile", type=str,
@@ -53,12 +58,6 @@ parser.add_argument(
help="Provide file with lengths for genes to normalize coverage by")
args = parser.parse_args()
-import sys
-import csv
-import numpy as np
-
-if not args.infile or not args.mapfile or not args.hierarchy:
- sys.exit(parser.print_help())
def ReadLengths(f):
@@ -171,7 +170,8 @@ def CalcHierarchy(mapping, annotations, coverage, operation, limit):
try:
gene_cov = coverage[gene]
except KeyError:
- sys.exit("ERROR: Could not find coverage for gene "+str(gene)+". Are you sure you have coverage information?\n")
+ sys.exit("ERROR: Could not find coverage for gene "+str(gene)+". \
+ Are you sure you have coverage information?\n")
covlist.append(gene_cov)
ann_c[annotation] = np.mean(covlist)
else:
@@ -184,12 +184,12 @@ def CalcHierarchy(mapping, annotations, coverage, operation, limit):
parents = mapping[annotation]
except KeyError:
if args.verbose:
- sys.stderr.write("WARNING: Could not find hierarchy parent for "+annotation+"\n")
+ sys.stderr.write("WARNING: Could not find hierarchy parent for " + annotation + "\n")
continue
for parent in parents:
if limit and parent not in limit:
if args.verbose:
- sys.stderr.write("Skipping parent "+ parent+"\n")
+ sys.stderr.write("Skipping parent " + parent + "\n")
continue
try:
hier_c[parent].append(count)
@@ -198,63 +198,68 @@ def CalcHierarchy(mapping, annotations, coverage, operation, limit):
(hier_sdev, hier_c) = Calculate(hier_c, operation)
return (hier_sdev, hier_c)
-if args.limit:
- limit = ReadLimits(args.limit)
-else:
- limit = []
-
-lengths = {}
-if args.lengthnorm:
- lengths = ReadLengths(args.lengthnorm)
-
-mapping = ReadMap(args.mapfile)
-annotations = ReadMap(args.infile) # # Read annotations the same way as above, then get length of the list for counts
-coverage = ReadCoverage(args.coverage, lengths)
-(max_hier, hierarchy) = ReadHierarchy(args.hierarchy)
-
-(hier_sdev, hier_counts) = CalcHierarchy(mapping, annotations, coverage, args.operation, limit)
-
-if args.outfile:
- hout = open(args.outfile, 'w')
-else:
- hout = sys.stdout
-houtcsv = csv.writer(hout, delimiter='\t')
-
-if args.name:
- name = args.name
-else:
- name = (args.infile).split("/")[-1]
-
-out = [name]
-if args.singlecol:
- out.insert(0, "X")
-else:
- for i in range(1, max_hier+1):
- out.append("Level" + str(i))
-houtcsv.writerow(out)
-
-if args.sdev:
- sdevout = open(args.sdev, 'w')
- sdevout.write("X.sdev\t"+name+"\n")
-
-for hier, count in hier_counts.iteritems():
- out = [count]
- try:
- h = hierarchy[hier]
- except KeyError:
- h = ["Unknown"]
+if __name__ == '__main__':
+ if not args.infile or not args.mapfile or not args.hierarchy:
+ sys.exit(parser.print_help())
+
+ if args.limit:
+ limit = ReadLimits(args.limit)
+ else:
+ limit = []
+
+ lengths = {}
+ if args.lengthnorm:
+ lengths = ReadLengths(args.lengthnorm)
+
+ mapping = ReadMap(args.mapfile)
+ annotations = ReadMap(args.infile) # Read annotations the same way as above, then get length of the list for counts
+ coverage = ReadCoverage(args.coverage, lengths)
+
+ (max_hier, hierarchy) = ReadHierarchy(args.hierarchy)
+
+ (hier_sdev, hier_counts) = CalcHierarchy(mapping, annotations, coverage, args.operation, limit)
+
+ if args.outfile:
+ hout = open(args.outfile, 'w')
+ else:
+ hout = sys.stdout
+ houtcsv = csv.writer(hout, delimiter='\t')
+
+ if args.name:
+ name = args.name
+ else:
+ name = (args.infile).split("/")[-1]
+
+ out = [name]
if args.singlecol:
- out.insert(0, hier)
+ out.insert(0, "X")
else:
- out += hierarchy[hier]
+ for i in range(1, max_hier+1):
+ out.append("Level" + str(i))
+ houtcsv.writerow(out)
+
+ if args.sdev:
+ sdevout = open(args.sdev, 'w')
+ sdevout.write("X.sdev\t"+name+"\n")
+
+ for hier, count in hier_counts.iteritems():
+ out = [count]
+ try:
+ h = hierarchy[hier]
+ except KeyError:
+ h = ["Unknown"]
+ if args.singlecol:
+ out.insert(0, hier)
+ else:
+ out += hierarchy[hier]
+ try:
+ sdevout.write(hier+"\t"+str(hier_sdev[hier])+"\n")
+ except NameError:
+ pass
+ houtcsv.writerow(out)
+ hout.close()
+
try:
- sdevout.write(hier+"\t"+str(hier_sdev[hier])+"\n")
+ sdevout.close()
except NameError:
pass
- houtcsv.writerow(out)
-hout.close()
-
-try:
- sdevout.close()
-except NameError:
- pass