fixed comments

anuradhawick · Jan 9, 2020 · ef3e411 · ef3e411
1 parent bfceff8
commit ef3e411
Showing 1 changed file with 36 additions and 36 deletions.
diff --git a/MetaBCC-LR b/MetaBCC-LR
@@ -95,42 +95,42 @@ else:
     else:
         cmdFilter = """"{0}/bin/filter" "{1}" "{2}/filteredReads.fa" fa""".format(os.path.dirname(__file__), readsPath, output)
 
-# o = os.system(cmdFilter)
-# checkProc(o, "Filtering reads")
-
-# print("Running DSK")
-# cmdDSK = """dsk -verbose 0 -file "{0}/filteredReads.fa" -kmer-size 15 -abundance-min 10 -out-dir "{0}/DSK" -max-memory 9000 -nb-cores {1}""".format(output, threads)
-# o = os.system(cmdDSK)
-# checkProc(o, "Running DSK")
-
-# print("Reading DSK output")
-# cmdDSKRead = """python {0}/src/scan-dsk.py {1}/DSK/filteredReads.h5 {1}/DSK/ {2}""".format(os.path.dirname(__file__), output, threads)
-# o = os.system(cmdDSKRead)
-# checkProc(o, "Reading DSK output")
-
-# print("Gathering DSK data")
-# cmdGather = """cat "{0}"/DSK/*.chunk > "{0}/DSK/15mersCounts" """.format(output)
-# o = os.system(cmdGather)
-# checkProc(o, "Gathering DSK data")
-
-# print("Counting Trimers")
-# cmd = """mkdir -p "{0}/profiles" """.format(output)
-# o = os.system(cmd)
-# checkProc(o, "Making directory for profiles")
-
-# cmd = """"{0}/bin/countTrimers" "{1}/filteredReads.fa" "{1}/profiles/3mers" {2}""".format(os.path.dirname(__file__), output, threads)
-# o = os.system(cmd)
-# checkProc(o, "Counting Trimers")
-
-# print("Counting 15-mer profiles")
-# cmd = """"{0}/bin/search15mers" "{1}/DSK/15mersCounts" "{1}/filteredReads.fa" "{1}/profiles/15mers" {2}""".format(os.path.dirname(__file__), output, threads)
-# o = os.system(cmd)
-# checkProc(o, "Counting 15-mer profiles")
-
-# print("Obtaining read lengths")
-# cmd = """awk "{{ if(NR%2==0) print length($1) }}" "{0}/filteredReads.fa" > "{0}/filteredReadLengths.txt" """.format(output)
-# o = os.system(cmd)
-# checkProc(o, "Obtaining read lengths")
+o = os.system(cmdFilter)
+checkProc(o, "Filtering reads")
+
+print("Running DSK")
+cmdDSK = """dsk -verbose 0 -file "{0}/filteredReads.fa" -kmer-size 15 -abundance-min 10 -out-dir "{0}/DSK" -max-memory 9000 -nb-cores {1}""".format(output, threads)
+o = os.system(cmdDSK)
+checkProc(o, "Running DSK")
+
+print("Reading DSK output")
+cmdDSKRead = """python {0}/src/scan-dsk.py {1}/DSK/filteredReads.h5 {1}/DSK/ {2}""".format(os.path.dirname(__file__), output, threads)
+o = os.system(cmdDSKRead)
+checkProc(o, "Reading DSK output")
+
+print("Gathering DSK data")
+cmdGather = """cat "{0}"/DSK/*.chunk > "{0}/DSK/15mersCounts" """.format(output)
+o = os.system(cmdGather)
+checkProc(o, "Gathering DSK data")
+
+print("Counting Trimers")
+cmd = """mkdir -p "{0}/profiles" """.format(output)
+o = os.system(cmd)
+checkProc(o, "Making directory for profiles")
+
+cmd = """"{0}/bin/countTrimers" "{1}/filteredReads.fa" "{1}/profiles/3mers" {2}""".format(os.path.dirname(__file__), output, threads)
+o = os.system(cmd)
+checkProc(o, "Counting Trimers")
+
+print("Counting 15-mer profiles")
+cmd = """"{0}/bin/search15mers" "{1}/DSK/15mersCounts" "{1}/filteredReads.fa" "{1}/profiles/15mers" {2}""".format(os.path.dirname(__file__), output, threads)
+o = os.system(cmd)
+checkProc(o, "Counting 15-mer profiles")
+
+print("Obtaining read lengths")
+cmd = """awk "{{ if(NR%2==0) print length($1) }}" "{0}/filteredReads.fa" > "{0}/filteredReadLengths.txt" """.format(output)
+o = os.system(cmd)
+checkProc(o, "Obtaining read lengths")
 
 print("Sampling Reads")
 if ids: