diff options
| -rwxr-xr-x | quikr.py | 5 | ||||
| -rwxr-xr-x | quikr_train.py | 2 |
2 files changed, 1 insertions, 6 deletions
@@ -37,7 +37,7 @@ def main(): parser.error( "Input fasta file not found") if not os.path.isfile(args.trained_matrix): - parser.error("custom trained matrix not found") + parser.error("Custom trained matrix not found") # use alternative lambda if args.lamb is not None: @@ -72,10 +72,8 @@ def quikr(input_fasta_location, trained_matrix, kmer, default_lambda): # We use the count program to count ____ if uname == "Linux" and os.path.isfile("./count-linux"): - print "Detected Linux" count_input = Popen(["./count-linux", "-r", str(kmer), "-1", "-u", input_fasta_location], stdout=PIPE) elif uname == "Darwin" and os.path.isfile("./count-osx"): - print "Detected Mac OS X" count_input = Popen(["count-osx", "-r", str(kmer), "-1", "-u", input_fasta_location], stdout=PIPE) @@ -91,7 +89,6 @@ def quikr(input_fasta_location, trained_matrix, kmer, default_lambda): xstar, rnorm = scipy.optimize.nnls(trained_matrix, counts) - xstar = xstar / xstar.sum(0) return xstar diff --git a/quikr_train.py b/quikr_train.py index b86afb9..5089e2a 100755 --- a/quikr_train.py +++ b/quikr_train.py @@ -48,10 +48,8 @@ def quikr_train(input_file_location, kmer): uname = platform.uname()[0] if uname == "Linux": - print "Detected Linux" input_file = Popen(["./probabilities-by-read-linux", str(kmer), input_file_location, kmer_file_name], stdout=PIPE) elif uname == "Darwin": - print "Detected Mac OS X" input_file = Popen(["./probabilities-by-read-osx", str(kmer), input_file_location, kmer_file_name]) # load and normalize the matrix by dividing each element by the sum of it's column. |