From b8f5709b8bebb1ebe53505505b1360cc21e1691b Mon Sep 17 00:00:00 2001
From: Calvin <calvin@EESI>
Date: Fri, 15 Feb 2013 17:47:49 -0500
Subject: tried to run it, fixed ftr several times
---
quikr.py | 24 +++++++++++++-----------
quikr_train.py | 16 +++++++---------
2 files changed, 20 insertions(+), 20 deletions(-)
mode change 100644 => 100755 quikr.py
diff --git a/quikr.py b/quikr.py
old mode 100644
new mode 100755
index 2c6815c..1feb82d
--- a/quikr.py
+++ b/quikr.py
@@ -1,3 +1,4 @@
+#!/usr/bin/python
import os
import sys
import scipy.optimize.nnls
@@ -29,9 +30,12 @@ def main():
if not os.path.isfile(args.fasta):
parser.error( "Input fasta file not found")
-
+
# If we are using a custom trained matrix, we need to do some basic checks
- if args.trained is not None:
+ if args.trained_matrix is not None:
+
+ if not os.path.isfile(args.trained_matrix):
+ parser.error("custom trained matrix not be found")
if args.kmer is None:
parser.error("A kmer is required when using a custom matrix")
@@ -43,14 +47,10 @@ def main():
input_lambda = 10000
# If we aren't using a custom trained matrix, load in the defaults
else:
- trained_matrix_location = "trainset7_112011N6Aaux.mat"
+ trained_matrix_location = "output.npy"
input_lambda = 10000
kmer = 6
-
- if not os.path.isfile(args.trained):
- parser.error("custom trained matrix not be found")
-
- xstar = quikr(args.fasta, trained_matrix_location, kmer, input_lambda)
+ xstar = quikr(args.fasta, trained_matrix_location, kmer, input_lambda)
return 0
@@ -74,10 +74,10 @@ def quikr(input_fasta_location, trained_matrix_location, 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 " + kmer, "-1", "-u", input_fasta_location], stdout=PIPE)
+ 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 6", "-1", "-u", input_fasta_location], stdout=PIPE)
+ count_input = Popen(["count-osx", "-r", str(kmer), "-1", "-u", input_fasta_location], stdout=PIPE)
# load the output of our count program and form a probability vector from the counts
@@ -86,9 +86,11 @@ def quikr(input_fasta_location, trained_matrix_location, kmer, default_lambda):
counts = default_lambda * counts
- trained_matrix = np.loadtxt(trained_matrix_location)
+ trained_matrix = np.load(trained_matrix_location)
# perform the non-negative least squares
+ # import pdb; pdb.set_trace()
+ counts = np.rot90(counts)
xstar = scipy.optimize.nnls(trained_matrix, counts)
xstar = xstar / sum(xstar)
diff --git a/quikr_train.py b/quikr_train.py
index 94a8c4e..b14ddcd 100755
--- a/quikr_train.py
+++ b/quikr_train.py
@@ -1,3 +1,4 @@
+#!/usr/bin/python
import numpy as np
import os
import sys
@@ -36,22 +37,21 @@ def quikr_train(input_file_location, kmer):
Takes a input fasta file, and kmer, returns a custom trained matrix
"""
-
- print "input fasta training file: " + input_file_location
- print "kmer: " + kmer
+ kmer_file_name = str(kmer) + "mers.txt"
- kmer_file_name = kmer + "mers.txt"
- print kmer_file_name
+ if not os.path.isfile(kmer_file_name):
+ print "could not find kmer file"
+ exit()
uname = platform.uname()[0]
if uname == "Linux":
print "Detected Linux"
- input_file = Popen(["./probabilities-by-read-linux", kmer, input_file_location, kmer_file_name], stdout=PIPE)
+ 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", kmer, input_file_location, kmer_file_name])
+ 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.
matrix = np.loadtxt(input_file.stdout)
@@ -59,7 +59,5 @@ def quikr_train(input_file_location, kmer):
return normalized
-
-
if __name__ == "__main__":
sys.exit(main())
--
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