# HG changeset patch
# User iuc
# Date 1568208511 14400
# Node ID 5320a0774e03d79be62a88b2e4b7bb7d1a29448e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
diff -r 000000000000 -r 5320a0774e03 calculate_contrast_threshold.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/calculate_contrast_threshold.py Wed Sep 11 09:28:31 2019 -0400
@@ -0,0 +1,186 @@
+#!/usr/bin/python
+
+import getopt
+import math
+import sys
+
+import numpy as np
+
+"""
+Program to calculate the contrast thresholds for heatmap from tagPileUp CDT
+"""
+
+
+def rebin(a, new_shape):
+ M, N = a.shape
+ m, n = new_shape
+ if m >= M:
+ # repeat rows in data matrix
+ a = np.repeat(a, math.ceil(float(m) / M), axis=0)
+
+ M, N = a.shape
+ m, n = new_shape
+
+ row_delete_num = M % m
+ col_delete_num = N % n
+
+ np.random.seed(seed=0)
+
+ if row_delete_num > 0:
+ # select deleted rows with equal intervals
+ row_delete = np.linspace(0, M - 1, num=row_delete_num, dtype=int)
+ # sort the random selected deleted row ids
+ row_delete = np.sort(row_delete)
+ row_delete_plus1 = row_delete[1:-1] + \
+ 1 # get deleted rows plus position
+ # get deleted rows plus position (top +1; end -1)
+ row_delete_plus1 = np.append(
+ np.append(row_delete[0] + 1, row_delete_plus1), row_delete[-1] - 1)
+ # put the info of deleted rows into the next rows by mean
+ a[row_delete_plus1, :] = (
+ a[row_delete, :] + a[row_delete_plus1, :]) / 2
+ a = np.delete(a, row_delete, axis=0) # random remove rows
+
+ if col_delete_num > 0:
+ # select deleted cols with equal intervals
+ col_delete = np.linspace(0, N - 1, num=col_delete_num, dtype=int)
+ # sort the random selected deleted col ids
+ col_delete = np.sort(col_delete)
+ col_delete_plus1 = col_delete[1:-1] + \
+ 1 # get deleted cols plus position
+ # get deleted cols plus position (top +1; end -1)
+ col_delete_plus1 = np.append(
+ np.append(col_delete[0] + 1, col_delete_plus1), col_delete[-1] - 1)
+ # put the info of deleted cols into the next cols by mean
+ a[:, col_delete_plus1] = (
+ a[:, col_delete] + a[:, col_delete_plus1]) / 2
+ a = np.delete(a, col_delete, axis=1) # random remove columns
+
+ M, N = a.shape
+
+ # compare the heatmap matrix
+ a_compress = a.reshape((m, int(M / m), n, int(N / n))).mean(3).mean(1)
+ return np.array(a_compress)
+
+
+def load_Data(input_file, quantile, absolute, header, start_col, row_num, col_num, min_upper_lim):
+ data0 = []
+ with open(input_file, 'r') as data:
+ if header == 'T':
+ data.readline()
+
+ for rec in data:
+ tmp = [(x.strip()) for x in rec.split('\t')]
+ data0.append(tmp[start_col:])
+ data0 = np.array(data0, dtype=float)
+
+ if row_num == -999:
+ row_num = data0.shape[0]
+ if col_num == -999:
+ col_num = data0.shape[1]
+
+ # rebin data0
+ if row_num < data0.shape[0] and col_num < data0.shape[1]:
+ data0 = rebin(data0, (row_num, col_num))
+ elif row_num < data0.shape[0]:
+ data0 = rebin(data0, (row_num, data0.shape[1]))
+ elif col_num < data0.shape[1]:
+ data0 = rebin(data0, (data0.shape[0], col_num))
+
+ # Calculate contrast limits here
+ rows, cols = np.nonzero(data0)
+ upper_lim = np.percentile(data0[rows, cols], quantile)
+ lower_lim = 0
+ if absolute != -999:
+ upper_lim = absolute
+
+ # Setting an absolute threshold to a minimum,
+ # in cases the 95th percentile contrast is <= user defined min_upper_lim
+ if quantile > 0.0:
+ print("\nQUANTILE: {}".format(quantile))
+ print("Quantile calculated UPPER LIM: {}".format(upper_lim))
+ print("LOWER LIM: {}".format(lower_lim))
+ if upper_lim <= min_upper_lim:
+ print("setting heatmap upper_threshold to min_upper_lim\n")
+ upper_lim = min_upper_lim
+
+ outfile = open('calcThreshold.txt', 'w')
+ outfile.write("upper_threshold:{}\nlower_threshold:{}\nrow_num:{}\ncol_num:{}\nheader:{}\nstart_col:{}".format(
+ upper_lim, lower_lim, row_num, col_num, header, start_col))
+ print('heatmap_upper_threshold:' + str(upper_lim))
+ print('heatmap_lower_threshold:' + str(lower_lim))
+ outfile.flush()
+ outfile.close()
+
+
+############################################################################
+# python cdt_to_heatmap.py -i test.tabular.split_line -o test.tabular.split_line.png -q 0.9 -c black -d T -s 2 -r 500 -l 300 -b test.colorsplit
+############################################################################
+usage = """
+Usage:
+This script calculates the contrast thresholds from Tag pile up heatmap data. Outputs a text file that contains the parameters for the heatmap script.
+
+python calculateThreshold.py -i -q -m -t -d -s -r -l '
+
+Example:
+python calculateThreshold.py -i test.tabular.split_line -q 90 -m 5 -d T -s 2 -r 600 -l 300
+"""
+
+if __name__ == '__main__':
+
+ # check for command line arguments
+ if len(sys.argv) < 2 or not sys.argv[1].startswith("-"):
+ sys.exit(usage)
+ # get arguments
+ try:
+ optlist, alist = getopt.getopt(sys.argv[1:], 'hi:o:q:t:c:d:s:r:l:m:')
+ except getopt.GetoptError:
+ sys.exit(usage)
+
+ # default quantile contrast saturation = 0.9
+ quantile = 90.0
+ min_upper_lim = 5.0
+ # absolute contrast saturation overrides quantile
+ absolute = -999
+
+ # default figure width/height is defined by matrix size
+ # if user-defined size is smaller than matrix, activate rebin function
+ row_num = -999
+ col_num = -999
+
+ for opt in optlist:
+ if opt[0] == "-h":
+ sys.exit(usage)
+ elif opt[0] == "-i":
+ input_file = opt[1]
+ elif opt[0] == "-q":
+ quantile = float(opt[1])
+ elif opt[0] == '-t':
+ absolute = float(opt[1])
+ elif opt[0] == "-d":
+ header = opt[1]
+ elif opt[0] == "-s":
+ start_col = int(opt[1])
+ elif opt[0] == "-r":
+ row_num = int(opt[1])
+ elif opt[0] == "-l":
+ col_num = int(opt[1])
+ elif opt[0] == "-m":
+ min_upper_lim = float(opt[1])
+
+ print("Header present:", header)
+ print("Start column:", start_col)
+ print("Row number (pixels):", row_num)
+ print("Col number (pixels):", col_num)
+ print("Min Upper Limit while using Quantile:", min_upper_lim)
+ if absolute != -999:
+ print("Absolute tag contrast threshold:", absolute)
+ else:
+ print("Percentile tag contrast threshold:", quantile)
+
+ if absolute == -999 and quantile <= 0:
+ print("\nInvalid threshold!!!")
+ sys.exit(usage)
+
+ load_Data(input_file, quantile, absolute,
+ header, start_col, row_num, col_num, min_upper_lim)
diff -r 000000000000 -r 5320a0774e03 calculate_contrast_threshold.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/calculate_contrast_threshold.xml Wed Sep 11 09:28:31 2019 -0400
@@ -0,0 +1,122 @@
+
+ from tag pileup CDT
+
+
+ numpy
+ python
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+ @unpublished{None,
+ author = {Kuntala, Prashant Kumar and Lai, William KM },
+ title = {None},
+ year = {None},
+ eprint = {None},
+ url = {http://www.pughlab.psu.edu/}
+ }
+
+
+
diff -r 000000000000 -r 5320a0774e03 test-data/calcThreshold_b.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/calcThreshold_b.txt Wed Sep 11 09:28:31 2019 -0400
@@ -0,0 +1,6 @@
+upper_threshold:5.0
+lower_threshold:0
+row_num:600
+col_num:300
+header:T
+start_col:2
\ No newline at end of file
diff -r 000000000000 -r 5320a0774e03 test-data/calcThreshold_t.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/calcThreshold_t.txt Wed Sep 11 09:28:31 2019 -0400
@@ -0,0 +1,6 @@
+upper_threshold:10.0
+lower_threshold:0
+row_num:600
+col_num:300
+header:T
+start_col:2
\ No newline at end of file
diff -r 000000000000 -r 5320a0774e03 test-data/sample.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample.tabular Wed Sep 11 09:28:31 2019 -0400
@@ -0,0 +1,20 @@
+YORF NAME 0 1 2 3 4 5 6 7
+10001 10001 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
+10002 10002 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+10003 10003 0.0 0.0 0.0 1.0 0.0 1.0 0.0 0.0
+10004 10004 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0
+10005 10005 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0
+10006 10006 1.0 2.0 2.0 0.0 1.0 0.0 0.0 0.0
+10007 10007 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+10008 10008 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
+10009 10009 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+10011 10011 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0
+10012 10012 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
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+10015 10015 1.0 1.0 1.0 0.0 1.0 1.0 1.0 0.0
+10016 10016 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0
+10017 10017 0.0 0.0 0.0 0.0 0.0 1.0 0.0 1.0
+10018 10018 0.0 0.0 0.0 0.0 1.0 1.0 0.0 0.0
+10019 10019 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0
+10020 10020 0.0 2.0 1.0 0.0 1.0 0.0 0.0 0.0