# HG changeset patch
# User iuc
# Date 1726420125 0
# Node ID 00b3da7776a0ddabb95014bc518fba49a3493479
# Parent 61946b8bd43b9bd80b3f6240b4e19cadfb9fcc56
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 06c54e8066ecbc6292167e7c5bdfb8af945a41ba
diff -r 61946b8bd43b -r 00b3da7776a0 bigwig_outlier_bed.py
--- a/bigwig_outlier_bed.py Thu Jul 25 14:38:34 2024 +0000
+++ b/bigwig_outlier_bed.py Sun Sep 15 17:08:45 2024 +0000
@@ -146,7 +146,7 @@
else:
bwex = np.r_[False, bw <= self.bwbot, False]
bwexd = np.diff(bwex)
- bwexdnz = bwexd.nonzero()[0]
+ bwexdnz = bwexd.nonzero()[0] # start and end transition of each segment - nice!
bwregions = np.reshape(bwexdnz, (-1, 2))
return bwregions
@@ -155,10 +155,9 @@
potentially multiple
"""
bed.sort()
- beds = ["%s\t%d\t%d\t%s\t%d" % x for x in bed]
with open(bedfname, "w") as bedf:
- bedf.write("\n".join(beds))
- bedf.write("\n")
+ for b in bed:
+ bedf.write("%s\t%d\t%d\t%s\t%d\n" % b)
def makeTableRow(self, bw, bwlabel, chr):
"""
@@ -194,7 +193,6 @@
restab = []
bwlabels = self.bwlabels
bwnames = self.bwnames
- bwnames.sort()
reshead = "bigwig\tcontig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot"
for i, bwname in enumerate(bwnames):
bwlabel = bwlabels[i].replace(" ", "")
@@ -251,8 +249,11 @@
self.bwbot = np.quantile(bw, self.qlo)
bwlo = self.processVals(bw, isTop=False)
for j, seg in enumerate(bwlo):
+ seglen = seg[1] - seg[0]
if seg[1] - seg[0] >= self.bedwin:
- score = -1 * np.sum(bw[seg[0]:seg[1]]) / float(seglen)
+ score = (
+ -1 * np.sum(bw[seg[0]:seg[1]]) / float(seglen)
+ )
bedlo.append(
(
chr,
diff -r 61946b8bd43b -r 00b3da7776a0 bigwig_outlier_bed.xml
--- a/bigwig_outlier_bed.xml Thu Jul 25 14:38:34 2024 +0000
+++ b/bigwig_outlier_bed.xml Sun Sep 15 17:08:45 2024 +0000
@@ -3,7 +3,7 @@
0.2.0
3.12.3
- 0
+ 1
topic_0157
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