Andreas Tille pushed to branch upstream at Debian Med / tiddit
Commits:
5573c455 by Andreas Tille at 2020-06-16T22:08:50+02:00
New upstream version 2.12.0+dfsg
- - - - -
5 changed files:
- TIDDIT.py
- src/TIDDIT.cpp
- src/TIDDIT_calling.py
- src/TIDDIT_coverage.py
- + versioned_singularity/TIDDIT.2.12.0
Changes:
=====================================
TIDDIT.py
=====================================
@@ -8,7 +8,7 @@ wd=os.path.dirname(os.path.realpath(__file__))
sys.path.insert(0, '{}/src/'.format(wd))
import TIDDIT_calling
-version = "2.11.0"
+version = "2.12.0"
parser =
argparse.ArgumentParser("""TIDDIT-{}""".format(version),add_help=False)
parser.add_argument('--sv' , help="call structural variation",
required=False, action="store_true")
parser.add_argument('--cov' , help="generate a coverage bed file",
required=False, action="store_true")
=====================================
src/TIDDIT.cpp
=====================================
@@ -46,7 +46,7 @@ int main(int argc, char **argv) {
int min_variant_size= 100;
int sample = 100000000;
string outputFileHeader ="output";
- string version = "2.11.0";
+ string version = "2.12.0";
//collect all options as a vector
vector<string> arguments(argv, argv + argc);
=====================================
src/TIDDIT_calling.py
=====================================
@@ -234,9 +234,21 @@ def cluster(args):
for chrA in chromosomes:
calls[chrA] =[]
print ("{}".format(chrA))
+ signals_chrA={}
+ signals=[
[hit[0],hit[1],hit[2],hit[3],hit[4],hit[5],hit[6],hit[7],hit[8]] for hit in
args.c.execute('SELECT
chrB,posA,posB,forwardA,qualA,forwardB,qualB,resolution,name FROM TIDDITcall
WHERE chrA == \'{}\''.format(chrA)).fetchall()]
+
for chrB in chromosomes:
- signal_data=numpy.array([
[hit[0],hit[1],hit[2],hit[3],hit[4],hit[5],hit[6],hit[7]] for hit in
args.c.execute('SELECT posA,posB,forwardA,qualA,forwardB,qualB,resolution,name
FROM TIDDITcall WHERE chrA == \'{}\' AND chrB ==
\'{}\''.format(chrA,chrB)).fetchall()])
+ if not chrB in signals_chrA:
+ signals_chrA[chrB] = []
+
+ for signal in signals:
+ signals_chrA[signal[0]].append(signal[1:])
+ for chrB in signals_chrA:
+ signals_chrA[chrB]=numpy.array(signals_chrA[chrB])
+
+ for chrB in chromosomes:
+ signal_data=signals_chrA[chrB]
if not len(signal_data):
continue
=====================================
src/TIDDIT_coverage.py
=====================================
@@ -88,7 +88,7 @@ def
determine_ploidy(args,chromosomes,coverage_data,Ncontent,library_stats):
print ("make sure that the contigs of the bam file and
the reference match")
quit()
- if len(cov):
+ if cov.size:
coverage_norm=numpy.median(cov)
else:
coverage_norm=1
@@ -107,7 +107,11 @@ def
determine_ploidy(args,chromosomes,coverage_data,Ncontent,library_stats):
else:
cov=coverage_data[chromosome][numpy.where(
(coverage_data[chromosome][:,1] > args.Q) | (coverage_data[chromosome][:,1] ==
0) ),0]
- chromosomal_average=numpy.median(cov)
+ if cov.size:
+ chromosomal_average=numpy.median(cov)
+ else:
+ chromosomal_average=0
+
if not args.force_ploidy:
try:
ploidies[chromosome]=int(round((chromosomal_average)/coverage_norm*args.n))
=====================================
versioned_singularity/TIDDIT.2.12.0
=====================================
@@ -0,0 +1,23 @@
+BootStrap: debootstrap
+OSVersion: trusty
+MirrorURL: http://us.archive.ubuntu.com/ubuntu/
+
+
+%runscript
+ echo "This is what happens when you run the container..."
+
+
+%post
+ echo "Hello from inside the container"
+ sed -i 's/$/ universe/' /etc/apt/sources.list
+ apt-get update
+ apt-get -y --force-yes install build-essential cmake make zlib1g-dev
python python-dev python-setuptools git wget libbz2-dev unzip
+ easy_install pip
+ pip install numpy cython
+
+ wget https://github.com/SciLifeLab/TIDDIT/archive/TIDDIT-2.12.0.zip
+ unzip TIDDIT-2.12.0.zip
+
+ mv TIDDIT-TIDDIT-2.12.0/* /bin/
+ cd /bin/ && ./INSTALL.sh
+ chmod +x /bin/TIDDIT.py
View it on GitLab:
https://salsa.debian.org/med-team/tiddit/-/commit/5573c4550fe1b5ff049305fdc12a9d08c59d4f52
--
View it on GitLab:
https://salsa.debian.org/med-team/tiddit/-/commit/5573c4550fe1b5ff049305fdc12a9d08c59d4f52
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