mirror of
https://github.com/ilyakooo0/nixpkgs.git
synced 2024-09-11 07:15:54 +03:00
Merge pull request #283881 from apraga/hap-py-0.3.15
This commit is contained in:
commit
4d49db587d
50
pkgs/by-name/ha/hap-py/boost-library-flags.patch
Normal file
50
pkgs/by-name/ha/hap-py/boost-library-flags.patch
Normal file
@ -0,0 +1,50 @@
|
||||
--- a/CMakeLists.txt 2023-02-01 23:55:18.171758209 +0100
|
||||
+++ b/CMakeLists.txt 2023-02-02 19:32:16.574426531 +0100
|
||||
@@ -23,25 +23,11 @@
|
||||
set (VCFEVAL_AVAILABLE 0)
|
||||
endif()
|
||||
|
||||
-execute_process(
|
||||
- COMMAND ${CMAKE_SOURCE_DIR}/external/make_dependencies.sh
|
||||
- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
|
||||
- RESULT_VARIABLE EXTERNAL_SUCCESS)
|
||||
|
||||
-if(NOT "${EXTERNAL_SUCCESS}" STREQUAL "0")
|
||||
- message(FATAL_ERROR "Building external dependencies has failed")
|
||||
-endif()
|
||||
-
|
||||
-set(Boost_USE_STATIC_LIBS ON) # only find static libs
|
||||
set(Boost_USE_MULTITHREADED ON)
|
||||
-set(Boost_USE_STATIC_RUNTIME ON)
|
||||
|
||||
# un-break library finding
|
||||
-set(Boost_NO_BOOST_CMAKE ON)
|
||||
-set(Boost_NO_SYSTEM_PATHS ON)
|
||||
|
||||
-set(BOOST_ROOT ${CMAKE_BINARY_DIR})
|
||||
-message("Using our own Boost, which was built at ${HAPLOTYPES_SOURCE_DIR}/external/boost_install")
|
||||
|
||||
find_package(Boost 1.55.0 COMPONENTS thread iostreams regex unit_test_framework filesystem system program_options REQUIRED)
|
||||
include_directories(${Boost_INCLUDE_DIRS})
|
||||
@@ -51,7 +51,8 @@
|
||||
link_directories (${CMAKE_BINARY_DIR}/lib)
|
||||
|
||||
# make sure we use the bundled zlib version
|
||||
-set(ZLIB_LIBRARIES ${CMAKE_BINARY_DIR}/lib/libz.a)
|
||||
+# Additional flags for nix, found by trial and error
|
||||
+set(ZLIB_LIBRARIES -lz -lbz2 -lcurl -lcrypto -llzma)
|
||||
|
||||
include_directories (${HAPLOTYPES_SOURCE_DIR}/external/klib)
|
||||
include_directories (${HAPLOTYPES_SOURCE_DIR}/external/intervaltree)
|
||||
@@ -84,11 +86,6 @@
|
||||
${CMAKE_THREAD_LIBS_INIT})
|
||||
|
||||
|
||||
-execute_process(COMMAND git describe --tags --always
|
||||
- OUTPUT_VARIABLE HAPLOTYPES_VERSION
|
||||
- WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
|
||||
- OUTPUT_STRIP_TRAILING_WHITESPACE
|
||||
-)
|
||||
|
||||
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/src/c++/include/Version.hh.in"
|
||||
"${CMAKE_BINARY_DIR}/include/Version.hh")
|
92
pkgs/by-name/ha/hap-py/package.nix
Normal file
92
pkgs/by-name/ha/hap-py/package.nix
Normal file
@ -0,0 +1,92 @@
|
||||
{
|
||||
autoconf,
|
||||
bcftools,
|
||||
boost,
|
||||
bzip2,
|
||||
cmake,
|
||||
curl,
|
||||
fetchFromGitHub,
|
||||
htslib,
|
||||
lib,
|
||||
makeWrapper,
|
||||
perl,
|
||||
python3,
|
||||
rtg-tools,
|
||||
samtools,
|
||||
stdenv,
|
||||
xz,
|
||||
zlib,
|
||||
}:
|
||||
|
||||
let
|
||||
# Bcftools needs perl
|
||||
runtime = [
|
||||
bcftools
|
||||
htslib
|
||||
my-python
|
||||
perl
|
||||
samtools
|
||||
];
|
||||
my-python-packages =
|
||||
p: with p; [
|
||||
bx-python
|
||||
pysam
|
||||
pandas
|
||||
psutil
|
||||
scipy
|
||||
];
|
||||
my-python = python3.withPackages my-python-packages;
|
||||
in
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "hap.py";
|
||||
version = "0.3.15";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "Illumina";
|
||||
repo = pname;
|
||||
rev = "v${version}";
|
||||
sha256 = "sha256-K8XXhioMGMHw56MKvp0Eo8S6R36JczBzGRaBz035zRQ=";
|
||||
};
|
||||
# For illumina script
|
||||
BOOST_ROOT = "${boost.out}";
|
||||
ZLIBSTATIC = "${zlib.static}";
|
||||
# For cmake : boost lib and includedir are in differernt location
|
||||
BOOST_LIBRARYDIR = "${boost.out}/lib";
|
||||
BOOST_INCLUDEDIR = "${boost.dev}/include";
|
||||
|
||||
patches = [
|
||||
# Compatibility with nix for boost and library flags : zlib, bzip2, curl, crypto, lzma
|
||||
./boost-library-flags.patch
|
||||
# Update to python3
|
||||
./python3.patch
|
||||
];
|
||||
nativeBuildInputs = [
|
||||
autoconf
|
||||
cmake
|
||||
makeWrapper
|
||||
];
|
||||
buildInputs = [
|
||||
boost
|
||||
bzip2
|
||||
curl
|
||||
htslib
|
||||
my-python
|
||||
rtg-tools
|
||||
xz
|
||||
zlib
|
||||
];
|
||||
|
||||
postFixup = ''
|
||||
wrapProgram $out/bin/hap.py \
|
||||
--set PATH ${lib.makeBinPath runtime} \
|
||||
--add-flags "--engine-vcfeval-path=${rtg-tools}/bin/rtg"
|
||||
'';
|
||||
|
||||
meta = with lib; {
|
||||
description = "Compare genetics variants against a gold dataset";
|
||||
homepage = "https://github.com/Illumina/hap.py";
|
||||
license = licenses.bsd2;
|
||||
maintainers = with maintainers; [ apraga ];
|
||||
mainProgram = "hap.py";
|
||||
};
|
||||
}
|
342
pkgs/by-name/ha/hap-py/python3.patch
Normal file
342
pkgs/by-name/ha/hap-py/python3.patch
Normal file
@ -0,0 +1,342 @@
|
||||
diff --git a/src/c++/lib/tools/Roc.cpp b/src/c++/lib/tools/Roc.cpp
|
||||
index fabe2be..2c6bb49 100644
|
||||
--- a/src/c++/lib/tools/Roc.cpp
|
||||
+++ b/src/c++/lib/tools/Roc.cpp
|
||||
@@ -34,6 +34,9 @@
|
||||
*/
|
||||
|
||||
#include "helpers/Roc.hh"
|
||||
+#include <stdexcept>
|
||||
+#include <limits>
|
||||
+
|
||||
|
||||
#include <algorithm>
|
||||
#include <cmath>
|
||||
diff --git a/src/cmake/cxx.cmake b/src/cmake/cxx.cmake
|
||||
old mode 100755
|
||||
new mode 100644
|
||||
diff --git a/src/python/Haplo/happyroc.py b/src/python/Haplo/happyroc.py
|
||||
index 152bd18..e439957 100644
|
||||
--- a/src/python/Haplo/happyroc.py
|
||||
+++ b/src/python/Haplo/happyroc.py
|
||||
@@ -97,7 +97,7 @@ def roc(roc_table, output_path,
|
||||
header = l.split("\t")
|
||||
else:
|
||||
rec = {}
|
||||
- for k, v in itertools.izip(header, l.split("\t")):
|
||||
+ for k, v in zip(header, l.split("\t")):
|
||||
rec[k] = v
|
||||
|
||||
if filter_handling:
|
||||
@@ -160,11 +160,11 @@ def roc(roc_table, output_path,
|
||||
|
||||
if "all" not in result:
|
||||
# minimal empty DF
|
||||
- minidata = [{"Type": "SNP", "Subtype": "*", "Filter": "ALL", "Genotype": "*", "Subset": "*", "QQ": "*"} for _ in xrange(2)]
|
||||
+ minidata = [{"Type": "SNP", "Subtype": "*", "Filter": "ALL", "Genotype": "*", "Subset": "*", "QQ": "*"} for _ in range(2)]
|
||||
minidata[1]["Type"] = "INDEL"
|
||||
result["all"] = pandas.DataFrame(minidata, columns=RESULT_ALLCOLUMNS)
|
||||
for i, c in enumerate(RESULT_ALLCOLUMNS):
|
||||
- result["all"][c] = result["all"][c].astype(RESULT_ALLDTYPES[i], raise_on_error=False)
|
||||
+ result["all"][c] = result["all"][c].astype(RESULT_ALLDTYPES[i], errors="ignore")
|
||||
|
||||
for k, v in result.items():
|
||||
result[k] = _postprocessRocData(pandas.DataFrame(v, columns=RESULT_ALLCOLUMNS))
|
||||
diff --git a/src/python/Haplo/partialcredit.py b/src/python/Haplo/partialcredit.py
|
||||
index d9e22bb..0f2b2cf 100644
|
||||
--- a/src/python/Haplo/partialcredit.py
|
||||
+++ b/src/python/Haplo/partialcredit.py
|
||||
@@ -202,7 +202,7 @@ def partialCredit(vcfname,
|
||||
try:
|
||||
res = runParallel(pool,
|
||||
preprocessWrapper,
|
||||
- itertools.izip(itertools.repeat(vcfname), locations),
|
||||
+ zip(itertools.repeat(vcfname), locations),
|
||||
{"reference": reference,
|
||||
"decompose": decompose,
|
||||
"leftshift": leftshift,
|
||||
diff --git a/src/python/Haplo/quantify.py b/src/python/Haplo/quantify.py
|
||||
index 042d13e..b1d362e 100755
|
||||
--- a/src/python/Haplo/quantify.py
|
||||
+++ b/src/python/Haplo/quantify.py
|
||||
@@ -152,7 +152,7 @@ def run_quantify(filename,
|
||||
run_str += " -v %s" % pipes.quote(write_vcf)
|
||||
|
||||
if regions:
|
||||
- for k, v in regions.iteritems():
|
||||
+ for k, v in regions.items():
|
||||
run_str += " -R '%s:%s'" % (k, v)
|
||||
|
||||
if roc_regions:
|
||||
diff --git a/src/python/Somatic/Mutect.py b/src/python/Somatic/Mutect.py
|
||||
index 7ac923c..81f08b5 100755
|
||||
--- a/src/python/Somatic/Mutect.py
|
||||
+++ b/src/python/Somatic/Mutect.py
|
||||
@@ -148,7 +148,7 @@ def extractMutectSNVFeatures(vcfname, tag, avg_depth=None):
|
||||
n_allele_alt_count = 0
|
||||
else:
|
||||
n_allele_alt_count = 0
|
||||
- for a in xrange(0, len(alleles_alt)):
|
||||
+ for a in range(0, len(alleles_alt)):
|
||||
n_allele_alt_count += float(rec[n_sample + "AD"][a + 1])
|
||||
|
||||
if n_allele_alt_count + n_allele_ref_count == 0:
|
||||
@@ -163,7 +163,7 @@ def extractMutectSNVFeatures(vcfname, tag, avg_depth=None):
|
||||
t_allele_alt_count = 0
|
||||
else:
|
||||
t_allele_alt_count = 0
|
||||
- for a in xrange(0, len(alleles_alt)):
|
||||
+ for a in range(0, len(alleles_alt)):
|
||||
t_allele_alt_count += float(rec[t_sample + "AD"][a + 1])
|
||||
|
||||
if t_allele_alt_count + t_allele_ref_count == 0:
|
||||
@@ -344,7 +344,7 @@ def extractMutectIndelFeatures(vcfname, tag, avg_depth=None):
|
||||
n_allele_alt_count = 0
|
||||
else:
|
||||
n_allele_alt_count = 0
|
||||
- for a in xrange(0, len(alleles_alt)):
|
||||
+ for a in range(0, len(alleles_alt)):
|
||||
n_allele_alt_count += float(rec[n_sample + "AD"][a + 1])
|
||||
|
||||
if n_allele_alt_count + n_allele_ref_count == 0:
|
||||
@@ -359,7 +359,7 @@ def extractMutectIndelFeatures(vcfname, tag, avg_depth=None):
|
||||
t_allele_alt_count = 0
|
||||
else:
|
||||
t_allele_alt_count = 0
|
||||
- for a in xrange(0, len(alleles_alt)):
|
||||
+ for a in range(0, len(alleles_alt)):
|
||||
t_allele_alt_count += float(rec[t_sample + "AD"][a + 1])
|
||||
|
||||
if t_allele_alt_count + t_allele_ref_count == 0:
|
||||
diff --git a/src/python/Tools/bcftools.py b/src/python/Tools/bcftools.py
|
||||
index 6146b7a..6d80d14 100755
|
||||
--- a/src/python/Tools/bcftools.py
|
||||
+++ b/src/python/Tools/bcftools.py
|
||||
@@ -128,8 +128,8 @@ def concatenateParts(output, *args):
|
||||
to_delete.append(tf2.name)
|
||||
to_delete.append(tf1.name + ".csi")
|
||||
to_delete.append(tf2.name + ".csi")
|
||||
- half1 = [tf1.name] + list(args[:len(args)/2])
|
||||
- half2 = [tf2.name] + list(args[len(args)/2:])
|
||||
+ half1 = [tf1.name] + list(args[:len(args)//2])
|
||||
+ half2 = [tf2.name] + list(args[len(args)//2:])
|
||||
concatenateParts(*half1)
|
||||
runBcftools("index", tf1.name)
|
||||
concatenateParts(*half2)
|
||||
diff --git a/src/python/Tools/metric.py b/src/python/Tools/metric.py
|
||||
index 71ccc99..372626d 100755
|
||||
--- a/src/python/Tools/metric.py
|
||||
+++ b/src/python/Tools/metric.py
|
||||
@@ -115,7 +115,7 @@ def replaceNaNs(xobject):
|
||||
if type(xobject[k]) is dict or type(xobject[k]) is list or type(xobject[k]) is float:
|
||||
xobject[k] = replaceNaNs(xobject[k])
|
||||
elif type(xobject) is list:
|
||||
- for k in xrange(0, len(xobject)):
|
||||
+ for k in range(0, len(xobject)):
|
||||
if type(xobject[k]) is dict or type(xobject[k]) is list or type(xobject[k]) is float:
|
||||
xobject[k] = replaceNaNs(xobject[k])
|
||||
elif type(xobject) is float:
|
||||
diff --git a/src/python/Tools/parallel.py b/src/python/Tools/parallel.py
|
||||
index 9d49760..5fcb37e 100755
|
||||
--- a/src/python/Tools/parallel.py
|
||||
+++ b/src/python/Tools/parallel.py
|
||||
@@ -17,9 +17,9 @@ import logging
|
||||
import traceback
|
||||
import subprocess
|
||||
import multiprocessing
|
||||
-import cPickle
|
||||
+import pickle
|
||||
import tempfile
|
||||
-from itertools import islice, izip, repeat
|
||||
+from itertools import islice, repeat
|
||||
|
||||
from . import LoggingWriter
|
||||
|
||||
@@ -93,7 +93,7 @@ def runParallel(pool, fun, par, *args, **kwargs):
|
||||
|
||||
"""
|
||||
if pool:
|
||||
- result = pool.map(parMapper, izip(par, repeat( { "fun": fun, "args": args, "kwargs": kwargs } )))
|
||||
+ result = pool.map(parMapper, zip(par, repeat( { "fun": fun, "args": args, "kwargs": kwargs } )))
|
||||
else:
|
||||
result = []
|
||||
for c in par:
|
||||
diff --git a/src/python/Tools/sessioninfo.py b/src/python/Tools/sessioninfo.py
|
||||
index 75650ec..b49bf59 100644
|
||||
--- a/src/python/Tools/sessioninfo.py
|
||||
+++ b/src/python/Tools/sessioninfo.py
|
||||
@@ -34,7 +34,6 @@ def sessionInfo():
|
||||
'version': version,
|
||||
'runInfo': [{"key": "commandline", "value": " ".join(sys.argv)}],
|
||||
'uname': " / ".join(platform.uname()),
|
||||
- 'dist': " / ".join(platform.dist()),
|
||||
'mac_ver': " / ".join([platform.mac_ver()[0], platform.mac_ver()[2]]),
|
||||
'python_implementation': platform.python_implementation(),
|
||||
'python_version': platform.python_version(),
|
||||
diff --git a/src/python/Tools/vcfcallerinfo.py b/src/python/Tools/vcfcallerinfo.py
|
||||
index eb7e86e..947f2c4 100755
|
||||
--- a/src/python/Tools/vcfcallerinfo.py
|
||||
+++ b/src/python/Tools/vcfcallerinfo.py
|
||||
@@ -33,8 +33,8 @@ class CallerInfo(object):
|
||||
|
||||
def asDict(self):
|
||||
kvd = ["name", "version", "parameters"]
|
||||
- return {"aligners": [dict(y for y in itertools.izip(kvd, x)) for x in self.aligners],
|
||||
- "callers": [dict(y for y in itertools.izip(kvd, x)) for x in self.callers]}
|
||||
+ return {"aligners": [dict(y for y in zip(kvd, x)) for x in self.aligners],
|
||||
+ "callers": [dict(y for y in zip(kvd, x)) for x in self.callers]}
|
||||
|
||||
def addVCF(self, vcfname):
|
||||
""" Add caller versions from a VCF
|
||||
diff --git a/src/python/hap.py b/src/python/hap.py
|
||||
index 8045936..93279a4 100755
|
||||
--- a/src/python/hap.py
|
||||
+++ b/src/python/hap.py
|
||||
@@ -188,7 +188,7 @@ def main():
|
||||
parser.print_help()
|
||||
exit(1)
|
||||
|
||||
- print "Hap.py %s" % Tools.version
|
||||
+ print("Hap.py %s" % Tools.version)
|
||||
if args.version:
|
||||
exit(0)
|
||||
|
||||
diff --git a/src/python/ovc.py b/src/python/ovc.py
|
||||
index 2837255..20b4442 100755
|
||||
--- a/src/python/ovc.py
|
||||
+++ b/src/python/ovc.py
|
||||
@@ -34,7 +34,7 @@ lines = 1
|
||||
for line in f:
|
||||
l = line.split("\t")
|
||||
if len(l) > 3 and (last-1) > int(l[1]):
|
||||
- print "Overlap at %s:%i (line %i)" % (l[0], int(l[1]), lines)
|
||||
+ print(Overlap at %s:%i (line %i)) % (l[0], int(l[1]), lines)
|
||||
exit(1)
|
||||
elif len(l) > 3:
|
||||
last = int(l[2])
|
||||
diff --git a/src/python/pre.py b/src/python/pre.py
|
||||
index 5ca1644..a37a4b2 100755
|
||||
--- a/src/python/pre.py
|
||||
+++ b/src/python/pre.py
|
||||
@@ -47,8 +47,8 @@ import Haplo.partialcredit
|
||||
def hasChrPrefix(chrlist):
|
||||
""" returns if list of chr names has a chr prefix or not """
|
||||
|
||||
- noprefix = map(str, range(23)) + ["X", "Y", "MT"]
|
||||
- withprefix = ["chr" + x for x in map(str, range(23)) + ["X", "Y", "M"]]
|
||||
+ noprefix = [str(x) for x in range(23)] + ["X", "Y", "MT"]
|
||||
+ withprefix = ["chr" + str(x) for x in range(23)] + ["X", "Y", "M"]
|
||||
|
||||
count_noprefix = len(list(set(noprefix) & set(chrlist)))
|
||||
count_prefix = len(list(set(withprefix) & set(chrlist)))
|
||||
@@ -126,7 +126,7 @@ def preprocess(vcf_input,
|
||||
|
||||
if gender == "auto":
|
||||
logging.info(mf)
|
||||
- if "female" in mf:
|
||||
+ if b"female" in mf:
|
||||
gender = "female"
|
||||
else:
|
||||
gender = "male"
|
||||
@@ -392,7 +392,7 @@ def main():
|
||||
exit(0)
|
||||
|
||||
if args.version:
|
||||
- print "pre.py %s" % Tools.version # noqa:E999
|
||||
+ print(pre.py %s) % Tools.version # noqa:E999
|
||||
exit(0)
|
||||
|
||||
args.input = args.input[0]
|
||||
diff --git a/src/python/qfy.py b/src/python/qfy.py
|
||||
index 4f247ee..59ed68a 100755
|
||||
--- a/src/python/qfy.py
|
||||
+++ b/src/python/qfy.py
|
||||
@@ -203,8 +203,8 @@ def quantify(args):
|
||||
|
||||
# in default mode, print result summary to stdout
|
||||
if not args.quiet and not args.verbose:
|
||||
- print "Benchmarking Summary:"
|
||||
- print essential_numbers.to_string(index=False)
|
||||
+ print("Benchmarking Summary:")
|
||||
+ print(essential_numbers.to_string(index=False))
|
||||
|
||||
# keep this for verbose output
|
||||
if not args.verbose:
|
||||
@@ -213,12 +213,12 @@ def quantify(args):
|
||||
except:
|
||||
pass
|
||||
|
||||
- for t in res.iterkeys():
|
||||
+ for t in res.keys():
|
||||
metrics_output["metrics"].append(dataframeToMetricsTable("roc." + t, res[t]))
|
||||
|
||||
# gzip JSON output
|
||||
if args.write_json:
|
||||
with gzip.open(args.reports_prefix + ".metrics.json.gz", "w") as fp:
|
||||
- json.dump(metrics_output, fp)
|
||||
+ fp.write(json.dumps(metrics_output, default=np_encoder).encode('ascii'))
|
||||
|
||||
|
||||
@@ -362,7 +363,7 @@ def main():
|
||||
exit(0)
|
||||
|
||||
if args.version:
|
||||
- print "qfy.py %s" % Tools.version
|
||||
+ print(qfy.py %s) % Tools.version
|
||||
exit(0)
|
||||
|
||||
if args.fp_bedfile and args.preprocessing_truth_confregions:
|
||||
diff --git a/src/python/som.py b/src/python/som.py
|
||||
index e942351..c01d522 100755
|
||||
--- a/src/python/som.py
|
||||
+++ b/src/python/som.py
|
||||
@@ -640,7 +640,7 @@ def main():
|
||||
"overlap):\n" + ambie.to_string(index=False))
|
||||
# in default mode, print result summary to stdout
|
||||
if not args.quiet and not args.verbose:
|
||||
- print "FP/ambiguity classes with info (multiple classes can " \
|
||||
+ print(FP/ambiguity classes with info (multiple classes can ) \
|
||||
"overlap):\n" + ambie.to_string(index=False)
|
||||
ambie.to_csv(args.output + ".ambiclasses.csv")
|
||||
metrics_output["metrics"].append(dataframeToMetricsTable("ambiclasses", ambie))
|
||||
@@ -659,7 +659,7 @@ def main():
|
||||
formatters={'reason': '{{:<{}s}}'.format(ambie['reason'].str.len().max()).format}, index=False))
|
||||
# in default mode, print result summary to stdout
|
||||
if not args.quiet and not args.verbose:
|
||||
- print "Reasons for defining as ambiguous (multiple reasons can overlap):\n" + ambie.to_string(
|
||||
+ print(Reasons for defining as ambiguous (multiple reasons can overlap):\n) + ambie.to_string(
|
||||
formatters={'reason': '{{:<{}s}}'.format(ambie['reason'].str.len().max()).format}, index=False)
|
||||
ambie.to_csv(args.output + ".ambireasons.csv")
|
||||
metrics_output["metrics"].append(dataframeToMetricsTable("ambireasons", ambie))
|
||||
@@ -936,7 +936,7 @@ def main():
|
||||
logging.info("\n" + res.to_string())
|
||||
# in default mode, print result summary to stdout
|
||||
if not args.quiet and not args.verbose:
|
||||
- print "\n" + res.to_string()
|
||||
+ print(\n) + res.to_string()
|
||||
|
||||
res["sompyversion"] = vstring
|
||||
|
||||
diff --git a/src/python/qfy.py b/src/python/qfy.py
|
||||
index 59ed68a..be8d7e1 100755
|
||||
--- a/src/python/qfy.py
|
||||
+++ b/src/python/qfy.py
|
||||
@@ -33,6 +33,7 @@ import pandas
|
||||
import json
|
||||
import tempfile
|
||||
import gzip
|
||||
+import numpy as np
|
||||
|
||||
scriptDir = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
|
||||
sys.path.append(os.path.abspath(os.path.join(scriptDir, '..', 'lib', 'python27')))
|
||||
@@ -45,6 +46,10 @@ import Haplo.happyroc
|
||||
import Haplo.gvcf2bed
|
||||
from Tools import fastasize
|
||||
|
||||
+# Cannot convert data to json without a custom enconder
|
||||
+def np_encoder(object):
|
||||
+ if isinstance(object, np.generic):
|
||||
+ return object.item()
|
||||
|
||||
def quantify(args):
|
||||
""" Run quantify and write tables """
|
Loading…
Reference in New Issue
Block a user