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nixpkgs/pkgs/by-name/ha/hap-py/python3.patch
Alexis Praga 5db72db7fa hap-py: use rtgtools vcfeval as default core 
For best results (quality and running time), the
authors advice to use RTGtools vcfeval as the
engine.

Depends on #230394
2024-04-07 21:05:23 +02:00

342 lines
14 KiB
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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 """
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