342 lines
14 KiB
Diff
342 lines
14 KiB
Diff
diff --git a/src/c++/lib/tools/Roc.cpp b/src/c++/lib/tools/Roc.cpp
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index fabe2be..2c6bb49 100644
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--- a/src/c++/lib/tools/Roc.cpp
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+++ b/src/c++/lib/tools/Roc.cpp
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@@ -34,6 +34,9 @@
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*/
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#include "helpers/Roc.hh"
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+#include <stdexcept>
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+#include <limits>
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+
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#include <algorithm>
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#include <cmath>
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diff --git a/src/cmake/cxx.cmake b/src/cmake/cxx.cmake
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old mode 100755
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new mode 100644
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diff --git a/src/python/Haplo/happyroc.py b/src/python/Haplo/happyroc.py
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index 152bd18..e439957 100644
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--- a/src/python/Haplo/happyroc.py
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+++ b/src/python/Haplo/happyroc.py
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@@ -97,7 +97,7 @@ def roc(roc_table, output_path,
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header = l.split("\t")
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else:
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rec = {}
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- for k, v in itertools.izip(header, l.split("\t")):
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+ for k, v in zip(header, l.split("\t")):
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rec[k] = v
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if filter_handling:
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@@ -160,11 +160,11 @@ def roc(roc_table, output_path,
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if "all" not in result:
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# minimal empty DF
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- minidata = [{"Type": "SNP", "Subtype": "*", "Filter": "ALL", "Genotype": "*", "Subset": "*", "QQ": "*"} for _ in xrange(2)]
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+ minidata = [{"Type": "SNP", "Subtype": "*", "Filter": "ALL", "Genotype": "*", "Subset": "*", "QQ": "*"} for _ in range(2)]
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minidata[1]["Type"] = "INDEL"
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result["all"] = pandas.DataFrame(minidata, columns=RESULT_ALLCOLUMNS)
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for i, c in enumerate(RESULT_ALLCOLUMNS):
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- result["all"][c] = result["all"][c].astype(RESULT_ALLDTYPES[i], raise_on_error=False)
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+ result["all"][c] = result["all"][c].astype(RESULT_ALLDTYPES[i], errors="ignore")
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for k, v in result.items():
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result[k] = _postprocessRocData(pandas.DataFrame(v, columns=RESULT_ALLCOLUMNS))
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diff --git a/src/python/Haplo/partialcredit.py b/src/python/Haplo/partialcredit.py
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index d9e22bb..0f2b2cf 100644
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--- a/src/python/Haplo/partialcredit.py
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+++ b/src/python/Haplo/partialcredit.py
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@@ -202,7 +202,7 @@ def partialCredit(vcfname,
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try:
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res = runParallel(pool,
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preprocessWrapper,
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- itertools.izip(itertools.repeat(vcfname), locations),
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+ zip(itertools.repeat(vcfname), locations),
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{"reference": reference,
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"decompose": decompose,
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"leftshift": leftshift,
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diff --git a/src/python/Haplo/quantify.py b/src/python/Haplo/quantify.py
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index 042d13e..b1d362e 100755
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--- a/src/python/Haplo/quantify.py
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+++ b/src/python/Haplo/quantify.py
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@@ -152,7 +152,7 @@ def run_quantify(filename,
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run_str += " -v %s" % pipes.quote(write_vcf)
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if regions:
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- for k, v in regions.iteritems():
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+ for k, v in regions.items():
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run_str += " -R '%s:%s'" % (k, v)
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if roc_regions:
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diff --git a/src/python/Somatic/Mutect.py b/src/python/Somatic/Mutect.py
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index 7ac923c..81f08b5 100755
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--- a/src/python/Somatic/Mutect.py
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+++ b/src/python/Somatic/Mutect.py
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@@ -148,7 +148,7 @@ def extractMutectSNVFeatures(vcfname, tag, avg_depth=None):
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n_allele_alt_count = 0
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else:
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n_allele_alt_count = 0
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- for a in xrange(0, len(alleles_alt)):
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+ for a in range(0, len(alleles_alt)):
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n_allele_alt_count += float(rec[n_sample + "AD"][a + 1])
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if n_allele_alt_count + n_allele_ref_count == 0:
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@@ -163,7 +163,7 @@ def extractMutectSNVFeatures(vcfname, tag, avg_depth=None):
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t_allele_alt_count = 0
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else:
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t_allele_alt_count = 0
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- for a in xrange(0, len(alleles_alt)):
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+ for a in range(0, len(alleles_alt)):
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t_allele_alt_count += float(rec[t_sample + "AD"][a + 1])
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if t_allele_alt_count + t_allele_ref_count == 0:
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@@ -344,7 +344,7 @@ def extractMutectIndelFeatures(vcfname, tag, avg_depth=None):
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n_allele_alt_count = 0
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else:
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n_allele_alt_count = 0
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- for a in xrange(0, len(alleles_alt)):
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+ for a in range(0, len(alleles_alt)):
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n_allele_alt_count += float(rec[n_sample + "AD"][a + 1])
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if n_allele_alt_count + n_allele_ref_count == 0:
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@@ -359,7 +359,7 @@ def extractMutectIndelFeatures(vcfname, tag, avg_depth=None):
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t_allele_alt_count = 0
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else:
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t_allele_alt_count = 0
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- for a in xrange(0, len(alleles_alt)):
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+ for a in range(0, len(alleles_alt)):
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t_allele_alt_count += float(rec[t_sample + "AD"][a + 1])
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if t_allele_alt_count + t_allele_ref_count == 0:
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diff --git a/src/python/Tools/bcftools.py b/src/python/Tools/bcftools.py
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index 6146b7a..6d80d14 100755
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--- a/src/python/Tools/bcftools.py
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+++ b/src/python/Tools/bcftools.py
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@@ -128,8 +128,8 @@ def concatenateParts(output, *args):
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to_delete.append(tf2.name)
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to_delete.append(tf1.name + ".csi")
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to_delete.append(tf2.name + ".csi")
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- half1 = [tf1.name] + list(args[:len(args)/2])
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- half2 = [tf2.name] + list(args[len(args)/2:])
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+ half1 = [tf1.name] + list(args[:len(args)//2])
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+ half2 = [tf2.name] + list(args[len(args)//2:])
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concatenateParts(*half1)
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runBcftools("index", tf1.name)
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concatenateParts(*half2)
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diff --git a/src/python/Tools/metric.py b/src/python/Tools/metric.py
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index 71ccc99..372626d 100755
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--- a/src/python/Tools/metric.py
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+++ b/src/python/Tools/metric.py
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@@ -115,7 +115,7 @@ def replaceNaNs(xobject):
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if type(xobject[k]) is dict or type(xobject[k]) is list or type(xobject[k]) is float:
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xobject[k] = replaceNaNs(xobject[k])
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elif type(xobject) is list:
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- for k in xrange(0, len(xobject)):
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+ for k in range(0, len(xobject)):
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if type(xobject[k]) is dict or type(xobject[k]) is list or type(xobject[k]) is float:
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xobject[k] = replaceNaNs(xobject[k])
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elif type(xobject) is float:
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diff --git a/src/python/Tools/parallel.py b/src/python/Tools/parallel.py
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index 9d49760..5fcb37e 100755
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--- a/src/python/Tools/parallel.py
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+++ b/src/python/Tools/parallel.py
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@@ -17,9 +17,9 @@ import logging
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import traceback
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import subprocess
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import multiprocessing
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-import cPickle
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+import pickle
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import tempfile
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-from itertools import islice, izip, repeat
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+from itertools import islice, repeat
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from . import LoggingWriter
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@@ -93,7 +93,7 @@ def runParallel(pool, fun, par, *args, **kwargs):
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"""
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if pool:
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- result = pool.map(parMapper, izip(par, repeat( { "fun": fun, "args": args, "kwargs": kwargs } )))
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+ result = pool.map(parMapper, zip(par, repeat( { "fun": fun, "args": args, "kwargs": kwargs } )))
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else:
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result = []
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for c in par:
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diff --git a/src/python/Tools/sessioninfo.py b/src/python/Tools/sessioninfo.py
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index 75650ec..b49bf59 100644
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--- a/src/python/Tools/sessioninfo.py
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+++ b/src/python/Tools/sessioninfo.py
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@@ -34,7 +34,6 @@ def sessionInfo():
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'version': version,
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'runInfo': [{"key": "commandline", "value": " ".join(sys.argv)}],
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'uname': " / ".join(platform.uname()),
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- 'dist': " / ".join(platform.dist()),
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'mac_ver': " / ".join([platform.mac_ver()[0], platform.mac_ver()[2]]),
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'python_implementation': platform.python_implementation(),
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'python_version': platform.python_version(),
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diff --git a/src/python/Tools/vcfcallerinfo.py b/src/python/Tools/vcfcallerinfo.py
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index eb7e86e..947f2c4 100755
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--- a/src/python/Tools/vcfcallerinfo.py
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+++ b/src/python/Tools/vcfcallerinfo.py
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@@ -33,8 +33,8 @@ class CallerInfo(object):
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def asDict(self):
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kvd = ["name", "version", "parameters"]
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- return {"aligners": [dict(y for y in itertools.izip(kvd, x)) for x in self.aligners],
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- "callers": [dict(y for y in itertools.izip(kvd, x)) for x in self.callers]}
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+ return {"aligners": [dict(y for y in zip(kvd, x)) for x in self.aligners],
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+ "callers": [dict(y for y in zip(kvd, x)) for x in self.callers]}
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def addVCF(self, vcfname):
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""" Add caller versions from a VCF
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diff --git a/src/python/hap.py b/src/python/hap.py
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index 8045936..93279a4 100755
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--- a/src/python/hap.py
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+++ b/src/python/hap.py
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@@ -188,7 +188,7 @@ def main():
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parser.print_help()
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exit(1)
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- print "Hap.py %s" % Tools.version
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+ print("Hap.py %s" % Tools.version)
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if args.version:
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exit(0)
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diff --git a/src/python/ovc.py b/src/python/ovc.py
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index 2837255..20b4442 100755
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--- a/src/python/ovc.py
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+++ b/src/python/ovc.py
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@@ -34,7 +34,7 @@ lines = 1
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for line in f:
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l = line.split("\t")
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if len(l) > 3 and (last-1) > int(l[1]):
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- print "Overlap at %s:%i (line %i)" % (l[0], int(l[1]), lines)
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+ print(Overlap at %s:%i (line %i)) % (l[0], int(l[1]), lines)
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exit(1)
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elif len(l) > 3:
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last = int(l[2])
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diff --git a/src/python/pre.py b/src/python/pre.py
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index 5ca1644..a37a4b2 100755
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--- a/src/python/pre.py
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+++ b/src/python/pre.py
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@@ -47,8 +47,8 @@ import Haplo.partialcredit
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def hasChrPrefix(chrlist):
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""" returns if list of chr names has a chr prefix or not """
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- noprefix = map(str, range(23)) + ["X", "Y", "MT"]
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- withprefix = ["chr" + x for x in map(str, range(23)) + ["X", "Y", "M"]]
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+ noprefix = [str(x) for x in range(23)] + ["X", "Y", "MT"]
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+ withprefix = ["chr" + str(x) for x in range(23)] + ["X", "Y", "M"]
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count_noprefix = len(list(set(noprefix) & set(chrlist)))
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count_prefix = len(list(set(withprefix) & set(chrlist)))
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@@ -126,7 +126,7 @@ def preprocess(vcf_input,
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if gender == "auto":
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logging.info(mf)
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- if "female" in mf:
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+ if b"female" in mf:
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gender = "female"
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else:
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gender = "male"
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@@ -392,7 +392,7 @@ def main():
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exit(0)
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if args.version:
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- print "pre.py %s" % Tools.version # noqa:E999
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+ print(pre.py %s) % Tools.version # noqa:E999
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exit(0)
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args.input = args.input[0]
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diff --git a/src/python/qfy.py b/src/python/qfy.py
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index 4f247ee..59ed68a 100755
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--- a/src/python/qfy.py
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+++ b/src/python/qfy.py
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@@ -203,8 +203,8 @@ def quantify(args):
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# in default mode, print result summary to stdout
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if not args.quiet and not args.verbose:
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- print "Benchmarking Summary:"
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- print essential_numbers.to_string(index=False)
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+ print("Benchmarking Summary:")
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+ print(essential_numbers.to_string(index=False))
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# keep this for verbose output
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if not args.verbose:
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@@ -213,12 +213,12 @@ def quantify(args):
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except:
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pass
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- for t in res.iterkeys():
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+ for t in res.keys():
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metrics_output["metrics"].append(dataframeToMetricsTable("roc." + t, res[t]))
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# gzip JSON output
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if args.write_json:
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with gzip.open(args.reports_prefix + ".metrics.json.gz", "w") as fp:
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- json.dump(metrics_output, fp)
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+ fp.write(json.dumps(metrics_output, default=np_encoder).encode('ascii'))
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@@ -362,7 +363,7 @@ def main():
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exit(0)
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if args.version:
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- print "qfy.py %s" % Tools.version
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+ print(qfy.py %s) % Tools.version
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exit(0)
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if args.fp_bedfile and args.preprocessing_truth_confregions:
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diff --git a/src/python/som.py b/src/python/som.py
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index e942351..c01d522 100755
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--- a/src/python/som.py
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+++ b/src/python/som.py
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@@ -640,7 +640,7 @@ def main():
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"overlap):\n" + ambie.to_string(index=False))
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# in default mode, print result summary to stdout
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if not args.quiet and not args.verbose:
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- print "FP/ambiguity classes with info (multiple classes can " \
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+ print(FP/ambiguity classes with info (multiple classes can ) \
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"overlap):\n" + ambie.to_string(index=False)
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ambie.to_csv(args.output + ".ambiclasses.csv")
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metrics_output["metrics"].append(dataframeToMetricsTable("ambiclasses", ambie))
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@@ -659,7 +659,7 @@ def main():
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formatters={'reason': '{{:<{}s}}'.format(ambie['reason'].str.len().max()).format}, index=False))
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# in default mode, print result summary to stdout
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if not args.quiet and not args.verbose:
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- print "Reasons for defining as ambiguous (multiple reasons can overlap):\n" + ambie.to_string(
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+ print(Reasons for defining as ambiguous (multiple reasons can overlap):\n) + ambie.to_string(
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formatters={'reason': '{{:<{}s}}'.format(ambie['reason'].str.len().max()).format}, index=False)
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ambie.to_csv(args.output + ".ambireasons.csv")
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metrics_output["metrics"].append(dataframeToMetricsTable("ambireasons", ambie))
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@@ -936,7 +936,7 @@ def main():
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logging.info("\n" + res.to_string())
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# in default mode, print result summary to stdout
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if not args.quiet and not args.verbose:
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- print "\n" + res.to_string()
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+ print(\n) + res.to_string()
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res["sompyversion"] = vstring
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diff --git a/src/python/qfy.py b/src/python/qfy.py
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index 59ed68a..be8d7e1 100755
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--- a/src/python/qfy.py
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+++ b/src/python/qfy.py
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@@ -33,6 +33,7 @@ import pandas
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import json
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import tempfile
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import gzip
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+import numpy as np
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scriptDir = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
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sys.path.append(os.path.abspath(os.path.join(scriptDir, '..', 'lib', 'python27')))
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@@ -45,6 +46,10 @@ import Haplo.happyroc
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import Haplo.gvcf2bed
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from Tools import fastasize
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+# Cannot convert data to json without a custom enconder
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+def np_encoder(object):
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+ if isinstance(object, np.generic):
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+ return object.item()
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def quantify(args):
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""" Run quantify and write tables """
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