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What happens if I push all of nixpkgs
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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.cmakeold mode 100755new mode 100644diff --git a/src/python/Haplo/happyroc.py b/src/python/Haplo/happyroc.pyindex 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.pyindex 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.pyindex 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.pyindex 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.pyindex 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.pyindex 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.pyindex 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.pyindex 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.pyindex 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 VCFdiff --git a/src/python/hap.py b/src/python/hap.pyindex 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.pyindex 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.pyindex 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.pyindex 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.pyindex 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.pyindex 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 """