refmt with newest black

Author: aryarm

haptools/data/breakpoints.py

@@ -12,7 +12,6 @@
 
 from .data import Data
 
-
 # A haplotype block consists of
 # 1) pop   - A population label (str), like 'YRI'
 # 2) chrom - A chromosome name (str), like 'chr19' or simply '19'

haptools/data/genotypes.py

@@ -515,8 +515,7 @@ def check_biallelic(self, discard_also=False):
                 self._var_idx = None
             else:
                 raise ValueError(
-                    "Variant with ID {} at POS {}:{} is multiallelic for sample {}"
-                    .format(
+                    "Variant with ID {} at POS {}:{} is multiallelic for sample {}".format(
                         *tuple(self.variants[variant_idx[0]])[:3],
                         self.samples[samp_idx[0]],
                     )

haptools/data/haplotypes.py

@@ -12,7 +12,6 @@
 from .data import Data
 from .genotypes import GenotypesVCF
 
-
 # the current version of the hap format spec
 HAP_VERSION = "0.2.0"
 

haptools/data/tr_harmonizer.py

@@ -2,6 +2,7 @@
 Utilities for harmonizing tandem repeat VCF records.
 Handles VCFs generated by various TR genotyping tools
 """
+
 import re
 import math
 import enum
@@ -462,8 +463,7 @@ def _HarmonizeHipSTRRecord(vcfrecord: cyvcf2.Variant):
     ):
         raise TypeError(
             "Record at {}:{} is missing one of the mandatory HipSTR info fields START,"
-            " END, PERIOD. ".format(vcfrecord.CHROM, vcfrecord.POS)
-            + _beagle_error
+            " END, PERIOD. ".format(vcfrecord.CHROM, vcfrecord.POS) + _beagle_error
         )
     # determine full alleles and trimmed alleles
     pos = int(vcfrecord.POS)
@@ -536,8 +536,7 @@ def _HarmonizeAdVNTRRecord(vcfrecord: cyvcf2.Variant):
     if vcfrecord.INFO.get("RU") is None or vcfrecord.INFO.get("VID") is None:
         raise TypeError(
             "Record at {}:{} is missing one of the mandatory ADVNTR info fields RU,"
-            " VID. ".format(vcfrecord.CHROM, vcfrecord.POS)
-            + _beagle_error
+            " VID. ".format(vcfrecord.CHROM, vcfrecord.POS) + _beagle_error
         )
     ref_allele = vcfrecord.REF.upper()
     if vcfrecord.ALT:
@@ -651,8 +650,7 @@ def _HarmonizeEHRecord(vcfrecord: cyvcf2.Variant):
     if vcfrecord.INFO.get("VARID") is None or vcfrecord.INFO.get("RU") is None:
         raise TypeError(
             "Record at {}:{} is missing one of the mandatory ExpansionHunter info"
-            " fields VARID, RU. ".format(vcfrecord.CHROM, vcfrecord.POS)
-            + _beagle_error
+            " fields VARID, RU. ".format(vcfrecord.CHROM, vcfrecord.POS) + _beagle_error
         )
     record_id = vcfrecord.INFO["VARID"]
     motif = vcfrecord.INFO["RU"].upper()

tests/bench_genotypes.py

@@ -24,7 +24,6 @@
     GenotypesPLINKTR,
 )
 
-
 # COMMAND FOR GENERATING UKB PLOT:
 # tests/bench_genotypes.py \
 # --default-variants 18472 --default-samples 487409 --intervals-variants 1 80 4 \

tests/bench_transform.py

@@ -17,7 +17,6 @@
 from haptools.logging import getLogger
 from haptools.data import GenotypesVCF, Haplotypes, Haplotype, Variant
 
-
 # ---------------USAGE----------------
 # COMMAND FOR GENERATING THE MAIN PLOT:
 # tests/bench_transform.py --name 'hap-loop' --reps 5 --archive archive.pickle \

tests/test_data.py

@@ -24,7 +24,6 @@
     GenotypesPLINKTR,
 )
 
-
 DATADIR = Path(__file__).parent.joinpath("data")
 
 

tests/test_outputvcf.py

@@ -16,7 +16,6 @@
     write_breakpoints,
 )
 
-
 DATADIR = Path(__file__).parent.joinpath("data")
 
 
@@ -740,8 +739,7 @@ def test_model_files():
             faulty_model, mapdir, chroms, popsize, vcf_file, sampleinfo_file, False
         )
     assert (
-        (str(e.value))
-        == "Current generation 1 - previous generation 4 = -3"
+        (str(e.value)) == "Current generation 1 - previous generation 4 = -3"
         " is less than 1. Please ensure the generations given in the first column"
         " are correct."
     )

tests/test_simgenotype.py

@@ -6,7 +6,6 @@
 from haptools.data import Data
 from haptools.__main__ import main
 
-
 DATADIR = Path(__file__).parent.joinpath("data")
 
 

tests/test_simphenotype.py

@@ -16,7 +16,6 @@
     GenotypesPLINK,
 )
 
-
 DATADIR = Path(__file__).parent.joinpath("data")