flake8 fixes

prinia/__init__.py

-from builtins import (ascii, bytes, chr, dict, filter, hex, input,
-                      int, map, next, oct, open, pow, range, round,
-                      str, super, zip)
 __author__ = 'ahbbollen'

prinia/design.py

-from builtins import (ascii, bytes, chr, dict, filter, hex, input,
-                      map, next, oct, open, pow, range, round,
-                      str, super, zip)
+from builtins import (map, open, str)
 __author__ = 'ahbbollen'
 
 from tempfile import NamedTemporaryFile
@@ -17,7 +15,8 @@ from .primer3 import Primer3, parse_primer3_output
 from .utils import (NoPrimersException, calc_gc, NEW_VCF,
                     generate_fastq_from_primers, is_at_least_version_samtools)
 
-PRIMER3_SCRIPT = os.path.join(os.path.join(os.path.dirname(__file__) ,"static"), 'getprimers.sh')
+PRIMER3_SCRIPT = os.path.join(os.path.join(os.path.dirname(__file__),
+                                           "static"), 'getprimers.sh')
 
 
 def get_sequence_fasta(region, reference=None, padding=True):
@@ -76,16 +75,17 @@ def samtools_version_check(samtools_exe):
         return True
 
 
-def aln_primers(primers, bwa_exe=None, samtools_exe=None, ref=None, output_bam=None):
+def aln_primers(primers, bwa_exe=None, samtools_exe=None, ref=None,
+                output_bam=None):
     """
-    Align primers with BWA. 
-    This only works with BWA-ALN due to the short read length. 
+    Align primers with BWA.
+    This only works with BWA-ALN due to the short read length.
     :param primers: List of primers
     :param bwa_exe: Path to BWA
     :param samtools_exe: Path to samtools
     :param ref: Path to reference fasta
     :param output_bam: Path to final bam file
-    :return: instance of pysam.AlignmentFile 
+    :return: instance of pysam.AlignmentFile
     """
     fq1 = NamedTemporaryFile()
     fq2 = NamedTemporaryFile()
@@ -104,7 +104,8 @@ def aln_primers(primers, bwa_exe=None, samtools_exe=None, ref=None, output_bam=N
         raise ValueError("bwa aln crashed with error code {0}".format(r))
 
     sam = NamedTemporaryFile()
-    sam_args = [bwa_exe, 'sampe', ref, sai1.name, sai2.name, fq1.name, fq2.name]
+    sam_args = [bwa_exe, 'sampe', ref, sai1.name, sai2.name, fq1.name,
+                fq2.name]
     r = check_call(sam_args, stdout=sam)
     if r != 0:
         raise ValueError("bwa sampe crashed with error code {0}".format(r))
@@ -113,20 +114,27 @@ def aln_primers(primers, bwa_exe=None, samtools_exe=None, ref=None, output_bam=N
     bam_args = [samtools_exe, 'view', '-Shb', sam.name]
     r = check_call(bam_args, stdout=bam)
     if r != 0:
-        raise ValueError("samtools view crashed with error code {0}".format(r))
+        raise ValueError(
+            "samtools view crashed with error code {0}".format(r)
+        )
 
     if samtools_version_check(samtools_exe):
-        final_args = [samtools_exe, 'sort', '-O', 'bam', '-o', output_bam, bam.name]
+        final_args = [samtools_exe, 'sort', '-O', 'bam', '-o', output_bam,
+                      bam.name]
     else:
         final_args = [samtools_exe, 'sort', "-f", bam.name, output_bam]
     r = check_call(final_args)
     if r != 0:
-        raise ValueError("samtools sort crashed with error code {0}".format(r))
+        raise ValueError(
+            "samtools sort crashed with error code {0}".format(r)
+        )
 
     index_args = [samtools_exe, "index", output_bam]
     r = check_call(index_args)
     if r != 0:
-        raise ValueError("samtools index crashed with error code {0}".format(r))
+        raise ValueError(
+            "samtools index crashed with error code {0}".format(r)
+        )
 
     # cleanup
     for i in [fq1, fq2, sai1, sai2, sam, bam]:
@@ -159,7 +167,8 @@ def _has_alternative_alignments(aligned_segment):
     return "XA" in [x[0] for x in tags]
 
 
-def create_primer_from_pair(read1, read2, position=0, reverse_as_complement=True):
+def create_primer_from_pair(read1, read2, position=0,
+                            reverse_as_complement=True):
     """Create primer from read pair"""
     if reverse_as_complement:
         seq = Seq(read2.query_sequence)
@@ -182,11 +191,11 @@ def create_primer_from_pair(read1, read2, position=0, reverse_as_complement=True
 
 def create_primers_bwa(bam_handle, variant=None, region=None):
     """
-    Find correct pairs in a bam file containing primers for a variant or region    
+    Find correct pairs in a bam file containing primers for a variant or region
     This requires to hold the bam file in memory. Use only with small bam files
     :param bam_handle: pysam.AlignmentFile instance
     :param variant: variant
-    :param region: region 
+    :param region: region
     :return: generator of primers
     """
     if variant is not None and region is not None:
@@ -236,13 +245,16 @@ def create_primers_bwa(bam_handle, variant=None, region=None):
             continue
 
         if variant is not None:
-            yield create_primer_from_pair(pair['r1'], pair['r2'], variant.position_g_start)
+            yield create_primer_from_pair(pair['r1'], pair['r2'],
+                                          variant.position_g_start)
         else:
-            position = int(region.start) + int((float((int(region.stop) - int(region.start)))/2))
+            position = int(region.start) + int((float(
+                (int(region.stop) - int(region.start)))/2))
             yield create_primer_from_pair(pair['r1'], pair['r2'], position)
 
 
-def find_best_bwa(bam, variant=None, region=None, accept_snp=False, field=None, max_freq=None, dbsnp=None):
+def find_best_bwa(bam, variant=None, region=None, accept_snp=False,
+                  field=None, max_freq=None, dbsnp=None):
     primers = []
     for primer in create_primers_bwa(bam, variant=variant, region=region):
         if not accept_snp and max_freq is not None and dbsnp is not None:
@@ -280,7 +292,7 @@ def _freq_in_query(query, field):
 def find_snps(primer, db_snp=None, field="AF"):
     try:
         import vcf
-    except:
+    except ImportError:
         return None
 
     if db_snp is None:
@@ -293,10 +305,12 @@ def find_snps(primer, db_snp=None, field="AF"):
 
     contigs = list(reader.contigs.keys())
     if len(contigs) == 0:
-        raise ValueError("The VCF file does not contain contigs in the header.")
-    if "chr" in contigs[0] and not "chr" in primer.chromosome:
+        raise ValueError(
+            "The VCF file does not contain contigs in the header."
+        )
+    if "chr" in contigs[0] and "chr" not in primer.chromosome:
         chrom = "chr" + primer.chromosome
-    elif "chr" in primer.chromosome and not "chr" in contigs[0]:
+    elif "chr" in primer.chromosome and "chr" not in contigs[0]:
         chrom = primer.chromosome.split("chr")[1]
     else:
         chrom = primer.chromosome
@@ -308,7 +322,8 @@ def find_snps(primer, db_snp=None, field="AF"):
 
     left_n, left_freqs = _freq_in_query(query, field)
 
-    # can't have two pysam queries open at the same time, so have to do this this way
+    # can't have two pysam queries open at the same time,
+    # so have to do this this way
     if NEW_VCF:
         right_query = reader.fetch(chrom, int(primer.right_pos), right_end)
     else:
@@ -336,8 +351,10 @@ def chop_region(region, size):
     """
     if len(region) <= size:
         return [region]
-    first = Region(chromosome=region.chr, start=region.start, stop=region.start+size,
-                   acc_nr=region.acc_nr, padding_left=region.padding_left, padding_right=region.padding_right,
+    first = Region(chromosome=region.chr, start=region.start,
+                   stop=region.start+size,
+                   acc_nr=region.acc_nr, padding_left=region.padding_left,
+                   padding_right=region.padding_right,
                    other=region.other_information)
     regions = [first]
     while sum([len(x) for x in regions]) < len(region):
@@ -347,8 +364,10 @@ def chop_region(region, size):
         else:
             stop = last.stop + size
 
-        nex = Region(chromosome=region.chr, start=last.stop, stop=stop, acc_nr=region.acc_nr,
-                     padding_left=region.padding_left, padding_right=region.padding_right,
+        nex = Region(chromosome=region.chr, start=last.stop,
+                     stop=stop, acc_nr=region.acc_nr,
+                     padding_left=region.padding_left,
+                     padding_right=region.padding_right,
                      other=region.other_information)
         regions.append(nex)
     return regions
@@ -375,23 +394,30 @@ def get_primer_from_region(region, reference, product_size, n_prims,
                                   product_size=product_size,
                                   n_primers=n_prims, prim3_exe=primer3_exe,
                                   **prim_args)
-        bam = aln_primers(raw_primers, bwa_exe=bwa_exe, samtools_exe=samtools_exe,
+        bam = aln_primers(raw_primers, bwa_exe=bwa_exe,
+                          samtools_exe=samtools_exe,
                           ref=reference, output_bam=output_bam)
-        prims = find_best_bwa(bam, region=reg, dbsnp=dbsnp, field=field, max_freq=max_freq)
+        prims = find_best_bwa(bam, region=reg, dbsnp=dbsnp, field=field,
+                              max_freq=max_freq)
         tmp_reg = []
         tmp_prim = []
 
         # filter out primers too close to the variant
         for primer in prims:
-            if not (int(primer.left_pos) + int(primer.left_len) + min_margin) < int(reg.start):
+            if not (int(primer.left_pos) + int(primer.left_len) + min_margin
+                    ) < int(reg.start):
                 continue
             if not (int(primer.right_pos) - min_margin) > int(reg.stop):
                 continue
 
-            n_region = Region(start=int(primer.left_pos), stop=int(primer.right_pos)+len(primer.right),
-                              chromosome=primer.chromosome, padding_left=0, padding_right=0,
+            n_region = Region(start=int(primer.left_pos),
+                              stop=int(primer.right_pos)+len(primer.right),
+                              chromosome=primer.chromosome,
+                              padding_left=0, padding_right=0,
                               acc_nr="NA", other="NA")
-            primer.fragment_sequence = get_sequence_fasta(n_region, reference=reference, padding=False)
+            primer.fragment_sequence = get_sequence_fasta(n_region,
+                                                          reference=reference,
+                                                          padding=False)
             if strict and len(primer.fragment_sequence) > max_length:
                 continue
             else:

prinia/lovd.py

-from builtins import (ascii, bytes, chr, dict, filter, hex, input,
-                      map, next, oct, open, pow, range, round,
-                      str, super, zip)
+from builtins import (map, open, str, zip)
 
 __author__ = 'ahbbollen'
 
@@ -39,7 +37,9 @@ def var_from_lovd(path):
             elif seen_header:
                 data_lines += 1
                 contents = line.split("\t")
-                assert len(contents) == len(d.keys()), "Different amount of values in data line?"
+                if len(contents) != len(d.keys()):
+                    raise ValueError("Number of data fields does not "
+                                     "match number of headers.")
                 for header, field in zip(d.keys(), contents):
                     if field.strip('""'):
                         d[header].append(field.strip('""'))
@@ -52,7 +52,3 @@ def var_from_lovd(path):
     comments["n_line"] = data_lines
 
     return Variant.from_dict(d, comments)
-
-
-
-

prinia/miracle_xml.py

-from builtins import (ascii, bytes, chr, dict, filter, hex, input,
-                      map, next, oct, open, pow, range, round,
-                      str, super, zip)
-
 """
 Parsing of Miracle XML files
 """
@@ -12,12 +8,14 @@ from io import StringIO
 from datetime import datetime
 from lxml import etree
 
-DEFAULT_XSD = os.path.join(os.path.join(os.path.dirname(__file__), "static"), 'variant.xsd')
-REGION_XSD = os.path.join(os.path.join(os.path.dirname(__file__), "static"), 'region.xsd')
-
-from .models import *
+from .models import Variant, Primer
 from .utils import calc_gc, datehash
 
+DEFAULT_XSD = os.path.join(os.path.join(os.path.dirname(__file__), "static"),
+                           'variant.xsd')
+REGION_XSD = os.path.join(os.path.join(os.path.dirname(__file__), "static"),
+                          'region.xsd')
+
 try:
     from itertools import zip_longest as longzip
 except ImportError:
@@ -95,7 +93,8 @@ def miracle_to_primer_and_var(xml, xsd=DEFAULT_XSD):
             var.allele = 'Heterozygous'
         elif item.find('UITSLAG_CODE').text == 'HOM':
             var.allele = 'Homozygous'
-        # FIXME: should include cases of maternally hemizygous and paternally hemizygous
+        # FIXME: should include cases of maternally hemizygous and
+        # paternally hemizygous
         else:
             var.allele = 'NA'
 
@@ -182,15 +181,19 @@ def primer_to_xml(root, prim, var):
     return root
 
 
-def vars_and_primers_to_xml(variants, primers, xml_path=None, xsd=DEFAULT_XSD, old=True):
+def vars_and_primers_to_xml(variants, primers, xml_path=None, xsd=DEFAULT_XSD,
+                            old=True):
     panel = int(variants[0].in_gene_panel) == 1
 
     if old:
-        xsd = os.path.join(os.path.join(os.path.dirname(__file__), 'static'), 'variant.xsd')
+        xsd = os.path.join(os.path.join(os.path.dirname(__file__), 'static'),
+                           'variant.xsd')
     else:
-        xsd = os.path.join(os.path.join(os.path.dirname(__file__), 'static'), 'variant_new.xsd')
+        xsd = os.path.join(os.path.join(os.path.dirname(__file__), 'static'),
+                           'variant_new.xsd')
 
-    document, results = common_xml(variants[0].miracle_id, variants[0].datum, panel, old=old)
+    document, results = common_xml(variants[0].miracle_id, variants[0].datum,
+                                   panel, old=old)
     i = 1
 
     for var, prim in longzip(variants, primers, fillvalue=None):
@@ -218,7 +221,7 @@ def vars_and_primers_to_xml(variants, primers, xml_path=None, xsd=DEFAULT_XSD, o
         name = etree.SubElement(gene, "NAAM")
         name.text = var.gene_name
 
-        loc = etree.SubElement(gene, "LOCATIE")
+        loc = etree.SubElement(gene, "LOCATIE")  # noqa
         build = etree.SubElement(variant, "BUILD")
         build.text = var.refseq_build
 
@@ -244,9 +247,11 @@ def vars_and_primers_to_xml(variants, primers, xml_path=None, xsd=DEFAULT_XSD, o
 
         if prim is not None:
             frag_len = etree.SubElement(prims, "FRAGMENT_LENGTH")
-            # fragment is the region between the end of the forward primer, and the start of the reverse primer
+            # fragment is the region between the end of the forward primer,
+            #  and the start of the reverse primer
 
-            frag_len.text = str(int(prim.right_pos) - (int(prim.left_pos) + len(prim.left)))
+            frag_len.text = str(int(prim.right_pos) - (int(prim.left_pos) +
+                                                       len(prim.left)))
 
             gc_perc = etree.SubElement(prims, "GC_PERC")
 
@@ -254,7 +259,7 @@ def vars_and_primers_to_xml(variants, primers, xml_path=None, xsd=DEFAULT_XSD, o
                 gc_perc.text = str(int(calc_gc(prim.fragment_sequence)))
             except ValueError:
                 gc_perc.text = '0'
-            _ = primer_to_xml(prims, prim, var)
+            _ = primer_to_xml(prims, prim, var)  # noqa
         else:
             comment = etree.SubElement(uitslag, "OPMERKING")
             comment.text = "NO PRIMERS FOUND"
@@ -308,11 +313,15 @@ def vars_and_primers_to_xml(variants, primers, xml_path=None, xsd=DEFAULT_XSD, o
     return xml
 
 
-def regions_and_primers_to_xml(variants, primers, xml_path=None, xsd=REGION_XSD, sample='', build="GRCh37", old=True):
+def regions_and_primers_to_xml(variants, primers, xml_path=None,
+                               xsd=REGION_XSD, sample='', build="GRCh37",
+                               old=True):
     if old:
-        xsd = os.path.join(os.path.join(os.path.dirname(__file__), 'static'),'region.xsd')
+        xsd = os.path.join(os.path.join(os.path.dirname(__file__), 'static'),
+                           'region.xsd')
     else:
-        xsd = os.path.join(os.path.join(os.path.dirname(__file__), 'static'), 'region_new.xsd')
+        xsd = os.path.join(os.path.join(os.path.dirname(__file__), 'static'),
+                           'region_new.xsd')
     document, results = common_xml(sample, '', old=old)
     i = 1
 
@@ -333,8 +342,10 @@ def regions_and_primers_to_xml(variants, primers, xml_path=None, xsd=REGION_XSD,
         code = etree.SubElement(gene, "CODE")
         if region.other_information != "NA":
             try:
-                code.text = region.other_information.split(",")[0].split("|")[0]
-            except:
+                code.text = region.other_information.split(
+                    ","
+                )[0].split("|")[0]
+            except IndexError:
                 code.text = ""
         else:
             code.text = ""
@@ -357,7 +368,8 @@ def regions_and_primers_to_xml(variants, primers, xml_path=None, xsd=REGION_XSD,
         if "NA" in region.other_information:
             f_code.text = prim.left_name + "." + datehash()
         else:
-            f_code.text = region.other_information.split("|")[0] + "_F." + datehash()
+            f_code.text = (region.other_information.split("|")[0] + "_F." +
+                           datehash())
         f_seq = etree.SubElement(primer_f, "SEQUENTIE")
         f_seq.text = prim.left
         f_coord = etree.SubElement(primer_f, "COORDINATE")
@@ -368,7 +380,8 @@ def regions_and_primers_to_xml(variants, primers, xml_path=None, xsd=REGION_XSD,
         if "NA" in region.other_information:
             r_code.text = prim.right_name + "." + datehash()
         else:
-            r_code.text = region.other_information.split("|")[0] + "_R." + datehash()
+            r_code.text = (region.other_information.split("|")[0] + "_R." +
+                           datehash())
         r_seq = etree.SubElement(primer_r, "SEQUENTIE")
         r_seq.text = prim.right
         r_coord = etree.SubElement(primer_r, "COORDINATE")

prinia/models.py

-from builtins import (ascii, bytes, chr, dict, filter, hex, input,
-                      map, next, oct, open, pow, range, round,
-                      str, super, zip)
+from builtins import (range, str)
 
 __author__ = 'ahbbollen'
 
@@ -48,14 +46,22 @@ class Variant(object):
             for k in dictionary.keys():
                 try:
                     setattr(x, k, dictionary[k][n])
-                except:
+                except:  # noqa
                     pass
 
             x.variant_on_genome = dictionary["VariantOnGenome/DNA"][n]
-            x.variant_on_transcript_dna = dictionary["VariantOnTranscript/DNA"][n]
-            x.variant_on_transcript_rna = dictionary["VariantOnTranscript/RNA"][n]
-            x.variant_on_transcript_protein = dictionary["VariantOnTranscript/Protein"][n]
-            x.variant_on_genome_origin = dictionary["VariantOnGenome/Genetic_origin"][n]
+            x.variant_on_transcript_dna = dictionary[
+                "VariantOnTranscript/DNA"
+            ][n]
+            x.variant_on_transcript_rna = dictionary[
+                "VariantOnTranscript/RNA"
+            ][n]
+            x.variant_on_transcript_protein = dictionary[
+                "VariantOnTranscript/Protein"
+            ][n]
+            x.variant_on_genome_origin = dictionary[
+                "VariantOnGenome/Genetic_origin"
+            ][n]
 
             if x.confirm_in_lab == "0":
                 x.confirm_in_lab = False
@@ -96,9 +102,10 @@ class Primer(object):
             setattr(self, kw, kv)
 
     @classmethod
-    def from_p3(cls, forward, reverse, fragment=None, chromosome=None, position=None):
+    def from_p3(cls, forward, reverse, fragment=None, chromosome=None,
+                position=None):
         # line looks like this:
-        #    0 CAGCACTGCTTGAGGGGAA                0 19  0 57.89 59.926  0.00  0.00 36.40  1.074
+        # 0 CAGCACTGCTTGAGGGGAA  0 19 0 57.89 59.926 0.00 0.00 36.40 1.074
         f_contents = [x for x in forward.strip().split(" ") if x]
         r_contents = [x for x in reverse.strip().split(" ") if x]
         primer = cls()
@@ -161,8 +168,10 @@ class Region(object):
 
     @classmethod
     def from_variant(cls, variant, padding_l=0, padding_r=0):
-        return cls(chromosome=variant.chromosome, acc_nr=variant.genomic_id_ncbi,
-                   start=variant.position_g_start, stop=variant.position_g_end,
+        return cls(chromosome=variant.chromosome,
+                   acc_nr=variant.genomic_id_ncbi,
+                   start=variant.position_g_start,
+                   stop=variant.position_g_end,
                    padding_left=padding_l,
                    padding_right=padding_r)
 
@@ -175,9 +184,14 @@ class Region(object):
         else:
             other = "NA"
 
-        return cls(chromosome=contents[0], acc_nr='NA',
-                   start=int(contents[1]), stop=int(contents[2]), padding_left=padding_l,
-                   padding_right=padding_r, ref=reference, other=other)
+        return cls(chromosome=contents[0],
+                   acc_nr='NA',
+                   start=int(contents[1]),
+                   stop=int(contents[2]),
+                   padding_left=padding_l,
+                   padding_right=padding_r,
+                   ref=reference,
+                   other=other)
 
     @classmethod
     def cut(cls, region, max_size, padded=False):

prinia/primer3.py

@@ -69,19 +69,17 @@ class Primer3(object):
                   "PRIMER_MIN_TM={it}\n" \
                   "PRIMER_MAX_TM={at}\n" \
                   "PRIMER_NUM_RETURN=200\n" \
-                  "=".format(
-            seq=self.template,
-            tar=self.target,
-            exc=self.excluded_region,
-            gc=self.opt_gc_perc,
-            size=self.opt_prim_length,
-            isize=self.opt_prim_length-5,
-            asize=self.opt_prim_length+5,
-            range=self.range,
-            osize=self.opt_size,
-            it=self.min_melting_t,
-            at=self.max_melting_t
-        )
+                  "=".format(seq=self.template, tar=self.target,
+                             exc=self.excluded_region,
+                             gc=self.opt_gc_perc,
+                             size=self.opt_prim_length,
+                             isize=self.opt_prim_length-5,
+                             asize=self.opt_prim_length+5,
+                             range=self.range,
+                             osize=self.opt_size,
+                             it=self.min_melting_t,
+                             at=self.max_melting_t
+                             )
 
         handle.write(cfg_str)
 
@@ -93,7 +91,7 @@ class Primer3(object):
         cfg.close()
         args = [self.primer3_exe, "-output", out.name, cfg.name]
 
-        _ = check_call(args)
+        _ = check_call(args)  # noqa
 
         retval = []
         with open(out.name) as handle:

prinia/primerdesign.py

-from builtins import (ascii, bytes, chr, dict, filter, hex, input,
-                      map, next, oct, open, pow, range, round,
-                      str, super, zip)
 """
-This script generates primer pairs from either LOVD input or BED files for regions.
+This script generates primer pairs from either LOVD input or BED files for
+regions.
 Output in Miracle XML or TSV
 """
 
 import argparse
 
-from prinia.lovd import *
-from prinia.design import *
-from prinia.miracle_xml import vars_and_primers_to_xml, regions_and_primers_to_xml
+from prinia.lovd import var_from_lovd
+from prinia.design import get_primer_from_region
+from prinia.models import Region
+from prinia.miracle_xml import (vars_and_primers_to_xml,
+                                regions_and_primers_to_xml)
 from prinia.utils import generate_fastq_from_primers, NoPrimersException
 
 __author__ = 'ahbbollen'
@@ -65,7 +65,8 @@ def primers_from_region(bed_path, padding, product_size, n_prims, reference,
             regs, prims = get_primer_from_region(region, reference,
                                                  product_size, n_prims,
                                                  bwa_exe, samtools_exe,
-                                                 primer3_exe, output_bam=output_bam,
+                                                 primer3_exe,
+                                                 output_bam=output_bam,
                                                  dbsnp=dbsnp, field=field,
                                                  max_freq=max_freq,
                                                  strict=strict,
@@ -84,7 +85,8 @@ def primers_to_xml(object, primers, xml, type='variants', sample=None):
     if type == 'variants':
         xml_out = vars_and_primers_to_xml(object, primers, xml)
     elif type == 'regions':
-        xml_out = regions_and_primers_to_xml(object, primers, xml, sample=sample)
+        xml_out = regions_and_primers_to_xml(object, primers, xml,
+                                             sample=sample)
     else:
         raise ValueError("Wrong type specified")
 
@@ -95,21 +97,25 @@ def primers_to_xml(object, primers, xml, type='variants', sample=None):
 def primers_to_tsv(object, primers, tsv, type='variants', sample='NA'):
     with open(tsv, "wb") as handle:
         if type == 'variants':
-            header = ['Sample', 'Chromosome', 'Hgvs (genomic)', 'transcript', 'hgvs (transcript)', 'fragment', 'forward', 'reverse']
+            header = ['Sample', 'Chromosome', 'Hgvs (genomic)', 'transcript',
+                      'hgvs (transcript)', 'fragment', 'forward', 'reverse']
         else:
-            header = ['Sample', 'Chr', 'Start', 'Stop', "size", "search_size", 'other_information',  'fragment', 'forward', 'reverse']
+            header = ['Sample', 'Chr', 'Start', 'Stop', "size", "search_size",
+                      'other_information',  'fragment', 'forward', 'reverse']
         headerline = "\t".join(header) + "\n"
         handle.write(headerline.encode())
 
         for o, prim in zip(object, primers):
             line = []
             if type == 'variants':
-                line += [o.miracle_id, o.chromosome, o.variant_on_genome, o.transcript_id_ncbi,
+                line += [o.miracle_id, o.chromosome, o.variant_on_genome,
+                         o.transcript_id_ncbi,
                          o.variant_on_transcript_dna]
             else:
-                line += [sample, o.chr, o.start, o.stop, len(o), o.size(padded=True), o.other_information]
+                line += [sample, o.chr, o.start, o.stop, len(o),
+                         o.size(padded=True), o.other_information]
             line += [prim.fragment_sequence, prim.left, prim.right]
-            linest = "\t".join(map(str,line)) + "\n"
+            linest = "\t".join(map(str, line)) + "\n"
             handle.write(linest.encode())
 
 
@@ -126,49 +132,77 @@ def main():
     group = parser.add_mutually_exclusive_group(required=True)
     group.add_argument("-l", "--lovd", help="Input LOVD file")
     group.add_argument('--region', help="Input region file")
-    parser.add_argument('-p', '--padding', help="Padding around regions or variants in bases. Defaults to 100",
+    parser.add_argument('-p', '--padding',
+                        help="Padding around regions or variants in bases. "
+                             "Defaults to 100",
                         type=int, default=100)
 
     output_group = parser.add_mutually_exclusive_group(required=True)
     output_group.add_argument('-x', '--xml', help="Output Miracle XML file")
     output_group.add_argument('-t', '--tsv', help="Output TSV file")
 
-    parser.add_argument('-b', '--bam', help="Path to output BAM file containing primers", required=True)
+    parser.add_argument('-b', '--bam',
+                        help="Path to output BAM file containing primers",
+                        required=True)
 
     parser.add_argument('-s', '--sample', help="Same ID for regions")