Commit ea30d85e authored by Sander Bollen's avatar Sander Bollen
Browse files

cleanup imports

parent 7b59581d
......@@ -3,23 +3,15 @@ from builtins import (ascii, bytes, chr, dict, filter, hex, input,
str, super, zip)
__author__ = 'ahbbollen'
from tempfile import TemporaryFile, NamedTemporaryFile
from tempfile import NamedTemporaryFile
from subprocess import check_call
import os
import re
import warnings
from time import sleep
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_dna
from fastools.fastools import get_reference
from pyfaidx import Fasta
from pysam import AlignmentFile
from .models import Primer, Region, BlatLine
from .models import Primer, Region
from .utils import NoPrimersException, calc_gc, NEW_VCF, generate_fastq_from_primers
PRIMER3_SCRIPT = os.path.join(os.path.join(os.path.dirname(__file__) ,"static"), 'getprimers.sh')
......@@ -416,4 +408,3 @@ def create_left_prim(primer, reference):
next_left.position = primer_r_pos
return next_left
......@@ -4,35 +4,8 @@ from builtins import (ascii, bytes, chr, dict, filter, hex, input,
__author__ = 'ahbbollen'
from collections import namedtuple
from datetime import datetime
BLAT_FIELDS = [
"match",
"mismatch",
"repmatch",
"N",
"Q_gap_count",
"Q_gap_bases",
"T_gap_count",
"T_gap_bases",
"strand",
"Q_name",
"Q_size",
"Q_start",
"Q_end",
"T_name",
"T_size",
"T_start",
"T_end",
"block_count",
"block_sizes",
"q_starts",
"t_starts"
]
BlatLine = namedtuple("BlatLine", BLAT_FIELDS)
class Variant(object):
"""
......@@ -245,7 +218,3 @@ class Region(object):
other=region.other_information)
return cut, remainder
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