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, ...@@ -3,23 +3,15 @@ from builtins import (ascii, bytes, chr, dict, filter, hex, input,
str, super, zip) str, super, zip)
__author__ = 'ahbbollen' __author__ = 'ahbbollen'
from tempfile import TemporaryFile, NamedTemporaryFile from tempfile import NamedTemporaryFile
from subprocess import check_call from subprocess import check_call
import os import os
import re
import warnings 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 pyfaidx import Fasta
from pysam import AlignmentFile 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 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') 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): ...@@ -416,4 +408,3 @@ def create_left_prim(primer, reference):
next_left.position = primer_r_pos next_left.position = primer_r_pos
return next_left return next_left
...@@ -4,35 +4,8 @@ from builtins import (ascii, bytes, chr, dict, filter, hex, input, ...@@ -4,35 +4,8 @@ from builtins import (ascii, bytes, chr, dict, filter, hex, input,
__author__ = 'ahbbollen' __author__ = 'ahbbollen'
from collections import namedtuple
from datetime import datetime 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): class Variant(object):
""" """
...@@ -245,7 +218,3 @@ class Region(object): ...@@ -245,7 +218,3 @@ class Region(object):
other=region.other_information) other=region.other_information)
return cut, remainder return cut, remainder
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