cleanup imports

prinia/design.py

@@ -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
-

prinia/models.py

@@ -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
-
-
-
-