diff --git a/cpt_find_spanins/cpt.py b/cpt_find_spanins/cpt.py
index d245cb7..8f15346 100755
--- a/cpt_find_spanins/cpt.py
+++ b/cpt_find_spanins/cpt.py
@@ -4,6 +4,7 @@
from Bio import SeqIO
from Bio.Data import CodonTable
import logging
+import regex as re
logging.basicConfig()
log = logging.getLogger()
@@ -147,7 +148,7 @@ def break_up_frame(self, s):
if index % 3 != 0:
continue
n = s[start:index]
- for (offset, n, t) in self.start_chop_and_trans(n):
+ for offset, n, t in self.start_chop_and_trans(n):
if n and len(t) >= self.min_len:
yield start + offset, n, t
start = index
@@ -294,7 +295,7 @@ def break_up_frame(self, s):
if index % 3 != 0:
continue
n = s[start:index]
- for (offset, n, t) in self.start_chop_and_trans(n):
+ for offset, n, t in self.start_chop_and_trans(n):
if n and len(t) >= self.min_len:
yield start + offset, n, t
start = index
diff --git a/cpt_find_spanins/findSpanin.py b/cpt_find_spanins/findSpanin.py
index 04da73a..818aea5 100755
--- a/cpt_find_spanins/findSpanin.py
+++ b/cpt_find_spanins/findSpanin.py
@@ -2,15 +2,12 @@
######### Much of this code is very "blocked", in the sense that one thing happens...then a function happens on the return...then another function...etc...etc...
import argparse
-import os
import re # new
-import itertools # new
-from collections import Counter, OrderedDict
+from collections import Counter
from spaninFuncs import (
getDescriptions,
grabLocs,
spaninProximity,
- splitStrands,
tuple_fasta,
lineWrapper,
)
diff --git a/cpt_find_spanins/findSpanin.xml b/cpt_find_spanins/findSpanin.xml
index b9051ed..cc10412 100755
--- a/cpt_find_spanins/findSpanin.xml
+++ b/cpt_find_spanins/findSpanin.xml
@@ -4,8 +4,11 @@
macros.xml
-
-
+
+ python
+ biopython
+ regex
+