# HG changeset patch
# User cpt
# Date 1726805942 0
# Node ID 46b252c89e9e2564d61cfb0912e1967e746b58ab
# Parent 673d1776d3b98e7d1454e0235b31d54494da9d70
planemo upload commit 25fff8b3887beeb66c2d53e2a32f9af9f34e40b6
diff -r 673d1776d3b9 -r 46b252c89e9e cpt.py
--- a/cpt.py Fri Jan 05 05:51:06 2024 +0000
+++ b/cpt.py Fri Sep 20 04:19:02 2024 +0000
@@ -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 @@
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 @@
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 -r 673d1776d3b9 -r 46b252c89e9e findSpanin.py
--- a/findSpanin.py Fri Jan 05 05:51:06 2024 +0000
+++ b/findSpanin.py Fri Sep 20 04:19:02 2024 +0000
@@ -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 -r 673d1776d3b9 -r 46b252c89e9e findSpanin.xml
--- a/findSpanin.xml Fri Jan 05 05:51:06 2024 +0000
+++ b/findSpanin.xml Fri Sep 20 04:19:02 2024 +0000
@@ -4,8 +4,11 @@
macros.xml
-
-
+
+ python
+ biopython
+ regex
+