# 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 +