# HG changeset patch
# User cpt
# Date 1726632126 0
# Node ID 08499fbf8697d07dce56b17c8b33cd77dbd5f0e4
# Parent 0a02ef22ce172106e6bdc95efbff09d961b8f2cd
planemo upload commit 96d9c038cdd9f83fcc55d2f20ab1057129d11589-dirty
diff -r 0a02ef22ce17 -r 08499fbf8697 cpt.py
--- a/cpt.py Fri Jan 05 05:56:25 2024 +0000
+++ b/cpt.py Wed Sep 18 04:02:06 2024 +0000
@@ -4,6 +4,7 @@
from Bio import SeqIO
from Bio.Data import CodonTable
import logging
+import 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 0a02ef22ce17 -r 08499fbf8697 generate-putative-isp.py
--- a/generate-putative-isp.py Fri Jan 05 05:56:25 2024 +0000
+++ b/generate-putative-isp.py Wed Sep 18 04:02:06 2024 +0000
@@ -5,20 +5,12 @@
import argparse
from cpt import OrfFinder
-from Bio import SeqIO
-from Bio import Seq
import re
from spaninFuncs import *
-import os
-# if __name__ == '__main__':
-# pass
-###############################################################################
if __name__ == "__main__":
- # Common parameters for both ISP / OSP portion of script
-
parser = argparse.ArgumentParser(
description="Get putative protein candidates for spanins"
)
@@ -212,15 +204,9 @@
pairs = tuple_fasta(fasta_file=args.out_isp_prot)
- # print(pairs)
-
have_tmd = [] # empty candidates list to be passed through the user input criteria
- for (
- each_pair
- ) in (
- pairs
- ): # grab transmembrane domains from spaninFuncts (queries for lysin snorkels # and a range of hydrophobic regions that could be TMDs)
+ for each_pair in pairs:
if len(each_pair[1]) <= args.max_isp:
try:
have_tmd += find_tmd(
diff -r 0a02ef22ce17 -r 08499fbf8697 generate-putative-isp.xml
--- a/generate-putative-isp.xml Fri Jan 05 05:56:25 2024 +0000
+++ b/generate-putative-isp.xml Wed Sep 18 04:02:06 2024 +0000
@@ -2,7 +2,6 @@
constructs a putative list of potential i-spanin from an input genomic FASTA
macros.xml
-