Mercurial > repos > cpt > cpt_putative_isp

changeset 3:08499fbf8697 draft

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planemo upload commit 96d9c038cdd9f83fcc55d2f20ab1057129d11589-dirty
author cpt
date Wed, 18 Sep 2024 04:02:06 +0000
parents 0a02ef22ce17
children bc16792ecfd2
files cpt.py generate-putative-isp.py generate-putative-isp.xml
diffstat 3 files changed, 4 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- 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
--- 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(
--- 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 @@
     <description>constructs a putative list of potential i-spanin from an input genomic FASTA</description>
     <macros>
         <import>macros.xml</import>
-    
     </macros>
     <expand macro="requirements">
     </expand>