Re-implements regex use

The cpt module depended on `regex` and some extra features from it
(opposed to vanilla re from python)

Next, some formatting was applied automatically by my linter.

[#15]

cpt_putative_isp/cpt.py

@@ -4,7 +4,7 @@
 from Bio import SeqIO
 from Bio.Data import CodonTable
 import logging
-import re
+import regex as re
 
 logging.basicConfig()
 log = logging.getLogger()

cpt_putative_isp/generate-putative-isp.py

@@ -5,20 +5,12 @@
 
 import argparse
 from cpt import OrfFinder
-from Bio import SeqIO
-from Bio import Seq
-import re
+import regex as 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(

cpt_putative_isp/generate-putative-isp.xml

@@ -2,9 +2,9 @@
     <description>constructs a putative list of potential i-spanin from an input genomic FASTA</description>
     <macros>
         <import>macros.xml</import>
-
     </macros>
     <expand macro="requirements">
+        <requirement type="package" version="2019.06.08">regex</requirement>
     </expand>
     <command detect_errors="aggressive"><![CDATA[
 python '$__tool_directory__/generate-putative-isp.py'