Mercurial > repos > cpt > cpt_find_spanins

changeset 4:673d1776d3b9 draft

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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:51:06 +0000
parents fd70980a516b
children 46b252c89e9e
files findSpanin.py findSpanin.xml
diffstat 2 files changed, 11 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/findSpanin.py	Mon Jun 05 02:42:01 2023 +0000
+++ b/findSpanin.py	Fri Jan 05 05:51:06 2024 +0000
@@ -19,6 +19,7 @@
 #### INPUT : putative_isp.fa & putative_osp.fa (in that order)
 #### PARAMETERS :
 
+
 ###############################################################################
 def write_output(candidates):
     """output file function...maybe not needed"""
@@ -132,7 +133,6 @@
             spanin_data["positive"]["amt_positive"] = 0
             spanin_data["positive"]["pos_amt_unique"] = 0
         if spanin_data["negative"]["coords"]:
-
             # do something else...
             # print('in other function')
             # print(spanin_data['negative']['coords'])
@@ -196,7 +196,6 @@
 
 
 if __name__ == "__main__":
-
     # Common parameters for both ISP / OSP portion of script
 
     parser = argparse.ArgumentParser(
@@ -330,8 +329,7 @@
                         for k, v in SPANIN_TYPES["EMBEDDED"].items():
                             # print(k)
                             f.writelines(
-                                ""
-                                + str(k)
+                                +str(k)
                                 + " ==> Amount of corresponding candidate o-spanins(s): "
                                 + str(len(v))
                                 + "\n"
@@ -339,8 +337,7 @@
                     if each_spanin_type == "SEPARATED":
                         for k, v in SPANIN_TYPES["SEPARATED"].items():
                             f.writelines(
-                                ""
-                                + str(k)
+                                +str(k)
                                 + " ==> Amount of corresponding candidate o-spanins(s): "
                                 + str(len(v))
                                 + "\n"
@@ -348,8 +345,7 @@
                     if each_spanin_type == "OVERLAPPED":
                         for k, v in SPANIN_TYPES["OVERLAPPED"].items():
                             f.writelines(
-                                ""
-                                + str(k)
+                                +str(k)
                                 + " ==> Amount of corresponding candidate o-spanins(s): "
                                 + str(len(v))
                                 + "\n"
@@ -414,15 +410,13 @@
                     if each_posp[6] == "+":
                         if each_posp[2] in pair_dict["pairs"]["pair_number"].keys():
                             f.write(
-                                ""
-                                + str(pair_dict["pairs"]["pair_number"][each_posp[2]])
+                                +str(pair_dict["pairs"]["pair_number"][each_posp[2]])
                                 + "\n"
                             )
                     elif each_posp[6] == "-":
                         if each_posp[1] in pair_dict["pairs"]["pair_number"].keys():
                             f.write(
-                                ""
-                                + str(pair_dict["pairs"]["pair_number"][each_posp[1]])
+                                +str(pair_dict["pairs"]["pair_number"][each_posp[1]])
                                 + "\n"
                             )
         else:
@@ -491,15 +485,13 @@
                         if each_posp[2] in pair_dict["pairs"]["pair_number"].keys():
                             # print('ovl ; +')
                             f.write(
-                                ""
-                                + str(pair_dict["pairs"]["pair_number"][each_posp[2]])
+                                +str(pair_dict["pairs"]["pair_number"][each_posp[2]])
                                 + "\n"
                             )
                     elif each_posp[6] == "-":
                         if each_posp[1] in pair_dict["pairs"]["pair_number"].keys():
                             f.write(
-                                ""
-                                + str(pair_dict["pairs"]["pair_number"][each_posp[1]])
+                                +str(pair_dict["pairs"]["pair_number"][each_posp[1]])
                                 + "\n"
                             )
         else:
@@ -565,15 +557,13 @@
                     if each_posp[6] == "+":
                         if each_posp[2] in pair_dict["pairs"]["pair_number"].keys():
                             f.write(
-                                ""
-                                + str(pair_dict["pairs"]["pair_number"][each_posp[2]])
+                                +str(pair_dict["pairs"]["pair_number"][each_posp[2]])
                                 + "\n"
                             )
                     elif each_posp[6] == "-":
                         if each_posp[1] in pair_dict["pairs"]["pair_number"].keys():
                             f.write(
-                                ""
-                                + str(pair_dict["pairs"]["pair_number"][each_posp[1]])
+                                +str(pair_dict["pairs"]["pair_number"][each_posp[1]])
                                 + "\n"
                             )
         else:
--- a/findSpanin.xml	Mon Jun 05 02:42:01 2023 +0000
+++ b/findSpanin.xml	Fri Jan 05 05:51:06 2024 +0000
@@ -2,7 +2,7 @@
     <description>With the outputs from the ISP and OSP candidate tools, cull the list down to candidate pairs</description>
     <macros>
         <import>macros.xml</import>
-        <import>cpt-macros.xml</import>
+    
     </macros>
     <expand macro="requirements">
     </expand>