Mercurial > repos > mheinzl > hd

changeset 5:445442a6aeb0 draft

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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit dda3de3fc961976844f5f44b756fe03e39d3b0db
author mheinzl
date Tue, 15 May 2018 10:56:52 -0400
parents ceb3a9b4bef5
children e76e404c1719
files hd.py hd.xml
diffstat 2 files changed, 11 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/hd.py	Tue May 15 10:47:06 2018 -0400
+++ b/hd.py	Tue May 15 10:56:52 2018 -0400
@@ -457,7 +457,7 @@
     #min_tagsList = []
     #diff11_zeros = []
     #min_tagsList_zeros = []
-    i = 0 # counter, only used to see how many HDs of tags were already calculated
+    c = 0 # counter, only used to see how many HDs of tags were already calculated
     if mate_b is False: # HD calculation for all a's
         half1_mate1 = array1_half
         half2_mate1 = array1_half2
@@ -496,21 +496,21 @@
             else:  # half1, corrects the variable of the HD from both halfs if it is a or b
                 d = d_1
                 d2 = d_2
-            min_valueList[i] = d + d2
-            min_tagsList[i] = tag
-            ham1.append[i] = d
-            ham2.append[i] = d2
+            min_valueList[c] = d + d2
+            min_tagsList[c] = tag
+            ham1.append[c] = d
+            ham2.append[c] = d2
             difference1 = abs(d - d2)
-            diff11[i] = difference1
+            diff11[c] = difference1
             rel_difference = round(float(difference1) / (d + d2), 1)
-            relativeDiffList[i] = rel_difference
+            relativeDiffList[c] = rel_difference
 
             #### tags which have identical parts:
             if d == 0 or d2 == 0:
-                min_tagsList_zeros[i] = tag
+                min_tagsList_zeros[c] = tag
                 difference1_zeros = abs(d - d2)
-                diff11_zeros[i] = difference1_zeros
-            i += 1
+                diff11_zeros[c] = difference1_zeros
+            c += 1
             
         #print(i)
     diff11 = [st for st in diff11 if st != 999]
@@ -712,9 +712,6 @@
         pdf_files = [title_savedFile_pdf]
         csv_files = [title_savedFile_csv]
 
-    print(type(onlyDuplicates))
-    print(onlyDuplicates)
-
     for f, name_file, pdf_f, csv_f in zip(files, names, pdf_files, csv_files):
         with open(csv_f, "w") as output_file, PdfPages(pdf_f) as pdf:
             print("dataset: ", name_file)
--- a/hd.xml	Tue May 15 10:47:06 2018 -0400
+++ b/hd.xml	Tue May 15 10:56:52 2018 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="hd" name="Duplex Sequencing Analysis:" version="0.0.5">
+<tool id="hd" name="Duplex Sequencing Analysis:" version="0.0.6">
     <requirements>
         <requirement type="package" version="2.7">python</requirement>
         <requirement type="package" version="1.4">matplotlib</requirement>