# HG changeset patch
# User nml
# Date 1505853297 14400
# Node ID 4e03573653fe72e642af3f3416e2e1da8706cb9a
# Parent  fc0f15ca12e051b659bbd776269de26b8b13b638
planemo upload commit 008f4667b70be22e9ddf496738b3f74bb942ed28

diff -r fc0f15ca12e0 -r 4e03573653fe split_by_allele.py
--- a/split_by_allele.py	Mon Oct 24 13:15:20 2016 -0400
+++ b/split_by_allele.py	Tue Sep 19 16:34:57 2017 -0400
@@ -1,62 +1,63 @@
 #!/usr/bin/env python
 import getopt
+import os
 import sys
-import os
+
 from Bio import SeqIO
 
-def split_allele_file(alleles,profiles):
-    
+ERROR_MSG = "Error could not parse out allele name and number from '%s'"
+
+
+def split_allele_file(alleles, profiles):
+
     writers = {}
 
     handle = open(alleles, "rU")
     for record in SeqIO.parse(handle, "fasta"):
-        
-        seqid=record.id
-        
-        #split out the alelle name from the version number
-        #attempting to split based on '-' first, if that fails, then '_'
+
+        seqid = record.id
+
+        # split out the alelle name from the version number
+        # attempting to split based on '-' first, if that fails, then '_'
         result = seqid.split('_')
-        
-        if len(result) !=2:
+
+        if len(result) != 2:
             result = seqid.split('-')
-            if len(result) ==2:
+            if len(result) == 2:
                 newid = '_'.join(result)
                 record.id = newid
             else:
-                print "Error could not parse out allele name and number from '%s'" % seqid
+                print(ERROR_MSG % seqid)
                 exit(0)
-            
-                
-        name,num = result
 
+        name, num = result
 
-        #if writer exist, then write to that current fasta file
+        # if writer exist, then write to that current fasta file
         if name in writers:
             SeqIO.write(record, writers[name], "fasta")
         else:
-            #new allele found, create new writer and add the first record
+            # new allele found, create new writer and add the first record
             file_name = name + '.fasta'
             output_fh = open(file_name, "w")
             SeqIO.write(record, output_fh, "fasta")
             writers[name] = output_fh
-            
+
     handle.close()
 
-    #creat config file based on the alleles found
-    with open('config.txt','w') as cfile:
+    # create config file based on the alleles found
+    with open('config.txt', 'w') as cfile:
         cfile.write("[loci]\n")
-        for name, writer in writers.iteritems() :
+        for name, writer in writers.items():
             path = os.path.realpath(writer.name)
-            cfile.write("%s\t%s\n" % (name,path))
+            cfile.write("%s\t%s\n" % (name, path))
         cfile.write("[profile]\n")
         cfile.write("profile\t%s\n" % profiles)
 
-        
     return
 
 
-alleles=None
-profiles=None
+alleles = None
+profiles = None
 
 """Input arguments"""
 options, remainder = getopt.getopt(sys.argv[1:], '', [
@@ -71,5 +72,4 @@
         profiles = arg
 
 if alleles and profiles:
-    split_allele_file(alleles,profiles)
-
+    split_allele_file(alleles, profiles)
diff -r fc0f15ca12e0 -r 4e03573653fe stringmlst.xml
--- a/stringmlst.xml	Mon Oct 24 13:15:20 2016 -0400
+++ b/stringmlst.xml	Tue Sep 19 16:34:57 2017 -0400
@@ -1,7 +1,8 @@
-<tool id="stringmlst" name="StringMLST" version="1.0.4">
+<tool id="stringmlst" name="StringMLST" version="1.1.0">
   <description>k-mer tool for multilocus sequence typing</description>
   <requirements>
-    <requirement type="package" version="2.1">stringmlst</requirement>
+    <requirement type="package" version="0.4.1">stringMLST</requirement>
+    <requirement type="package" version="1.70">biopython</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" />
diff -r fc0f15ca12e0 -r 4e03573653fe test-data/results.tsv
--- a/test-data/results.tsv	Mon Oct 24 13:15:20 2016 -0400
+++ b/test-data/results.tsv	Tue Sep 19 16:34:57 2017 -0400
@@ -1,2 +1,2 @@
 Sample	abcZ	bglA	cat	dapE	dat	ldh	lhkA	ST
-answer	2	1	11	3	3	1	7	5
+input	2	1	11	3	3	1	7	5
diff -r fc0f15ca12e0 -r 4e03573653fe tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Oct 24 13:15:20 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="stringmlst" version="2.1">
-    	<repository changeset_revision="75d83e0939c5" name="package_stringmlst_2_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>