Mercurial > repos > bornea > merge_scaffold

comparison MergeFiles.py @ 10:90045bffffaa draft

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author bornea
date Wed, 03 Aug 2016 15:22:44 -0400
parents 008bc143e72e
children 0e055df46eb0
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9:abe608eb4aa4 10:90045bffffaa
5 """ 5 """
6 ####################################################################################### 6 #######################################################################################
7 import sys 7 import sys
8 import urllib2 8 import urllib2
9 import os.path 9 import os.path
10 import pandas 10 import pandas as pd
11 ####################################################################################### 11 #######################################################################################
12 ## Description: ## 12 ## Description: ##
13 # This program will merge either 2 or 3 scaffold 13 # This program will merge either 2 or 3 scaffold
14 # sample report files together 14 # sample report files together
15 ## Required input: ## 15 ## Required input: ##
16 infile1 = sys.argv[1] # scaffold report #1 -- filename 16 infile1 = sys.argv[1] # scaffold report #1 -- filename
17 print infile1
17 infile2 = sys.argv[2] # scaffold report #2 -- filename 18 infile2 = sys.argv[2] # scaffold report #2 -- filename
19 print infile2
18 infile3 = sys.argv[3] # scaffold report #3 -- filename or "False" 20 infile3 = sys.argv[3] # scaffold report #3 -- filename or "False"
21 print infile3
19 baitfile = sys.argv[4] # Bait file -- filename 22 baitfile = sys.argv[4] # Bait file -- filename
23 print baitfile
20 outfile = sys.argv[5] # output filename 24 outfile = sys.argv[5] # output filename
21 class ScaffoldReturn(object): 25 class ScaffoldReturn(object):
22 def __init__(self, getdata, getproteins, getheader): 26 def __init__(self, getdata, getproteins, getheader):
23 self.data = getdata 27 self.data = getdata
24 self.proteins = getproteins 28 self.proteins = getproteins