Mercurial > repos > sanbi-uwc > plink_datatypes

annotate fam/fam.py @ 1:0e9c114c748f draft default tip

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planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
author sanbi-uwc
date Thu, 30 Aug 2018 07:41:55 -0400
parents 57bd7c6a72cd
children
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1
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
diff changeset
1 # -*- coding: utf-8 -*-
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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2 from galaxy import eggs
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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3
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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4
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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5 import pkg_resources
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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6 pkg_resources.require( "bx-python" )
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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7
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
diff changeset
8
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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9 import logging, os, sys, time, sets, tempfile, shutil
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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10 import data
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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11 from galaxy import util
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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12 from galaxy.datatypes.sniff import *
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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13 from cgi import escape
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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14 import urllib
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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15 from bx.intervals.io import *
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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16 from galaxy.datatypes import metadata
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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17 from galaxy.datatypes.metadata import MetadataElement
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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18 from galaxy.datatypes.tabular import Tabular
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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19
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
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20
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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21 class Fam( Tabular ):
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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22 """Tab delimited data in bim format"""
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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23 file_ext = "fam"
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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24
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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25 MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True )
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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26
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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27
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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28 def __init__ (self, **kwd):
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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29 """Initialize bim datatype"""
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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30 Tabular. __init__ (self, **kwd)
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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31 self.do_something_else()
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
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32
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
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33
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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34 def init_meta( self, dataset, copy_from=None ):
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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35 Tabular.init_meta( self, dataset, copy_from=copy_from )
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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36 if elems_len == 8:
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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37 try:
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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38 map( int, [hdr[6], hdr[7]] )
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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39 proceed = True
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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40 except:
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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41 pass
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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42
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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43
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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44 def sniff( self, filename ):
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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45 headers = get_headers( filename, '\t' )
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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46 try:
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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47 if len(headers) < 2:
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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48 return False
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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49 for hdr in headers:
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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50 if len( hdr ) > 1 and hdr[0] and not hdr[0].startswith( '#' ):
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
diff changeset
51 if len(hdr) != 8:
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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52 return False
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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53 try:
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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54 map( int, [hdr[6], hdr[7]] )
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
diff changeset
55 except:
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
diff changeset
56 return False
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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57 # Do other necessary checking here...
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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58 except:
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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59 return False
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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60 # If we haven't yet returned False, then...
0e9c114c748f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/tree/master/datatypes/plink_datatypes commit d0354c6155e1a44aab9c2fecf7a1a7f9e4bb22de
sanbi-uwc
parents: 0
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61 return True