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annotate specify.py @ 28:184d14e4270d

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Update to Miller Lab devshed revision 4ede22dd5500
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 17 Jul 2013 12:46:46 -0400
parents 8997f2ca8c7a
children
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1 #!/usr/bin/env python
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3 import gd_util
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4 import sys
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5 from Population import Population
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7 ################################################################################
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9 def parse_string(str_arg, ind_token2col):
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10 columns = []
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12 string = gd_util.unwrap_string(str_arg)
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13 tokens = find_tokens(string, ind_token2col)
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15 for token in tokens:
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16 col = ind_token2col[token]
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17 if col not in columns:
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18 columns.append(col)
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20 return columns
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22 def find_tokens(string, tokens):
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23 rv = []
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24 for token in tokens:
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25 if token in string:
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26 if token not in rv:
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27 rv.append(token)
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28 return rv
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30 ################################################################################
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32 if len(sys.argv) != 6:
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33 gd_util.die('Usage')
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35 input, output, ind_arg, cb_arg, str_arg = sys.argv[1:]
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37 p_total = Population()
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38 p_total.from_wrapped_dict(ind_arg)
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40 p_cb = Population()
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41 p_cb.from_wrapped_dict(cb_arg)
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43 if not p_total.is_superset(p_cb):
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44 gd_util.die('There is a checked individual that does not appear in the SNP table')
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46 ################################################################################
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48 ind_col2name = {}
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49 ind_token2col = {}
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50 for col in p_total.column_list():
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51 individual = p_total.individual_with_column(col)
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52 name = individual.name
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53 ind_col2name[col] = name
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54 first_token = name.split()[0]
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55 if first_token not in ind_token2col:
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56 ind_token2col[first_token] = col
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57 else:
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58 gd_util.die('duplicate first token: {0}'.format(first_token))
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60 out_cols = p_cb.column_list()
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61 str_cols = parse_string(str_arg, ind_token2col)
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63 with open(output, 'w') as fh:
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64 for col in sorted(ind_col2name.keys()):
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65 if col in out_cols or col in str_cols:
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66 print >> fh, '\t'.join([str(x) for x in [col, ind_col2name[col], '']])
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68 sys.exit(0)
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