Mercurial > repos > devteam > table_annovar

annotate replace_NA.py @ 0:525e6995fe44 draft default tip

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planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:58:50 -0500
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 #!/usr/bin/env python
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2
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3 # Reads a tabular file and replaces a target sequence (currently 'NA') with a number in columns that have numerical values.
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4 # Limitations: (a) can only take input from stdin and (b) cannot specify target or replacement.
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5
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 import sys
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 import os
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 import tempfile
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 # Constants.
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 SEPARATOR = '\t'
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12 TARGET = 'NA'
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13 REPLACEMENT = -1
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14 # List of known numerical columns.
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 NUMERICAL_COLUMNS = ['1000g2012apr_all', 'esp6500si_all']
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 # Use tempfile to store data.
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 temp_out = tempfile.NamedTemporaryFile(delete=False)
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 # Use first line to set up data structure and identify numerical columns.
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 first_line = sys.stdin.readline()
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22 fields = first_line.strip().split(SEPARATOR)
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23 numerical_cols = []
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24 for i, f in enumerate(fields):
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25 if f in NUMERICAL_COLUMNS:
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 numerical_cols.append(i)
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28 # Data structure is a 2-element list for each fields; first element is # of string elements and second element is # of number elements.
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 col_type_counts = [ [0, 0] for i in range( len(fields) ) ]
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 # Set up function to process lines.
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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32 def process_line_fields(fields):
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33 '''
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34 Process fields in a line.
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35 '''
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36 for i, f in enumerate(fields):
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 # Ignore targets in calculation.
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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38 if f == TARGET:
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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39 continue
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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41 # Assume it's a number.
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42 type_index = 1
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43 try:
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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44 float(f)
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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45 except:
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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46 # Not a number.
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47 type_index = 0
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48 col_type_counts[i][type_index] += 1
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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49
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50
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51 # Process first line.
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52 process_line_fields(fields)
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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53 temp_out.write(first_line)
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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54
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55 # Process N-1 lines.
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56 for line in sys.stdin:
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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57 fields = line.strip().split(SEPARATOR)
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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58 process_line_fields(fields)
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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59 temp_out.write(line)
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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60
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61 # Close temp file so that it can be read.
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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62 temp_name = temp_out.name
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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63 temp_out.close()
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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64
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65 # Get column type based on label or consensus.
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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66 col_types = range(len(col_type_counts))
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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67 for i, counts in enumerate(col_type_counts):
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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68 if i in numerical_cols:
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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69 col_type = 'number'
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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70 elif counts[0] > counts[1]:
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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71 col_type = 'string'
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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72 else:
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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73 col_type = 'number'
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74 col_types[i] = col_type
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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75
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76 # Replace target in number columns.
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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77 for line in open(temp_name, 'r'):
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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78 fields = line.strip().split(SEPARATOR)
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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79 for i, f in enumerate(fields):
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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80 if fields[i] == TARGET and col_types[i] == 'number':
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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81 fields[i] = str(REPLACEMENT)
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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82 print SEPARATOR.join(fields)
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83
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84 # Clean up temp file.
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85 temp_out.close()
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86 os.unlink(temp_out.name)
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87
525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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525e6995fe44 planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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