Mercurial > repos > devteam > column_maker

annotate column_maker.py @ 10:beec6ecc7d3c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
author iuc
date Thu, 22 Aug 2024 08:25:32 +0000
parents 33b81f9ea109
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4dadd821722f Imported from capsule None
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parents:
diff changeset
1 #!/usr/bin/env python
4
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
devteam
parents: 2
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2 """
9
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
3 This tool takes a tab-delimited textfile as input and creates new columns in
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
4 the file which are the result of a computation performed on every row in the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
5 original file. The tool will skip over empty and comment (starting with a #)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
6 lines within the file. It does not change the formatting of any original,
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
7 retained columns.
4
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
devteam
parents: 2
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8 """
0
4dadd821722f Imported from capsule None
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9
6
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
devteam
parents: 5
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10 import argparse
9
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
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11 import enum
4
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
devteam
parents: 2
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12 import re
7
e7c273e8d4d6 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
devteam
parents: 6
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13 import sys
9
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
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14 # Functions that may be used in the compute expression
8
227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"
devteam
parents: 7
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15 from math import ( # noqa: F401
10
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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16 acos,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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17 acosh,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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18 asin,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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19 asinh,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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20 atan,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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21 atan2,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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22 atanh,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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23 cbrt,
8
227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"
devteam
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24 ceil,
10
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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25 comb,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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26 copysign,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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27 cos,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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28 cosh,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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29 degrees,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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30 dist,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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31 erf,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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32 erfc,
8
227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"
devteam
parents: 7
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33 exp,
10
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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34 exp2,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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35 expm1,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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36 fabs,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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37 factorial,
8
227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"
devteam
parents: 7
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38 floor,
10
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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39 fmod,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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40 frexp,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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41 fsum,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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42 gamma,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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43 gcd,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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44 hypot,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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45 inf,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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46 isclose,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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47 isfinite,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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48 isinf,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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49 isnan,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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50 isqrt,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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51 ldexp,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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52 lgamma,
8
227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"
devteam
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53 log,
227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"
devteam
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54 log10,
10
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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55 log1p,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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56 log2,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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57 modf,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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58 nextafter,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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59 perm,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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60 pi,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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61 pow,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
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62 prod,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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63 remainder,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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64 sin,
9
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iuc
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65 sqrt,
10
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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66 tan,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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67 tanh,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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68 tau,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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69 trunc,
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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70 ulp,
8
227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"
devteam
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71 )
227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"
devteam
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72
9
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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73 from numpy import format_float_positional
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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74
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parents: 8
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75
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76 class Mode(enum.Enum):
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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77 APPEND = ''
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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78 INSERT = 'I'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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79 REPLACE = 'R'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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80
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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81
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82 def from_str(s, to_type):
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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83 if to_type is list:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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84 return [part.strip(' ') for part in s.split(',')]
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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85 else:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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86 return to_type(s)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
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87
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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88
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89 def to_str(obj):
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
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90 if type(obj) is list:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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91 return ','.join([to_str(i) for i in obj])
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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92 if args.avoid_scientific_notation and type(obj) is float:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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93 return format_float_positional(obj)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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94 return str(obj)
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95
0
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96
6
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97 parser = argparse.ArgumentParser()
9
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98 parser.add_argument('input', type=str, help='input file')
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99 parser.add_argument('output', type=str, help='output file')
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100 parser.add_argument(
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101 '-t', '--column-types', nargs='?', required=True,
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102 help='A comma-separated list of column types in the input file'
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103 )
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104 parser.add_argument(
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105 '--avoid-scientific-notation', action='store_true',
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106 help='avoid scientific notation'
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107 )
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108 parser.add_argument(
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109 '--header', action='store_true',
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110 help='The input has a header line with column names. '
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111 'Actions must specify names of newly calculated columns.'
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112 )
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113 parser.add_argument(
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114 '--fail-on-non-existent-columns', action='store_true',
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115 help='If an action references a column number that is not existent '
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116 'when the expression gets computed, the default behavior is to treat '
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117 'this as a case of rows for which the expression cannot be computed. '
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118 'The behavior of the tool will then depend on which of the '
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119 'non-computable switches is in effect. With this flag, in contrast, '
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120 'the tool will fail directly upon encountering a non-existing column.'
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121 )
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122 non_computable = parser.add_mutually_exclusive_group()
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123 non_computable.add_argument('--fail-on-non-computable', action='store_true')
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124 non_computable.add_argument('--skip-non-computable', action='store_true')
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125 non_computable.add_argument('--keep-non-computable', action='store_true')
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126 non_computable.add_argument('--non-computable-blank', action='store_true')
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127 non_computable.add_argument('--non-computable-default')
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128
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129 group = parser.add_mutually_exclusive_group(required=True)
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130 group.add_argument(
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131 '-a', '--actions', nargs='*', type=str,
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132 help='One or more action(s) of the format EXPR;[COL_ADD_SPEC];[COL_NAME]'
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133 )
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134 group.add_argument(
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135 '-f', '--file', type=str,
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136 help='File to read actions from (mutually exclusive with -a)'
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137 )
6
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138 args = parser.parse_args()
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139
9
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140 if not args.column_types:
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141 with open(args.input) as fh:
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142 if not fh.readline():
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143 # Generally, the input must have at least one column to be
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144 # considered tabular, but empty files are ok and should produce
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145 # empty output.
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146 with open(args.output, 'w') as out:
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147 pass
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148 sys.exit()
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149 sys.exit(
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150 "Missing column types. "
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151 "In Galaxy, click the pencil icon on the history item and "
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152 "select the Auto-detect option to correct it. "
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153 "This tool can only be used with tab-delimited data."
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154 )
7
e7c273e8d4d6 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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155
9
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156 in_column_types = [t.strip() for t in args.column_types.split(',')]
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157 in_columns = len(in_column_types)
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158
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159 # Prepare initial column variable names and type cast representations
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160 # for column data types
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161 cols, type_casts = [], []
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162 for n, col_type in enumerate(in_column_types, start=1):
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163 col_name = "c%d" % n
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164 cols.append(col_name)
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165 col_str = ', '.join(cols) # 'c1, c2, c3, c4'
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166
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167 # Define lambda for type-casting of original row fields
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168 try:
9
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169 cast_types = eval(
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170 'lambda fields: [from_str(s, t) for s, t in zip(fields, [%s])]'
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171 % args.column_types
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172 )
10
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173 except Exception as err:
9
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174 sys.exit(
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175 'While parsing column types, the following problem occured: "%s"'
10
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176 % err
9
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177 )
0
4dadd821722f Imported from capsule None
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178
9
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179 # Get and parse actions
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180 if args.file:
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181 actions = []
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182 with open(args.file) as i:
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183 for line in i:
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184 line = line.strip()
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185 if line:
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186 actions.append(line)
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187 else:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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188 actions = args.actions
0
4dadd821722f Imported from capsule None
devteam
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diff changeset
189
9
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190 # each action must be a full data row manipulation instruction of the form:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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191 # EXPR;[COL_ADD_SPEC];[COL_NAME]
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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192 # where EXPR is the actual expression to compute on the row,
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193 # COL_ADD_SPEC consists of a column index and a mode identifier for how the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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194 # new column should be added.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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195 # Examples: 3I (insert new col before current column 3),
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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196 # 2R (replace current column 2 with new column);
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197 # a missing COL_ADD_SPEC is interpreted as mode A (append new column at the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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198 # end of the row).
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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199 # COL_NAME is required with the --header option and specifies the name of the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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200 # new column; without --header, any COL_NAME gets ignored.
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201 operators = 'is|not|or|and'
10
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
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202 builtin_functions = (
9
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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203 'abs|all|any|ascii|bin|bool|chr|complex|divmod|float|format|hex|int|len|'
10
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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204 'list|map|max|min|oct|ord|pow|range|reversed|round|set|sorted|str|sum|type'
9
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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205 )
10
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
parents: 9
diff changeset
206
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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207 math_functions = (
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
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208 'acos|acosh|asin|asinh|atan|atan2|atanh|cbrt|ceil|comb|copysign|cos|cosh|degrees|'
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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209 'dist|erf|erfc|exp|exp2|expm1|fabs|factorial|floor|fmod|frexp|fsum|gamma|gcd|'
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
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210 'hypot|inf|isclose|isfinite|isinf|isnan|isqrt|ldexp|lgamma|log|log10|log1p|'
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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211 'log2|modf|nextafter|perm|pi|pow|prod|remainder|sin|'
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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212 'sqrt|tan|tanh|tau|trunc|ulp'
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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213 )
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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214 builtin_and_math_functions = builtin_functions + '|' + math_functions
9
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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215 imported_numpy_function = 'format_float_positional'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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216 string_and_list_methods = [
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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217 name for name in dir('') + dir([]) if not name.startswith('_')
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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218 ]
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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219 whitelist = r"^([c0-9\+\-\*\/\(\)\.\'\"><=,:! ]|%s|%s|%s|%s)*$" % (
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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220 operators,
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
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221 builtin_and_math_functions,
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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222 imported_numpy_function,
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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223 '|'.join(string_and_list_methods)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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224 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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225 valid_pat = re.compile(whitelist)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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226 ops = []
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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227 num_cols = in_columns
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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228 for ac in actions:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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229 try:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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230 expr_string, col_add_spec, new_col_name = ac.split(';')
10
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
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231 print(expr_string)
9
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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232 except ValueError:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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233 sys.exit(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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234 'Invalid Action: "%s". '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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235 'Required format: EXPR;[COL_ADD_SPEC];[COL_NAME]' % ac
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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236 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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237 if not valid_pat.match(expr_string):
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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238 sys.exit('Invalid expression: "%s"' % expr_string)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
239 try:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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240 expr_lambda = eval('lambda %s: %s' % (col_str, expr_string))
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
241 except Exception as e:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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242 if str(e).startswith('invalid syntax'):
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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243 sys.exit(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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244 'Expression "%s" caused a syntax error during parsing.'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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245 % expr_string
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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246 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
247 else:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
248 sys.exit(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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249 'While parsing expression "%s" the following problem occured: '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
250 '"%s"' % (expr_string, str(e))
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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251 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
252 try:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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253 new_col_idx = int(col_add_spec[:-1] or '0') - 1
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
254 except ValueError:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
255 sys.exit(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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256 'COL_ADD_SPECS need to start with a (1-based) column index. '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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257 'Could not parse a column index from "%s"' % col_add_spec
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
258 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
259 try:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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260 mode = Mode(col_add_spec[-1:])
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
261 except ValueError:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
262 sys.exit(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
263 'COL_ADD_SPECS need to end in a single-character mode identifier '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
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264 '("I", or "R"), or be empty (for Append mode). '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
265 'Could not parse a valid identifier from "%s"' % col_add_spec
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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parents: 8
diff changeset
266 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
267 if mode is Mode.REPLACE:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
268 if new_col_idx < 0 or new_col_idx >= num_cols:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
269 sys.exit(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
270 'Cannot replace the contents of column %d as specified by '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
271 'action "%s". No such column at this point of the '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
272 'computation' % (new_col_idx + 1, ac)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
273 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
274 if not new_col_name and args.header:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
275 sys.exit(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
276 'A name is required for any new columns when using an existing '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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277 'header line (--header option), but found none in action: '
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278 '"%s"' % ac
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279 )
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280 # Successfully parsed the instruction
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281 # Store the expression lambda, the index and name of the new column, and
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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282 # the original string representation of the expression (for use in
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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283 # potential later error messages).
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284 ops.append([expr_lambda, new_col_idx, mode, new_col_name, expr_string])
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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285 if mode is Mode.APPEND or mode is Mode.INSERT:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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286 # If the current expression results in an additional column,
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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287 # we need to handle the new field in subsequent lambda functions.
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288 num_cols += 1
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289 col_str += ', c%d' % num_cols
4
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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290
9
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291
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292 # ready to start parsing the input file
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293 print(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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294 'Computing %d new columns with instructions %s'
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295 % (num_cols - in_columns, actions)
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296 )
0
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297 skipped_lines = 0
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298 first_invalid_line = 0
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299 invalid_line = None
9
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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300 lines_computed = 0
0
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301 total_lines = 0
9
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302 non_existent_col_pat = re.compile(r"name 'c\d+' is not defined")
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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303
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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304 with open(args.input, encoding='utf-8') as fh, \
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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305 open(args.output, 'w', encoding='utf-8') as out:
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306 if args.header:
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307 # compute new header line from original
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308 header_cols = fh.readline().strip('\n').split('\t')
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309 for _, col_idx, mode, col_name, _ in ops:
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310 if mode is Mode.INSERT:
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311 header_cols.insert(col_idx, col_name)
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312 elif mode is Mode.REPLACE:
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313 header_cols[col_idx] = col_name
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314 else:
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315 header_cols.append(col_name)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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316 out.write('\t'.join(header_cols) + '\n')
0
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317
9
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318 # read data, skipping empty and comment lines, and perform computations
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319 # that will result in new columns
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iuc
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320 for i, line in enumerate(fh):
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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321 total_lines += 1
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iuc
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322 line = line.rstrip('\n')
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323 if not line or line.startswith('#'):
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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324 skipped_lines += 1
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iuc
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diff changeset
325 if not invalid_line:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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326 first_invalid_line = i + 1
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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327 invalid_line = line
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iuc
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328 continue
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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329 fields = line.split('\t')
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330 if len(fields) == in_columns:
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331 try:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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332 typed_fields = cast_types(fields)
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diff changeset
333 except ValueError as e:
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334 sys.exit(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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335 'Failed to convert some of the columns in line #%d to their '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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336 'expected types. The error was: "%s" for the line: "%s"'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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337 % (i, str(e), line)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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338 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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339 else:
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340 # A "suspicious" line with less or more fields than expected
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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341 # Type-casting for it might fail or not, but it is pointless to
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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342 # even try because subsequent computation of any expression will
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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343 # fail anyway as expression lambdas expect a fixed number of
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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344 # arguments.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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345 # Lets pass in a copy of the original string fields, let
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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346 # the computation of the first expression fail, then have that
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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347 # situation handled according to the non-computable settings in
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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348 # effect.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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349 typed_fields = fields[:]
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350 for fun, col_idx, mode, col_name, ex in ops:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
351 try:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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352 try:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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353 new_val = fun(*typed_fields)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
354 except NameError as e:
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iuc
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355 # Python 3.10+ would have the problematic name
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
356 # available as e.name
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357 if non_existent_col_pat.fullmatch(str(e)) and (
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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358 not args.fail_on_non_existent_columns
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diff changeset
359 ):
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
360 # Looks like a reference to a non-existent column
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
361 # and we are not supposed to fail on it directly.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
362 # Reraise and have it handled as a non-computable
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iuc
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diff changeset
363 # row.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
364 raise
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
365 # NameErrors are not row-specific, but indicate a
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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366 # general problem with the user-supplied expression.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
367 sys.exit(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
368 'While parsing expression "%s" the following '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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369 'problem occured: "%s"' % (ex, str(e))
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
370 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
371 except Exception as e:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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diff changeset
372 if args.skip_non_computable:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
373 # log that a line got skipped, then stop computing
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
374 # for this line
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
375 skipped_lines += 1
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
376 if not invalid_line:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
377 first_invalid_line = i + 1
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
378 invalid_line = line
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
379 break
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
380 if args.keep_non_computable:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
381 # write the original line unchanged and stop computing
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
382 # for this line
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
383 out.write(line + '\n')
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
384 break
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
385 if args.non_computable_blank:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
386 new_val = ''
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
387 elif args.non_computable_default is not None:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
388 new_val = args.non_computable_default
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
389 else:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
390 # --fail_on_non_computable
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
391 # (which is default behavior, too)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
392 sys.exit(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
393 'Could not compute a new column value using "%s" on '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
394 'line #%d: "%s". Error was "%s"'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
395 % (ex, i, line, str(e))
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
396 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
397 if mode is Mode.INSERT:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
398 fields.insert(col_idx, new_val)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
399 typed_fields.insert(col_idx, new_val)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
400 elif mode is Mode.REPLACE:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
401 if col_idx > len(fields):
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
402 # Intentionally allow "replacing" one column beyond
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
403 # current fields since this can be used to fix
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
404 # short lines in the input.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
405 sys.exit(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
406 'Cannot replace column #%d in line with %d columns: '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
407 '"%s"' % (col_idx + 1, len(fields), line)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
408 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
409 fields[col_idx:col_idx + 1] = [new_val]
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
410 typed_fields[col_idx:col_idx + 1] = [new_val]
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
411 else:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
412 fields.append(new_val)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
413 typed_fields.append(new_val)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
414 else:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
415 fields = [to_str(field) for field in fields]
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
416 out.write('\t'.join(fields) + '\n')
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
417 lines_computed += 1
0
4dadd821722f Imported from capsule None
devteam
parents:
diff changeset
418
4dadd821722f Imported from capsule None
devteam
parents:
diff changeset
419
9
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
420 valid_lines = total_lines - skipped_lines
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
421 if valid_lines > 0:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
422 print(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
423 'Computed new column values for %4.2f%% of %d lines written.'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
424 % (100.0 * lines_computed / valid_lines, valid_lines)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
425 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
426 elif args.fail_on_non_existent_columns:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
427 # Warn the user that there could be an issue with an expression.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
428 print(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
429 'Could not compute a new column for any input row! '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
430 'Please check your expression(s) "%s" for problems.'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
431 % actions
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
432 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
433 else:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
434 # Same, but the problem could also be a reference to a non-existent
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
435 # column.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
436 print(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
437 'Could not compute a new column for any input row! '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
438 'Please check your expression(s) "%s" for references to non-existent '
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
439 'columns or other problems.'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
440 % actions
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
441 )
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
442 if skipped_lines > 0:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
443 print('Skipped %d invalid lines starting at line #%d: "%s"' %
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
444 (skipped_lines, first_invalid_line, invalid_line))
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
445 if lines_computed < valid_lines:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
446 print(
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
447 'Rewrote %d lines unmodified because computation of a new value failed'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
448 % (valid_lines - lines_computed)
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
parents: 8
diff changeset
449 )