1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
|
.. include:: ../global.inc
.. _decorators.product:
.. index::
pair: @product; Syntax
.. seealso::
* :ref:`@product <new_manual.product>` in the **Ruffus** Manual
* :ref:`Decorators <decorators>` for more decorators
.. |input| replace:: `input`
.. _input: `decorators.product.input`_
.. |filter| replace:: `filter`
.. _filter: `decorators.product.filter`_
.. |input2| replace:: `input2`
.. _input2: `decorators.product.input2`_
.. |filter2| replace:: `filter2`
.. _filter2: `decorators.product.filter2`_
.. |extras| replace:: `extras`
.. _extras: `decorators.product.extras`_
.. |output| replace:: `output`
.. _output: `decorators.product.output`_
.. |matching_formatter| replace:: `matching_formatter`
.. _matching_formatter: `decorators.product.matching_formatter`_
################################################################################################################################################
product
################################################################################################################################################
************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
@product( |input|_, |filter|_, [|input2|_, |filter2|_, ...], |output|_, [|extras|_,...] )
************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
**Purpose:**
Generates the Cartesian **product**, i.e. all vs all comparisons, between multiple sets of |input|_ (e.g. **A B C D**, and **X Y Z**),
The effect is analogous to the python `itertools <http://docs.python.org/2/library/itertools.html#itertools.product>`__
function of the same name, i.e. a nested for loop.
.. code-block:: pycon
:emphasize-lines: 2
>>> from itertools import product
>>> # product('ABC', 'XYZ') --> AX AY AZ BX BY BZ CX CY CZ
>>> [ "".join(a) for a in product('ABC', 'XYZ')]
['AX', 'AY', 'AZ', 'BX', 'BY', 'BZ', 'CX', 'CY', 'CZ']
Only out of date tasks (comparing input and output files) will be run
|output|_ file names and strings in the extra parameters
are generated by string replacement via the :ref:`formatter()<decorators.formatter>` filter
from the |input|_. This can be, for example, a list of file names or the
|output|_ of up stream tasks.
.
The replacement strings require an extra level of nesting to refer to
parsed components.
#. The first level refers to which *set* in each tuple of |input|_.
#. The second level refers to which |input|_ file in any particular *set* of |input|_.
This will be clear in the following example:
**Example**:
Calculates the **@product** of **A,B** and **P,Q** and **X, Y** files
If |input|_ is three *sets* of file names
.. code-block:: python
:emphasize-lines: 1-10
set1 = [ 'a.start', # 0
'b.start'])
set2 = [ 'p.start', # 1
'q.start'])
set3 = [ ['x.1_start', 'x.2_start'], # 2
['y.1_start', 'y.2_start'] ]
The first job of:
.. code-block:: python
@product( input = set1, filter = formatter(),
input2 = set2, filter2 = formatter(),
input3 = set2, filter3 = formatter(),
...)
Will be
.. <<python
.. code-block:: python
:emphasize-lines: 1-6
# One from each set
['a.start']
# versus
['p.start']
# versus
['x.1_start', 'x.2_start'],
..
python
First level of nesting (one list of files from each set):
.. code-block:: python
:emphasize-lines: 1-6
['a.start'] # [0]
['p.start'] # [1]
['x.1_start', 'x.2_start'], # [2]
Second level of nesting (one file):
.. code-block:: python
:emphasize-lines: 1-6
'a.start' # [0][0]
'p.start' # [1][0]
'x.1_start' # [2][0]
Parse filename without suffix
.. code-block:: python
:emphasize-lines: 1-6
'a' # {basename[0][0]}
'p' # {basename[1][0]}
'x' # {basename[2][0]}
Python code:
.. code-block:: python
:emphasize-lines: 4,19,21,24,27,29-32,34-35,37-40
from ruffus import *
from ruffus.combinatorics import *
# Three sets of initial files
@originate([ 'a.start', 'b.start'])
def create_initial_files_ab(output_file):
with open(output_file, "w") as oo: pass
@originate([ 'p.start', 'q.start'])
def create_initial_files_pq(output_file):
with open(output_file, "w") as oo: pass
@originate([ ['x.1_start', 'x.2_start'],
['y.1_start', 'y.2_start'] ])
def create_initial_files_xy(output_files):
for o in output_files:
with open(o, "w") as oo: pass
# @product
@product( create_initial_files_ab, # Input
formatter("(.start)$"), # match input file set # 1
create_initial_files_pq, # Input
formatter("(.start)$"), # match input file set # 2
create_initial_files_xy, # Input
formatter("(.start)$"), # match input file set # 3
"{path[0][0]}/" # Output Replacement string
"{basename[0][0]}_vs_" #
"{basename[1][0]}_vs_" #
"{basename[2][0]}.product", #
# Extra parameter: path for
"{path[0][0]}", # 1st set of files, 1st file name
# Extra parameter: basename for
["{basename[0][0]}", # 1st set of files, 1st file name
"{basename[1][0]}", # 2nd
"{basename[2][0]}", # 3rd
])
def product_task(input_file, output_parameter, shared_path, basenames):
print "# basenames = ", " ".join(basenames)
print "input_parameter = ", input_file
print "output_parameter = ", output_parameter, "\n"
#
# Run
#
#pipeline_printout(verbose=6)
pipeline_run(verbose=0)
This results in:
.. code-block:: pycon
:emphasize-lines: 2,6,10,14,18,22,26,30
>>> pipeline_run(verbose=0)
# basenames = a p x
input_parameter = ('a.start', 'p.start', 'x.start')
output_parameter = /home/lg/temp/a_vs_p_vs_x.product
# basenames = a p y
input_parameter = ('a.start', 'p.start', 'y.start')
output_parameter = /home/lg/temp/a_vs_p_vs_y.product
# basenames = a q x
input_parameter = ('a.start', 'q.start', 'x.start')
output_parameter = /home/lg/temp/a_vs_q_vs_x.product
# basenames = a q y
input_parameter = ('a.start', 'q.start', 'y.start')
output_parameter = /home/lg/temp/a_vs_q_vs_y.product
# basenames = b p x
input_parameter = ('b.start', 'p.start', 'x.start')
output_parameter = /home/lg/temp/b_vs_p_vs_x.product
# basenames = b p y
input_parameter = ('b.start', 'p.start', 'y.start')
output_parameter = /home/lg/temp/b_vs_p_vs_y.product
# basenames = b q x
input_parameter = ('b.start', 'q.start', 'x.start')
output_parameter = /home/lg/temp/b_vs_q_vs_x.product
# basenames = b q y
input_parameter = ('b.start', 'q.start', 'y.start')
output_parameter = /home/lg/temp/b_vs_q_vs_y.product
**Parameters:**
.. _decorators.product.input:
* **input** = *tasks_or_file_names*
can be a:
#. Task / list of tasks.
File names are taken from the |output|_ of the specified task(s)
#. (Nested) list of file name strings.
File names containing ``*[]?`` will be expanded as a |glob|_.
E.g.:``"a.*" => "a.1", "a.2"``
.. _decorators.product.filter:
.. _decorators.product.matching_formatter:
* **filter** = *formater(...)*
a :ref:`formatter<decorators.formatter>` indicator object containing optionally
a python `regular expression (re) <http://docs.python.org/library/re.html>`_.
.. _decorators.product.input2:
.. _decorators.product.filter2:
Additional **input** and **filter** as needed:
* **input2** = *tasks_or_file_names*
* **filter2** = *formater(...)*
.. _decorators.product.output:
* **output** = *output*
Specifies the resulting output file name(s) after string substitution
.. _decorators.product.extras:
* **extras** = *extras*
Any extra parameters are passed verbatim to the task function
If you are using named parameters, these can be passed as a list, i.e. ``extras= [...]``
Any extra parameters are consumed by the task function and not forwarded further down the pipeline.
|
