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Last change
on this file was
8848,
checked in by epruesse, 12 years ago
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Added Python bindings using SWIG
Build and clean targets are "bindings" and "bindings_clean"; they
are not added to all and clean yet. The "test.py" shows a bit of
the python usage of the interface. You need to have swig installed,
of course.
The bindings are not build from arb_prot.h like the perl bindings.
Rather, ARB.i defines the exported functions. This is to make the
interface smaller and have an avenue of keeping it stable in case
the library interface needs to be changed. It also cuts down on
compile time a lot.
The idea is to eventually build the perl bindings with SWIG as well.
I haven't figured out how to provide the BIO:: module with the
ARB module yet, though, which would be required for backwards
compatability with pre-existing amc scripts.
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-
Property svn:executable set to
*
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File size:
1.1 KB
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| 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | # load ARB and os libraries |
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| 4 | import ARB,os,sys |
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| 5 | |
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| 6 | OK = "OK" |
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| 7 | FAIL = "FAIL" |
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| 8 | |
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| 9 | ## |
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| 10 | # define testcases |
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| 11 | ## |
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| 12 | |
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| 13 | def open_nonexistant(): |
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| 14 | """try opening nonexistant db""" |
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| 15 | err = FAIL |
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| 16 | try: |
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| 17 | arbdb = ARB.open("doesnotexist.arb","r") |
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| 18 | except Exception as e: |
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| 19 | err = OK |
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| 20 | print "Exception on attempt to open noexistant DB: " + err |
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| 21 | return err == OK |
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| 22 | |
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| 23 | def count_spec_in_demo_arb(): |
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| 24 | err = OK |
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| 25 | # open the demo database |
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| 26 | try: |
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| 27 | arbdb = ARB.open(os.environ["ARBHOME"] + "/demo.arb","r") |
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| 28 | except Exception as e: |
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| 29 | err = FAIL |
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| 30 | print "Opening demo.arb: " + err |
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| 31 | if (err != OK): return False |
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| 32 | |
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| 33 | # iterate through species and count |
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| 34 | num = 0 |
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| 35 | err = OK |
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| 36 | for species in arbdb.all_species(): |
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| 37 | num+=1 |
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| 38 | if (num != 100): |
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| 39 | err = FAIL |
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| 40 | print "Counting species (expecting 100): " + err |
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| 41 | return err == OK |
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| 42 | |
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| 43 | arbdb.close() |
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| 44 | |
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| 45 | ## |
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| 46 | # run tests |
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| 47 | ## |
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| 48 | |
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| 49 | print "Testing ARB-Python interface:" |
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| 50 | err = False |
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| 51 | err = err or not open_nonexistant() |
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| 52 | err = err or not count_spec_in_demo_arb() |
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| 53 | |
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| 54 | if (err == True): |
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| 55 | print "Some tests failed!" |
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| 56 | sys.exit(1) |
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| 57 | else: |
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| 58 | print "All tests completed successfully. :)" |
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| 59 | |
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