Python superyaml Examples

Example #1

File: test1.py Project: iandriver/Rnaseq

 def test_sections(self):
     sy=superyaml(domain=os.getcwd())
     d_sy=sy.load('sections.syml',{'these':'some other'})
     self.assertEqual(d_sy['these'],'some other')
     self.assertEqual(d_sy['this_color'],'red', 'this_color=red: got %s' % d_sy['this_color'])
     self.assertEqual(type(d_sy['section1']['flintstones']), type([]), "got a list for section1->flintstones")
     self.assertEqual(d_sy['section1']['flintstones'][0], 'fred', 'section1=fred: got %s' % d_sy['section1']['flintstones'][0])

Example #2

File: test1.py Project: iandriver/Rnaseq

 def test_basic(self):
     sy=superyaml(domain=os.getcwd())
     
     d={'this':'that', 'these':'those'}
     d_sy=sy.load('basic.syml',d)
     self.assertEqual(d['this'],'that')
     self.assertEqual(d['these'],'those')

Example #3

File: test_bowtie.py Project: phonybone/Rnaseq

    def test_bowtie(self):
        sy = superyaml(domain="/proj/hoodlab/share/vcassen/rna-seq/rnaseq/templates")
        d_sy = sy.load("bowtie.syml", {})
        warn(yaml.dump(d_sy))

        d_sy = sy.load("bowtie.syml", d_sy)
        warn(yaml.dump(d_sy))
        self.assertEquals(d_sy["exe"], "bowtie", 'got d[exe]=%s, expected "bowtie"' % d_sy["exe"])

Example #4

File: test_composite.py Project: iandriver/Rnaseq

    def test_composite(self):
        sy=superyaml(domain='/proj/hoodlab/share/vcassen/rna-seq/rnaseq/templates')
        readset=sy.load('readset.syml',{})

        bowtie=sy.load('bowtie.syml',readset)
        warn("bowtie 1",yaml.dump(bowtie))
        self.assertEquals(bowtie['exe'],'bowtie','got d[exe]=%s, expected "bowtie"' % bowtie['exe'])

        bowtie.update(readset)
        bowtie=sy.load('bowtie.syml',bowtie)
        warn("bowtie 2",yaml.dump(bowtie))

        expected=("%(exe)s %(ewbt)s %(args)s" % hashslice(bowtie,'exe','ewbt','args')) + " ${input} ${output}"
        warn("expected is %s" % expected)
        self.assertEquals(bowtie['usage'], expected,
                          'got bowtie[usage]=%s, expected %s' % (bowtie['usage'], expected))

Example #5

File: 11-test-linear.py Project: icefoxx/rna-seq-scripts

from superyaml import *
import yaml

sy=superyaml({'config_file': 'linear.yml',
              })
sy.load()


print "sy.config is %s" % yaml.dump(sy.config)

Example #6

File: 10-test-cyclic.py Project: icefoxx/rna-seq-scripts

from superyaml import *
import yaml

sy=superyaml({'config_file': 'cyclic.yml',
              })
sy.load()                               # should throw an exception


print "sy is %s" % yaml.dump(sy)

Example #7

File: test1.py Project: iandriver/Rnaseq

 def test_internal_substitution(self):
     sy=superyaml(domain=os.getcwd())
     d_sy=sy.load('internal_substitution.syml',{'these':'some other'})
     self.assertEqual(d_sy['these'],'some other')
     self.assertEqual(d_sy['this_color'],'red', 'this_color=red: got %s' % d_sy['this_color'])

Example #8

File: test1.py Project: iandriver/Rnaseq

 def test_basic_substitution(self):
     sy=superyaml(domain=os.getcwd())
     d_sy=sy.load('basic_substitution.syml',{'these':'some other'})
     self.assertEqual(d_sy['these'],'some other')

Example #9

File: 12-test-repeat.py Project: icefoxx/rna-seq-scripts

from superyaml import *
import yaml

sy=superyaml({'config_file': 'repeat.syml',
              })
sy.load()                               # should throw an exception


print "sy.config is %s" % yaml.dump(sy.config)

Example #10

File: 01-test-simple.py Project: icefoxx/rna-seq-scripts

from superyaml import *
import yaml

sy=superyaml({'config_file': 'simple.yml',
              })
sy.load()


print "sy.config is %s" % yaml.dump(sy.config)