def sample1_se_tiny_fq(tmpdir_factory):
"""
Single-end FASTQ file with 1010 reads
"""
d = tmpdir_for_func(tmpdir_factory)
fn = 'rnaseq_samples/sample1/sample1.tiny_R1.fastq.gz'
return _download_file(fn, d)
def generic_fixture(key, mapping, factory):
"""
Tries to handle as much of the magic as possible.
Parameters
----------
key : str
Key into the module-level config dict
mapping : dict
Maps paths from fixtures to input files expected by the snakefile
tmpdir : str
Path to temporary dir, usually created by utils.tmpdir_for_func
Returns
-------
After a successful Snakemake run, returns the dictionary of the config's
`output` key but with paths fixed to be relative to tmpdir. This returned
dict is ready to be used as a fixture by test functions.
"""
conf = config[key]
tmpdir = utils.tmpdir_for_func(factory)
input_data_func = utils.symlink_in_tempdir(mapping)
utils.run(utils.dpath(conf['wrapper']), conf['snakefile'], None,
input_data_func, tmpdir)
output = conf['output'].copy()
for k, v in output.items():
output[k] = os.path.join(tmpdir, v)
return output
def sample1_pe_tiny_fq(tmpdir_factory):
pair = []
d = tmpdir_for_func(tmpdir_factory)
for fn in [
'rnaseq_samples/sample1/sample1.tiny_R1.fastq.gz',
'rnaseq_samples/sample1/sample1.tiny_R2.fastq.gz'
]:
pair.append(_download_file(fn, d))
return pair
def bowtie2_indexes(dm6_fa, tmpdir_factory):
d = tmpdir_for_func(tmpdir_factory)
snakefile = '''
rule bowtie2:
input: fasta='dm6.fa'
output: index=['dm6.1.bt2', 'dm6.2.bt2']
log: 'bowtie2.log'
wrapper: 'file:wrapper'
'''
input_data_func = symlink_in_tempdir({dm6_fa: 'dm6.fa'})
def check():
assert 'Total time for backward call to driver' in open(
'bowtie2.log').readlines()[-1]
assert list(shell('bowtie2-inspect dm6 -n',
iterable=True)) == ['2L', '2R']
run(dpath('../wrappers/bowtie2/build'), snakefile, check, input_data_func,
d)
return aligners.bowtie2_index_from_prefix(os.path.join(d, 'dm6'))
def kallisto_index(tmpdir_factory, transcriptome):
d = tmpdir_for_func(tmpdir_factory)
snakefile = '''
rule kallisto:
input: fasta='transcriptome.fa'
output: index='transcriptome.idx'
log: 'log'
wrapper: 'file:wrapper'
'''
input_data_func = symlink_in_tempdir({
transcriptome: 'transcriptome.fa',
})
def check():
log = open('log').read()
assert '[build] target deBruijn graph'
run(dpath('../wrappers/kallisto/index'), snakefile, check, input_data_func,
d)
return os.path.join(d, 'transcriptome.idx')
def hisat2_indexes(dm6_fa, tmpdir_factory):
d = tmpdir_for_func(tmpdir_factory)
snakefile = '''
rule hisat2:
input: fasta='2L.fa'
output: index=['2L.1.ht2', '2L.2.ht2']
log: 'hisat.log'
wrapper: 'file:wrapper'
'''
input_data_func = symlink_in_tempdir(
{
dm6_fa: '2L.fa'
}
)
def check():
assert 'Total time for call to driver' in open('hisat.log').readlines()[-1]
assert list(shell('hisat2-inspect 2L -n', iterable=True)) == ['2L', '2R']
run(
dpath('../wrappers/hisat2/build'),
snakefile, check, input_data_func, d)
return aligners.hisat2_index_from_prefix(os.path.join(d, '2L'))
def salmon_index(tmpdir_factory, transcriptome):
d = tmpdir_for_func(tmpdir_factory)
snakefile = '''
rule salmon:
input: fasta='transcriptome.fa'
output: hash='salmon_index/hash.bin'
log: 'log'
wrapper: 'file:wrapper'
'''
input_data_func = symlink_in_tempdir(
{
transcriptome: 'transcriptome.fa',
}
)
def check():
log = open('log').read()
assert '[info] done building index' in log
run(
dpath('../wrappers/salmon/index'),
snakefile, check, input_data_func, d)
return os.path.join(d, 'salmon_index')
def sample1_se_tiny_bam(tmpdir_factory):
d = tmpdir_for_func(tmpdir_factory)
fn = 'rnaseq_samples/sample1/sample1.tiny.single.sorted.bam'
return _download_file(fn, d)
def sample1_pe_bam(tmpdir_factory):
d = tmpdir_for_func(tmpdir_factory)
fn = 'rnaseq_samples/sample1/sample1.small.paired.sorted.bam'
return _download_file(fn, d)
def annotation_refflat(tmpdir_factory):
fn = 'annotation/dm6.small.refflat'
d = tmpdir_for_func(tmpdir_factory)
return _download_file(fn, d)
def annotation(tmpdir_factory):
fn = 'annotation/dm6.small.gtf'
d = tmpdir_for_func(tmpdir_factory)
return _download_file(fn, d)
def dm6_fa(tmpdir_factory):
fn = 'seq/dm6.small.fa'
d = tmpdir_for_func(tmpdir_factory)
return _download_file(fn, d)
def transcriptome(tmpdir_factory):
d = tmpdir_for_func(tmpdir_factory)
fn = 'seq/dm6.small.transcriptome.fa'
return _download_file(fn, d)
def sample1_se_fq(tmpdir_factory):
d = tmpdir_for_func(tmpdir_factory)
fn = 'rnaseq_samples/sample1/sample1.small_R1.fastq.gz'
return _download_file(fn, d)
