def create_simdata_token_test_dir(directory):
"""
Create temporary test directories. The directory structure is of
consistent with that expected by
:py:const:`riboviz.test.SIMDATA_UMI_CONFIG`
and :py:const:`riboviz.test.SIMDATA_MULTIPLEX_CONFIG` after
application of :py:func:`tokenize_config_in_place` and assuming when
a workflow is run the user provides values for the environment
variable (:py:const:`riboviz.params.ENV_DIRS`) corresponding to
the tokens. The directory is structured as follows::
<directory>
data/
# Symholic links to <riboviz>/data/ files:
yeast_codon_pos_i200.RData
yeast_features.tsv
yeast_standard_asite_disp_length.txt
yeast_tRNAs.tsv
organisms/
# Symholic links to <riboviz>/vignette/input/ files:
yeast_rRNA_R64-1-1.fa
yeast_YAL_CDS_w_250utrs.fa
yeast_YAL_CDS_w_250utrs.gff3
samples/
simdata/
# Symholic links to <riboviz>/data/simdata/ files:
umi5_umi3_umi_adaptor.fastq
multiplex_umi_barcode_adaptor.fastq
multiplex_barcodes.tsv
The directories returned are as follows:
* organisms: ``<directory>/organisms/``
* samples: ``<directory>/samples/``
* data: ``<directory>/data/``
:param directory: Directory
:type directory: py._path.local.LocalPath
:return: organisms directory, samples directory, data directory
:rtype: tuple(str or unicode, str or unicode, str or unicode)
"""
organisms_dir = directory.mkdir("organisms")
samples_dir = directory.mkdir("samples")
simdata_dir = samples_dir.mkdir("simdata")
data_dir = directory.mkdir("data")
test.symlink_files(organisms_dir, test.ORGANISM_FILES)
test.symlink_files(simdata_dir, test.SIMDATA_INPUT_FILES)
test.symlink_files(data_dir, test.DATA_FILES)
return str(organisms_dir), str(samples_dir), str(data_dir)
def create_simdata_test_dir(directory):
"""
Create temporary test directories. The directory structure is of
consistent with that expected by
:py:const:`riboviz.test.SIMDATA_UMI_CONFIG`
and :py:const:`riboviz.test.SIMDATA_MULTIPLEX_CONFIG`. The
directory is structured as follows::
<directory>
data/
simdata/
# Symholic links to <riboviz>/data/simdata/ files:
umi5_umi3_umi_adaptor.fastq
multiplex_umi_barcode_adaptor.fastq
multiplex_barcodes.tsv
# Symholic links to <riboviz>/data/ files:
yeast_codon_pos_i200.RData
yeast_features.tsv
yeast_standard_asite_disp_length.txt
yeast_tRNAs.tsv
vignette/
input/
# Symholic links to <riboviz>/vignette/input/ files:
yeast_rRNA_R64-1-1.fa
yeast_YAL_CDS_w_250utrs.fa
yeast_YAL_CDS_w_250utrs.gff3
The directories returned are as follows:
* organisms: ``<directory>/vignette/input/``
* samples: ``<directory>/data/``
* data: ``<directory>/data/``
:param directory: Directory
:type directory: py._path.local.LocalPath
:return: organisms directory, samples directory, data directory
:rtype: tuple(str or unicode, str or unicode, str or unicode)
"""
input_dir = directory.mkdir("vignette").mkdir("input")
data_dir = directory.mkdir("data")
simdata_dir = data_dir.mkdir("simdata")
test.symlink_files(input_dir, test.ORGANISM_FILES)
test.symlink_files(simdata_dir, test.SIMDATA_INPUT_FILES)
test.symlink_files(data_dir, test.DATA_FILES)
return str(input_dir), str(simdata_dir), str(data_dir)
def create_vignette_test_dir(directory):
"""
Create temporary test directories. The directory structure is of
consistent with that expected by
:py:const:`ribeviz.test.VIGNETTE_CONFIG`. The
directory is structured as follows::
<directory>
data/
# Symholic links to <riboviz>/data/ files:
yeast_codon_pos_i200.RData
yeast_features.tsv
yeast_standard_asite_disp_length.txt
yeast_tRNAs.tsv
vignette/
input/
# Symholic links to <riboviz>/vignette/input/ files:
yeast_rRNA_R64-1-1.fa
yeast_YAL_CDS_w_250utrs.fa
yeast_YAL_CDS_w_250utrs.gff3
# Symholic links to <riboviz>/vignette/input/ files:
SRR1042855_s1mi.fastq.gz
SRR1042864_s1mi.fastq.gz
The directories returned are as follows:
* organisms: ``<directory>/vignette/input/``
* samples: ``<directory>/vignette/``
* data: ``<directory>/data/``
:param directory: Directory
:type directory: py._path.local.LocalPath
:return: organisms directory, samples directory, data directory
:rtype: tuple(str or unicode, str or unicode, str or unicode)
"""
vignette_dir = directory.mkdir("vignette")
input_dir = vignette_dir.mkdir("input")
data_dir = directory.mkdir("data")
test.symlink_files(input_dir, test.ORGANISM_FILES)
test.symlink_files(input_dir, test.VIGNETTE_INPUT_FILES)
test.symlink_files(data_dir, test.DATA_FILES)
return str(input_dir), str(vignette_dir), str(data_dir)
def create_vignette_default_token_test_dir(directory):
"""
Create temporary test directories. The directory structure is of
consistent with that expected by
:py:const:`riboviz.test.VIGNETTE_CONFIG` after
application of :py:func:`tokenize_config_in_place` and assuming when
a workflow is run the user does not provide values for the
environment variable (:py:const:`riboviz.params.ENV_DIRS`)
corresponding to the tokens. The directory is structured as
follows::
<directory>
# Symholic links to <riboviz>/data/ files:
yeast_codon_pos_i200.RData
yeast_features.tsv
yeast_standard_asite_disp_length.txt
yeast_tRNAs.tsv
# Symholic links to <riboviz>/vignette/input/ files:
yeast_rRNA_R64-1-1.fa
yeast_YAL_CDS_w_250utrs.fa
yeast_YAL_CDS_w_250utrs.gff3
input/
# Symholic links to <riboviz>/vignette/input/ files:
SRR1042855_s1mi.fastq.gz
SRR1042864_s1mi.fastq.gz
The directories returned are as follows:
* organisms: ``<directory>/``
* samples: ``<directory>/input/``
* data: ``<directory>/``
:param directory: Directory
:type directory: py._path.local.LocalPath
:return: organisms directory, samples directory, data directory
:rtype: tuple(str or unicode, str or unicode, str or unicode)
"""
input_dir = directory.mkdir("input")
test.symlink_files(directory, test.ORGANISM_FILES)
test.symlink_files(input_dir, test.VIGNETTE_INPUT_FILES)
test.symlink_files(directory, test.DATA_FILES)
return str(directory), str(input_dir), str(directory)