def __init__(self, design_filename, adapters):
""".. rubric:: Constructor
:param str design_filename: a CSV file that is compatible
with our :class:`sequana.expdesign.ExpDesignAdapter`
:param adapters: the type of adapters (PCRFree, Nextera,
Rubicon, TruSeq, SMARTer, Small)
The files of adapters are stored in Sequana and accessible with the
sequana_data function. So, for instance if adapters is set to Nextera,
the following file is used to identify the adapters::
sequana_data("adapters_Nextera_fwd.fa")
New adapters files can be added on request. Currently, Nextera and
PCRFree are available. Rubicon and TruSeq will be added soon.
"""
from sequana.expdesign import ExpDesignAdapter
self.design = ExpDesignAdapter(design_filename)
if self.design.df.index.name == "Sample_ID" or \
"Sample_ID" in self.design.df.columns:
self.design.df.set_index("Sample_ID", inplace=True)
else:
raise ValueError("Incorrect design file. Missing Sample_ID field")
self.adapters = adapters
file1 = sequana_data("adapters_%s_fwd.fa" % adapters)
file2 = sequana_data("adapters_%s_revcomp.fa" % adapters)
self._adapters_fwd = AdapterReader(file1)
self._adapters_revc = AdapterReader(file2) # !!! revcomp
def get_sequana_adapters(type_, direction):
"""Return path to a list of adapters in FASTA format
:param tag: PCRFree, Rubicon, Nextera
:param type_: fwd, rev, revcomp
:return: path to the adapter filename
"""
# search possible types
registered = _get_registered_adapters()
if type_ not in registered:
logger.error("This adapter type (%s) is not valid" % type_)
logger.error("choose one in %s types" % registered)
raise ValueError
directions = ["fwd", "rev", "revcomp"]
if direction not in directions:
logger.error("This kind of tag (%s) is not valid" % direction)
logger.error("choose one in %s " % directions)
raise ValueError
try:
this = sequana_data("adapters_%s_%s.fa" % (type_, direction))
logger.warning("Rename {} (remove the adapters_ prefix)".format(this))
return this
except:
return sequana_data("%s_%s.fa" % (type_, direction))
def _get_registered_adapters():
filenames = sequana_data('*', 'data/adapters')
filenames = [x for x in filenames if "_fwd" in x]
registered = [
x.lstrip("adapters_").replace("_fwd.fa", "") for x in filenames
]
registered = set(registered)
return registered
def __init__(self, design_filename, adapters):
""".. rubric:: Constructor
:param str design_filename: a CSV file that is compatible
with our :class:`sequana.expdesign.ExpDesignAdapter`
:param adapters: the type of adapters (PCRFree, Nextera,
Rubicon, TruSeq, SMARTer, Small)
The files of adapters are stored in Sequana and accessible with the
sequana_data function. So, for instance if adapters is set to Nextera,
the following file is used to identify the adapters::
sequana_data("adapters_Nextera_fwd.fa")
New adapters files can be added on request. See resources/data/adapters
for the full list. You can also use::
from sequana.adapters import _get_registered_adapters
_get_registered_adapters()
"""
from sequana.expdesign import ExpDesignAdapter
self.design = ExpDesignAdapter(design_filename)
if self.design.df.index.name == "Sample_ID" or \
"Sample_ID" in self.design.df.columns:
self.design.df.set_index("Sample_ID", inplace=True)
else:
raise ValueError("Incorrect design file. Missing Sample_ID field")
self.adapters = adapters
try:
file1 = sequana_data("adapters_%s_fwd.fa" % adapters)
logger.warning("rename your file removing prefix adatper")
except:
file1 = sequana_data("%s_fwd.fa" % adapters)
try:
file2 = sequana_data("adapters_%s_revcomp.fa" % adapters)
logger.warning("rename your file removing prefix adatper")
except:
file2 = sequana_data("%s_revcomp.fa" % adapters)
self._adapters_fwd = AdapterReader(file1)
self._adapters_revc = AdapterReader(file2) # !!! revcomp
def __init__(self, design_filename, adapters):
""".. rubric:: Constructor
:param str design_filename: a CSV file that is compatible
with our :class:`sequana.iem.IEM`
:param adapters: the type of adapters (PCRFree, Nextera,
Rubicon, TruSeq, SMARTer, Small)
The files of adapters are stored in Sequana and accessible with the
sequana_data function. So, for instance if adapters is set to Nextera,
the following file is used to identify the adapters::
sequana_data("adapters_Nextera_fwd.fa")
New adapters files can be added on request. See resources/data/adapters
for the full list. You can also use::
from sequana.adapters import _get_registered_adapters
_get_registered_adapters()
"""
from sequana.iem import IEM
self.design = IEM(design_filename)
self.adapters = adapters
try:
file1 = sequana_data("adapters_%s_fwd.fa" % adapters)
logger.warning("rename your file removing prefix adatper")
except:
file1 = sequana_data("%s_fwd.fa" % adapters)
try:
file2 = sequana_data("adapters_%s_revcomp.fa" % adapters)
logger.warning("rename your file removing prefix adatper")
except:
file2 = sequana_data("%s_revcomp.fa" % adapters)
self._adapters_fwd = AdapterReader(file1)
self._adapters_revc = AdapterReader(file2) # !!! revcomp
def _get_registered_adapters():
filenames = sequana_data('*', 'data/adapters')
filenames = [x for x in filenames if x.startswith("adapters")]
registered = [x.lstrip("adapters_").split("_",1)[0] for x in filenames]
registered = set(registered)
return registered
