def create_mapped_reads_count(self,
parent=None,
name=None,
url=None,
reference_genome=None,
metainfo=None):
"""
Create a Mapped Reads Count file from a local or remote mapped reads count file.
:param parent: accession of parent folder leave empty for ``Imported files``
:type parent: str
:param name: name of the file
:type name: str
:param url: URL of a file
:param reference_genome: reference genome accession
:type reference_genome: str
:param metainfo: metainfo object
:type metainfo: BioMetainfo
:return: file accession
:rtype: str
"""
metainfo = metainfo or BioMetainfo()
name and metainfo.add_string(BioMetainfo.NAME, name)
reference_genome and metainfo.add_file_reference(
BioMetainfo.REFERENCE_GENOME, reference_genome)
url and metainfo.add_external_link(BioMetainfo.DATA_LINK, url)
return self.__invoke_loader('genestack/mappedReadsCountLoader',
'importFile', parent, metainfo)
def create_microarray_assay(self,
parent,
name=None,
urls=None,
method=None,
organism=None,
metainfo=None):
"""
Create a Genestack Microarray Assay inside an Experiment folder. If ``parent`` is not an Experiment, an exception will be raised.
``name`` and ``urls`` are required fields. They can be specified through the arguments or via a metainfo object.
:param parent: accession of parent experiment
:type parent: str
:param name: name of the file
:type name: str
:param urls: list of urls
:type urls: list
:param method: method
:type method: str
:param organism: organism
:type organism: str
:param metainfo: metainfo object
:type metainfo: BioMetainfo
:return: file accession
:rtype: str
"""
metainfo = metainfo or BioMetainfo()
name and metainfo.add_string(BioMetainfo.NAME, name)
organism and metainfo.add_organism(BioMetainfo.ORGANISM, organism)
method and metainfo.add_string(BioMetainfo.METHOD, method)
if urls:
for url in urls:
metainfo.add_external_link(BioMetainfo.READS_LINK, url)
return self.__invoke_loader('genestack/experimentLoader',
'addMicroarrayAssay', parent, metainfo)
def create_report_file(self,
parent=None,
name=None,
urls=None,
metainfo=None):
"""
Create a Genestack Report File from a local or remote data file.
``name`` and ``urls`` are required fields.
They can be specified through the arguments or via a metainfo object.
:param parent: accession of parent folder leave empty for ``Imported files``
:type parent: str
:param name: name of the file
:type name: str
:param urls: URL or list of URLs of local file paths
:type urls: list or str
:param metainfo: metainfo object
:type metainfo: BioMetainfo
:return: file accession
:rtype: str
"""
metainfo = metainfo or BioMetainfo()
name and metainfo.add_string(BioMetainfo.NAME, name)
if urls:
for url in urls:
metainfo.add_external_link(BioMetainfo.DATA_LINK, url)
return self.__invoke_loader('genestack/reportLoader', 'importFile',
parent, metainfo)
def create_dbnsfp(self,
parent=None,
url=None,
name=None,
organism=None,
metainfo=None):
"""
Create a Genestack Variation Database file. ``name`` and ``url`` are required fields.
They can be specified through the arguments or via a metainfo object.
:param parent: accession of parent folder leave empty for ``Imported files``
:type parent: str
:param url: URL or local path
:type url: str
:param name: name of the file
:type name: str
:param organism: organism
:type organism: str
:param metainfo: metainfo object
:type metainfo: BioMetainfo
:return: file accession
:rtype: str
"""
metainfo = metainfo or BioMetainfo()
metainfo.add_string(BioMetainfo.DATABASE_ID, 'dbNSFP')
name and metainfo.add_string(BioMetainfo.NAME, name)
organism and metainfo.add_organism(BioMetainfo.ORGANISM, organism)
if url:
metainfo.add_external_link(BioMetainfo.DATA_LINK, url)
return self.__invoke_loader('genestack/variationDatabaseLoader',
'addDbNSFP', parent, metainfo)
def create_experiment(self,
parent=None,
name=None,
description=None,
metainfo=None):
"""
Create a Genestack Experiment. The ``name`` parameter is required.
It can be specified through the arguments or via a metainfo object.
:param parent: accession of parent folder. Leave empty for ``Imported files``
:type parent: str
:param name: name of the file
:type name: str
:param description: experiment description
:type description: str
:param metainfo: metainfo object
:type metainfo: BioMetainfo
:return: file accession
:rtype: str
"""
metainfo = metainfo or BioMetainfo()
name and metainfo.add_string(BioMetainfo.NAME, name)
description and metainfo.add_string(BioMetainfo.DESCRIPTION,
description)
return self.__invoke_loader('genestack/experimentLoader',
'addExperiment', parent, metainfo)
def create_wig(self,
parent=None,
name=None,
reference_genome=None,
url=None,
metainfo=None):
"""
Create a Genestack Wiggle Track from a local or remote WIG file.
``name`` and ``url`` are required fields. They can be specified through the arguments or via a metainfo object.
:param parent: accession of parent folder. Leave empty for ``Imported files``
:type parent: str
:param name: name of the file
:type name: str
:param reference_genome: accession of reference genome
:type reference_genome: str
:param url: URL or local path to file
:type url: str
:param metainfo: metainfo object
:type metainfo: BioMetainfo
:return: file accession
:rtype: str
"""
metainfo = metainfo or BioMetainfo()
name and metainfo.add_string(BioMetainfo.NAME, name)
reference_genome and metainfo.add_file_reference(
BioMetainfo.REFERENCE_GENOME, reference_genome)
url and metainfo.add_external_link(BioMetainfo.DATA_LINK, url)
return self.__invoke_loader('genestack/wigLoader', 'importFile',
parent, metainfo)
def create_reference_genome(self,
parent=None,
name=None,
description='',
sequence_urls=None,
annotation_url=None,
organism=None,
assembly=None,
release=None,
strain=None,
metainfo=None):
"""
Create a Genestack Reference Genome from a collection of local or remote FASTA sequence files, and a GTF or GFF
annotation file.
:param parent: accession of parent folder leave empty for ``Imported files``
:type parent: str
:param name: name of the file
:type name: str
:param description: experiment description
:type description: str
:param sequence_urls: list urls or local path to sequencing files.
:type sequence_urls: list
:param annotation_url: url to annotation file
:type annotation_url: str
:param organism: organism
:type organism: str
:param assembly: assembly
:type assembly: str
:param release: release
:type release: str
:param strain: strain
:type strain: str
:param metainfo: metainfo object
:type metainfo: BioMetainfo
:return:
"""
metainfo = metainfo or BioMetainfo()
name and metainfo.add_string(BioMetainfo.NAME, name)
organism and metainfo.add_organism(BioMetainfo.ORGANISM, organism)
strain and metainfo.add_string(BioMetainfo.STRAIN, strain)
assembly and metainfo.add_string(BioMetainfo.REFERENCE_GENOME_ASSEMBLY,
assembly)
release and metainfo.add_string(BioMetainfo.REFERENCE_GENOME_RELEASE,
release)
annotation_url and metainfo.add_external_link(
ANNOTATION_KEY, annotation_url, text='Annotations data link')
metainfo.add_string(metainfo.DESCRIPTION, description or '')
for seq_link in sequence_urls:
metainfo.add_external_link(SEQUENCE_KEY,
seq_link,
text='Sequence data link')
return self.__invoke_loader('genestack/referenceGenomeLoader',
'importFile', parent, metainfo)
def create_genome_annotation(self,
parent=None,
url=None,
name=None,
organism=None,
reference_genome=None,
strain=None,
metainfo=None):
"""
Create a Genestack Genome Annotation file from a local or remote file.
``name`` and ``url`` are required fields. They can be specified through the arguments or via a metainfo object.
:param parent: accession of parent folder. Leave empty for ``Imported files``
:type parent: str
:param url: URL or local path
:type url: str
:param name: name of the file
:type name: str
:param organism: organism
:type organism: str
:param reference_genome: reference genome accession
:type reference_genome: str
:param strain: strain
:type strain: str
:param metainfo: metainfo object
:type metainfo: BioMetainfo
:return: file accession
:rtype: str
"""
metainfo = metainfo or BioMetainfo()
name and metainfo.add_string(BioMetainfo.NAME, name)
organism and metainfo.add_organism(BioMetainfo.ORGANISM, organism)
strain and metainfo.add_string(BioMetainfo.STRAIN, strain)
reference_genome and metainfo.add_file_reference(
BioMetainfo.REFERENCE_GENOME, reference_genome)
if url:
metainfo.add_external_link(BioMetainfo.DATA_LINK, url)
return self.__invoke_loader('genestack/genome-annotation-loader',
'addGOAnnotationFile', parent, metainfo)
def create_unaligned_read(self,
parent=None,
name=None,
urls=None,
method=None,
organism=None,
metainfo=None):
"""
Create a Genestack Unaligned Reads file from one or several local or remote files. Most common file formats encoding
sequencing reads with quality scores are accepted (FASTQ 33/64, SRA, FASTA+QUAL, SFF, FAST5).
``name`` and ``urls`` are required fields. They can be specified through the arguments or via a metainfo object.
:param parent: accession of parent folder leave empty for ``Imported files``
:type parent: str
:param name: name of the file
:type name: str
:param urls: list of urls
:type urls: list
:param method: method
:type method: str
:param organism: organism
:type organism: str
:param metainfo: metainfo object
:type metainfo: BioMetainfo
:return: file accession
:rtype: str
"""
metainfo = metainfo or BioMetainfo()
name and metainfo.add_string(BioMetainfo.NAME, name)
organism and metainfo.add_organism(BioMetainfo.ORGANISM, organism)
method and metainfo.add_string(BioMetainfo.METHOD, method)
if urls:
for url in urls:
metainfo.add_external_link(BioMetainfo.READS_LINK, url)
return self.__invoke_loader('genestack/unalignedReadsLoader',
'importFile', parent, metainfo)
def create_bam(self,
parent=None,
name=None,
url=None,
metainfo=None,
organism=None,
strain=None,
reference_genome=None):
"""
Create a Genestack Aligned Reads file from a local or remote BAM file.
:param parent: accession of parent folder leave empty for ``Imported files``
:type parent: str
:param name: name of the file
:type name: str
:param url: URL of a BAM file; the index will be created at initialization
:param metainfo: metainfo object
:type metainfo: BioMetainfo
:param organism: organism
:type organism: str
:param strain: strain
:type strain:
:param reference_genome: reference genome accession
:type reference_genome: str
:return: file accession
:rtype: str
"""
metainfo = metainfo or BioMetainfo()
name and metainfo.add_string(BioMetainfo.NAME, name)
organism and metainfo.add_organism(BioMetainfo.ORGANISM, organism)
strain and metainfo.add_string(BioMetainfo.STRAIN, strain)
reference_genome and metainfo.add_file_reference(
BioMetainfo.REFERENCE_GENOME, reference_genome)
url and metainfo.add_external_link(BioMetainfo.BAM_FILE_LINK, url)
return self.__invoke_loader('genestack/alignedReadsLoader',
'importFile', parent, metainfo)
# parse the CSV file
with open(csv_input, 'r') as the_file:
reader = csv.DictReader(the_file, delimiter=",")
field_names = reader.fieldnames
# check if mandatory keys are in the CSV file
for mandatory_key in MANDATORY_KEYS:
if mandatory_key not in field_names:
raise GenestackException(
"The key '%s' must be supplied in the CSV file" %
mandatory_key)
for file_data in reader:
# for each entry, prepare a BioMetainfo object
metainfo = BioMetainfo()
for key in field_names:
# 'link' and 'organism' are treated separately, as they are added to the metainfo using specific methods
if key == "link":
url = file_data[key]
metainfo.add_external_link(key=BioMetainfo.READS_LINK,
text="link",
url=url,
fmt=file_format)
elif key == "organism":
metainfo.add_organism(BioMetainfo.ORGANISM, file_data[key])
# all the other keys are added as strings
else:
metainfo_key = SPECIAL_KEYS.get(key.lower(), key)
metainfo.add_string(metainfo_key, file_data[key])
reader = csv.DictReader(the_file, delimiter=",")
field_names = reader.fieldnames
if args.local_key not in field_names:
raise GenestackException("Error: the local key %s is not present in the supplied CSV file" % args.local_key)
for file_data in reader:
# find the corresponding file
local_identifier = file_data[local_key]
remote_file = identifier_map.get(local_identifier)
if not remote_file:
print "Warning: no match found for file name '%s'" % local_identifier
continue
# prepare a BioMetainfo object
metainfo = BioMetainfo()
for key in field_names:
# key parsing logic
value = file_data[key]
if value == "" or value is None:
continue
if key == args.local_key:
continue
if key == "organism":
metainfo.add_organism(BioMetainfo.ORGANISM, value)
else:
metainfo_key = SPECIAL_KEYS.get(key.lower(), key)
if parse_as_boolean(value) is not None:
metainfo.add_boolean(metainfo_key, parse_as_boolean(value))
else:
metainfo.add_string(metainfo_key, value)
# parse the CSV file
with open(csv_input, 'r') as the_file:
reader = csv.DictReader(the_file, delimiter=",")
field_names = reader.fieldnames
# check if mandatory keys are in the CSV file
for mandatory_key in MANDATORY_KEYS:
if mandatory_key not in field_names:
raise GenestackException("The key '%s' must be supplied in the CSV file" % mandatory_key)
for file_data in reader:
# for each entry, prepare a BioMetainfo object
metainfo = BioMetainfo()
for key in field_names:
# 'link' and 'organism' are treated separately, as they are added to the metainfo using specific methods
if key == "link":
url = file_data[key]
metainfo.add_external_link(key=BioMetainfo.READS_LINK, text="link", url=url, fmt=file_format)
elif key == "organism":
metainfo.add_organism(BioMetainfo.ORGANISM, file_data[key])
# all the other keys are added as strings
else:
metainfo_key = SPECIAL_KEYS.get(key.lower(), key)
metainfo.add_string(metainfo_key, file_data[key])
# create the sequencing assay on Genestack
created_file = importer.create_sequencing_assay(experiment, metainfo=metainfo)
def create_codon_table(self, parent=None, metainfo=None):
metainfo = metainfo or BioMetainfo()
return self.__invoke_loader('genestack/codonTableLoader',
'addCodonTable', parent, metainfo)
if args.local_key not in field_names:
raise GenestackException(
"Error: the local key %s is not present in the supplied CSV file"
% args.local_key)
for file_data in reader:
# find the corresponding file
local_identifier = file_data[local_key]
remote_file = identifier_map.get(local_identifier)
if not remote_file:
print "Warning: no match found for file name '%s'" % local_identifier
continue
# prepare a BioMetainfo object
metainfo = BioMetainfo()
for key in field_names:
# key parsing logic
value = file_data[key]
if value == "" or value is None:
continue
if key == args.local_key:
continue
if key == "organism":
metainfo.add_organism(BioMetainfo.ORGANISM, value)
else:
metainfo_key = SPECIAL_KEYS.get(key.lower(), key)
if parse_as_boolean(value) is not None:
metainfo.add_boolean(metainfo_key,
parse_as_boolean(value))
else:
