def biomart_iterator(columns,
biomart="ensembl",
dataset="hsapiens_gene_ensembl",
host='www.biomart.org'):
'''download a dataset from biomart and output as a
tab-separated table.
*columns* is a list with field to obtain.
*biomart* and *dataset* denote the
database and dataset to get the data from.
returns a iterator over rows.
'''
R.library("biomaRt")
mart = R.useMart(biomart=biomart, dataset=dataset, host=host)
result = R.getBM(attributes=rpy2.robjects.vectors.StrVector(columns),
mart=mart)
# result is a dataframe.
# rx returns a dataframe.
# rx()[0] returns a vector
for data in zip(*[result.rx(x)[0] for x in columns]):
yield dict(zip(columns, data))
def importFromBiomart(outfile,
columns,
biomart="ensembl",
dataset="hsapiens_gene_ensembl",
host='www.biomart.org'):
'''download a dataset from biomart and output as a
tab-separated table.
*columns* is a dictionary mapping biomart columns to columns in
the output tables. *biomart* and *dataset* denote the database and
dataset to get the data from.
'''
R.library("biomaRt")
keys = columns.keys()
mart = R.useMart(biomart=biomart, dataset=dataset, host=host)
result = R.getBM(attributes=keys, mart=mart)
outf = IOTools.openFile(outfile, "w")
outf.write("\t".join([columns[x] for x in keys]) + "\n")
# for x in ("mim_gene_accession", "mim_morbid_accession"):
# result[x] = [ ("", y)[y >= 0] for y in result[x] ]
for data in zip(*[result[x] for x in keys]):
outf.write("\t".join(map(str, data)) + "\n")
outf.close()
def biomart_iterator( columns,
biomart = "ensembl",
dataset = "hsapiens_gene_ensembl",
host = 'www.biomart.org' ):
'''download a dataset from biomart and output as a
tab-separated table.
*columns* is a list with field to obtain.
*biomart* and *dataset* denote the
database and dataset to get the data from.
returns a iterator over rows.
'''
R.library("biomaRt")
mart = R.useMart(biomart=biomart, dataset= dataset, host=host )
result = R.getBM( attributes=rpy2.robjects.vectors.StrVector(columns),
mart=mart )
# result is a dataframe.
# rx returns a dataframe.
# rx()[0] returns a vector
for data in zip( *[ result.rx(x)[0] for x in columns] ):
yield dict( zip(columns, data) )
def get_exons(mart):
"""Queries a Mart object to find all exons of its dataset attribute.
Forms a specific getBM query that is sent to the BioMart API to
retrieve information about the exons (and their exonic coordinates)
of a specific Dataset. The output is then transformed via the GRanges
Bioconductor package and seqnames converted to UCSC standard.
Args:
mart: an rpy2-converted biomaRt Mart object.
Returns:
An rpy2 DataFrame containing a table of relevant exon information.
DataFrame column headers are:
["seqnames", "start", "end", "width", "strand"]
"""
exons = R.getBM(attributes = StrVector(("chromosome_name",
"exon_chrom_start", "exon_chrom_end", "strand")),
mart=mart)
exons_ranges = R.GRanges(
seqnames=exons.rx2('chromosome_name'),
ranges=R.IRanges(start=exons.rx2('exon_chrom_start'),
end=exons.rx2('exon_chrom_end')),
strand='+' if exons.rx2('strand') == '1L' else '-')
# This was hell to find
# https://stackoverflow.com/questions/38806898/
set_method = R("`seqlevelsStyle<-`")
exons_ranges = set_method(exons_ranges, "UCSC")
as_data_frame = R("function(x) as.data.frame(x)")
exons_ranges_df = as_data_frame(exons_ranges)
return exons_ranges_df
def get_genes(mart):
"""Queries a Mart object to find all genes of its dataset attribute.
Forms a specific getBM query that is sent to the BioMart API to
retrieve information about the genes of a specifc Dataset. This
output is then converted from an rpy2 DataFrame to a pandas
DataFrame.
Args:
mart: an rpy2-converted biomaRt Mart object.
Returns:
An pandas DataFrame containing a table of relevant gene information.
DataFrame column headers are:
["gene_name", "chromosome_name", "start_position", "end_position"]
"""
genes = R.getBM(
attributes = StrVector(("external_gene_name", "chromosome_name",
"start_position", "end_position")),
mart=mart)
genes_df = pandas2ri.ri2py(genes)
genes_df.rename(columns={'external_gene_name': 'gene_name'}, inplace=True)
return genes_df
def importKEGGAssignments(outfile, mart, host, biomart_dataset):
''' import the KEGG annotations from the R KEGG.db
annotations package. Note that since KEGG is no longer
publically availible, this is not up-to-date and maybe removed
from bioconductor in future releases '''
R.library("KEGG.db")
R.library("biomaRt")
E.info("getting entrez to ensembl mapping ...")
mart = R.useMart(biomart=mart,
host=host,
path="/biomart/martservice",
dataset=biomart_dataset)
entrez2ensembl = R.getBM(attributes=ro.StrVector(
["ensembl_gene_id", "entrezgene"]),
mart=mart)
entrez = entrez2ensembl.rx2("entrezgene")
ensembl = entrez2ensembl.rx2("ensembl_gene_id")
entrez2ensembl = dict(zip(entrez, ensembl))
E.info("Done")
E.info("getting entrez to kegg mapping ... ")
entrez2path = R('as.list(KEGGEXTID2PATHID)')
E.info("Done")
E.info("Getting KEGG names")
pathnames = R('as.list(KEGGPATHID2NAME)')
pathid2name = dict(zip(pathnames.names, R.unlist(pathnames)))
E.info("Done")
outf = IOTools.openFile(outfile, "w")
outf.write("ontology\tgene_id\tkegg_ID\tkegg_name\tevidence\n")
for gene in entrez2path.names:
try:
gene = int(gene)
except ValueError:
continue
if gene in entrez2ensembl:
ensid = entrez2ensembl[gene]
else:
continue
for pathway in entrez2path.rx2(str(gene)):
pathid = re.match("[a-z]+([0-9]+)", pathway).groups()[0]
pathname = pathid2name[pathid]
outf.write("\t".join(["kegg", ensid,
str(pathway), pathname, "NA"]) + "\n")
def importKEGGAssignments(outfile, mart, host, biomart_dataset):
''' import the KEGG annotations from the R KEGG.db
annotations package. Note that since KEGG is no longer
publically availible, this is not up-to-date and maybe removed
from bioconductor in future releases '''
R.library("KEGG.db")
R.library("biomaRt")
E.info("getting entrez to ensembl mapping ...")
mart = R.useMart(biomart=mart,
host=host,
path="/biomart/martservice",
dataset=biomart_dataset)
entrez2ensembl = R.getBM(attributes=ro.StrVector(["ensembl_gene_id", "entrezgene"]),
mart=mart)
entrez = entrez2ensembl.rx2("entrezgene")
ensembl = entrez2ensembl.rx2("ensembl_gene_id")
entrez2ensembl = dict(zip(entrez, ensembl))
E.info("Done")
E.info("getting entrez to kegg mapping ... ")
entrez2path = R('as.list(KEGGEXTID2PATHID)')
E.info("Done")
E.info("Getting KEGG names")
pathnames = R('as.list(KEGGPATHID2NAME)')
pathid2name = dict(zip(pathnames.names, R.unlist(pathnames)))
E.info("Done")
outf = IOTools.openFile(outfile, "w")
outf.write("ontology\tgene_id\tkegg_ID\tkegg_name\tevidence\n")
for gene in entrez2path.names:
try:
gene = int(gene)
except ValueError:
continue
if gene in entrez2ensembl:
ensid = entrez2ensembl[gene]
else:
continue
for pathway in entrez2path.rx2(str(gene)):
pathid = re.match("[a-z]+([0-9]+)", pathway).groups()[0]
pathname = pathid2name[pathid]
outf.write(
"\t".join(["kegg", ensid, str(pathway), pathname, "NA"]) + "\n")
def convert_hgnc2ensembl(hgnc_id):
init_biomaRt()
v = R.c(hgnc_id)
res = R.getBM(attributes=R.c("ensembl_gene_id"), filters="hgnc_symbol", values=v, mart=__mart)
try:
return R.get("ensembl_gene_id", res)[0]
except:
print 'Error convert_hgnc2ensembl: '+str(hgnc_id)+' not found in database'
return None
def convert_list_ensembl2hgnc(ensembl_id_list):
init_biomaRt()
v = R.c(ensembl_id_list)
res = R.getBM(attributes=R.c("hgnc_symbol"), filters="ensembl_gene_id", values=v, mart=__mart)
try:
return R.get("hgnc_symbol", res)
except:
print 'Error convert_ensembl2hgnc: '+str(ensembl_id)+' not found in database'
return None
def biomart_iterator(columns,
biomart="ensembl",
dataset="hsapiens_gene_ensembl",
host='www.biomart.org',
path="/biomart/martservice",
filters=None,
values=None,
archive=False):
'''download a dataset from biomart and output as a
tab-separated table.
*columns* is a list with field to obtain.
*biomart* and *dataset* denote the
database and dataset to get the data from.
returns a iterator over rows.
'''
R.library("biomaRt")
mart = R.useMart(biomart=biomart,
dataset=dataset,
host=host,
path=path,
archive=archive)
if filters is not None:
filter_names = R.StrVector(filters)
else:
filter_names = ""
if values is not None:
filter_values = values
else:
filter_values = ""
# result is a dataframe
result = R.getBM(
attributes=rpy2.robjects.vectors.StrVector(columns),
filters=filter_names,
values=filter_values,
mart=mart)
# access via result.rx was broken in rpy2 2.4.2, thus try
# numeric access
assert tuple(result.colnames) == tuple(columns),\
"colnames in dataframe: %s different from expected: %s" % \
(str(tuple(result.colnames)), tuple(columns))
for data in zip(*[result[x] for x in range(len(columns))]):
yield dict(zip(columns, data))
def importFromBiomart(outfile,
columns,
biomart="ensembl",
dataset="hsapiens_gene_ensembl",
host='www.biomart.org'):
'''download a dataset from biomart and output as a
tab-separated table.
Arguments
---------
outfile : string
Filename of output file
columns : dict
Dictionary mapping biomart columns to columns in the output table.
biomart : string
Biomart name
dataset : string
Biomart dataset
host : string
Biomart host
'''
R.library("biomaRt")
keys = columns.keys()
# The default value for host in the biomaRt package is
# www.biomart.org but for some reason R errors if you specify
# host manually but then use the default - but it is fine if
# host is anything valid apart from www.biomart.org. So I have
# changed this to only specify a value if the value you
# are specifying is different to the default KB
if host == 'www.biomart.org':
mart = R.useMart(biomart=biomart, dataset=dataset)
else:
mart = R.useMart(biomart=biomart, dataset=dataset, host=host)
result = R.getBM(attributes=keys, mart=mart)
outf = IOTools.openFile(outfile, "w")
outf.write("\t".join([columns[x] for x in keys]) + "\n")
# for x in ("mim_gene_accession", "mim_morbid_accession"):
# result[x] = [ ("", y)[y >= 0] for y in result[x] ]
for data in zip(*[result[x] for x in keys]):
outf.write("\t".join(map(str, data)) + "\n")
outf.close()
def importFromBiomart(outfile,
columns,
biomart="ensembl",
dataset="hsapiens_gene_ensembl",
host='www.biomart.org'):
'''download a dataset from biomart and output as a
tab-separated table.
Arguments
---------
outfile : string
Filename of output file
columns : dict
Dictionary mapping biomart columns to columns in the output table.
biomart : string
Biomart name
dataset : string
Biomart dataset
host : string
Biomart host
'''
R.library("biomaRt")
keys = list(columns.keys())
# The default value for host in the biomaRt package is
# www.biomart.org but for some reason R errors if you specify
# host manually but then use the default - but it is fine if
# host is anything valid apart from www.biomart.org. So I have
# changed this to only specify a value if the value you
# are specifying is different to the default KB
if host == 'www.biomart.org':
mart = R.useMart(biomart=biomart, dataset=dataset)
else:
mart = R.useMart(biomart=biomart, dataset=dataset, host=host)
result = R.getBM(attributes=keys, mart=mart)
outf = IOTools.openFile(outfile, "w")
outf.write("\t".join([columns[x] for x in keys]) + "\n")
# for x in ("mim_gene_accession", "mim_morbid_accession"):
# result[x] = [ ("", y)[y >= 0] for y in result[x] ]
for data in zip(*[result[x] for x in keys]):
outf.write("\t".join(map(str, data)) + "\n")
outf.close()
def biomart_iterator(columns,
biomart="ensembl",
dataset="hsapiens_gene_ensembl",
host='www.biomart.org',
path="/biomart/martservice",
filters=None,
values=None,
archive=False):
'''download a dataset from biomart and output as a
tab-separated table.
Arguments
---------
columns : dict
List of fields to obtain.
biomart : string
Biomart name
dataset : string
Biomart dataset
host : string
Biomart host
filters : list
List of filter to use
values : list
Values of the filters
archive : bool
If True, use archived version
Returns
-------
iterator
Iterator over rows in biomart database. Each row
is dictionary mapping column names to values.
'''
R.library("biomaRt")
# The default value for host in the biomaRt package is
# www.biomart.org but for some reason R errors if you specify
# host manually but then use the default - but it is fine if
# host is anything valid apart from www.biomart.org. So I have
# changed this to only specify a value if the value you
# are specifying is different to the default KB
if host == 'www.biomart.org':
mart = R.useMart(biomart=biomart,
dataset=dataset,
path=path,
archive=archive)
else:
mart = R.useMart(biomart=biomart,
dataset=dataset,
host=host,
path=path,
archive=archive)
if filters is not None:
filter_names = rpy2.robjects.vectors.StrVector(filters)
else:
filter_names = ""
if values is not None:
filter_values = values
else:
filter_values = ""
# result is a dataframe
result = R.getBM(attributes=rpy2.robjects.vectors.StrVector(columns),
filters=filter_names,
values=filter_values,
mart=mart)
# access via result.rx was broken in rpy2 2.4.2, thus try
# numeric access
assert tuple(result.colnames) == tuple(columns),\
"colnames in dataframe: %s different from expected: %s" % \
(str(tuple(result.colnames)), tuple(columns))
for data in zip(*[result[x] for x in range(len(columns))]):
yield dict(zip(columns, data))
def return_bm_df(atts, mart):
atts_vector = StrVector([x for x in atts])
BM = R.getBM(attributes = atts_vector, mart = mart)
return r2pd_dataframe(BM)
def biomart_iterator(columns,
biomart="ensembl",
dataset="hsapiens_gene_ensembl",
host='www.biomart.org',
path="/biomart/martservice",
filters=None,
values=None,
archive=False):
'''download a dataset from biomart and output as a
tab-separated table.
Arguments
---------
columns : dict
List of fields to obtain.
biomart : string
Biomart name
dataset : string
Biomart dataset
host : string
Biomart host
filters : list
List of filter to use
values : list
Values of the filters
archive : bool
If True, use archived version
Returns
-------
iterator
Iterator over rows in biomart database. Each row
is dictionary mapping column names to values.
'''
R.library("biomaRt")
# The default value for host in the biomaRt package is
# www.biomart.org but for some reason R errors if you specify
# host manually but then use the default - but it is fine if
# host is anything valid apart from www.biomart.org. So I have
# changed this to only specify a value if the value you
# are specifying is different to the default KB
if host == 'www.biomart.org':
mart = R.useMart(biomart=biomart, dataset=dataset, path=path,
archive=archive)
else:
mart = R.useMart(biomart=biomart, dataset=dataset, host=host,
path=path, archive=archive)
if filters is not None:
filter_names = rpy2.robjects.vectors.StrVector(filters)
else:
filter_names = ""
if values is not None:
filter_values = values
else:
filter_values = ""
# result is a dataframe
result = R.getBM(
attributes=rpy2.robjects.vectors.StrVector(columns),
filters=filter_names,
values=filter_values,
mart=mart)
# access via result.rx was broken in rpy2 2.4.2, thus try
# numeric access
assert tuple(result.colnames) == tuple(columns),\
"colnames in dataframe: %s different from expected: %s" % \
(str(tuple(result.colnames)), tuple(columns))
for data in zip(*[result[x] for x in range(len(columns))]):
yield dict(list(zip(columns, data)))
def make_lookup(mart_name, dataset, attributes, filters=None, values=None,
unique_rows=True):
"""
Given a mart name, dataset name, and a list of attributes, return
a pandas.DataFrame indexed by the first attribute in the list provided.
In R, filters is a character vector, and values is either a single
character vector (if only one filter provided) or a list of character
vectors.
This function allows `filters` to be a dictionary where keys are filters
and values are...values.
>>> mart_name = 'ensembl'
>>> dataset = 'dmelanogaster_gene_ensembl'
>>> filters = ['flybase_gene_id', 'chromosome_name']
>>> attributes = ['flybase_gene_id', 'flybasename_gene', 'chromosome_name']
>>> values = [['FBgn0031208', 'FBgn0002121', 'FBgn0031209', 'FBgn0051973'], ['2L']]
>>> df = make_lookup(
... mart_name=mart_name,
... dataset=dataset,
... attributes=attributes,
... filters=filters,
... values=values)
Alternatively, make a dictionary of filters: values, in which case you
don't need to provide `values` separately:
>>> filters = {
... 'flybase_gene_id': ['FBgn0031208', 'FBgn0002121', 'FBgn0031209', 'FBgn0051973'],
... 'chromosome_name': ['2L']}
>>> df2 = make_lookup(
... mart_name=mart_name,
... dataset=dataset,
... attributes=attributes,
... filters=filters)
Confirm that both methods yield identical results:
>>> assert np.all(df.values == df2.values)
Check results:
>>> df.head()
flybasename_gene chromosome_name
flybase_gene_id
FBgn0002121 l(2)gl 2L
FBgn0031208 CG11023 2L
FBgn0031209 Ir21a 2L
FBgn0051973 Cda5 2L
<BLANKLINE>
[4 rows x 2 columns]
Indexing by gene ID (or whatever was the first attribute provided):
>>> df.ix['FBgn0031209']
flybasename_gene Ir21a
chromosome_name 2L
Name: FBgn0031209, dtype: object
Extracting data:
>>> df.ix['FBgn0031209']['flybasename_gene']
'Ir21a'
Or get all names:
>>> df['flybasename_gene']
flybase_gene_id
FBgn0002121 l(2)gl
FBgn0031208 CG11023
FBgn0031209 Ir21a
FBgn0051973 Cda5
Name: flybasename_gene, dtype: object
"""
mart = r.useDataset(dataset, mart=r.useMart(mart_name))
attributes = robjects.StrVector(attributes)
kwargs = dict(
attributes=attributes,
uniqueRows=unique_rows,
mart=mart
)
def _filter_and_values_to_RList(d):
"""`d` is a dictionary of filters: values. Returns a StrVector and
a ListVector of StrVectors"""
# Could use ListVector directly with the dict, but want to guarantee
# positional order of filters and values
f = robjects.StrVector(list(d.keys()))
v = robjects.ListVector(
rpy2.rlike.container.TaggedList(
d.values(),
tags=list(d.keys())
)
)
return f, v
if isinstance(filters, dict):
if values is not None:
raise ValueError("`values` are already specified in the "
"`filters` dictionary")
filter_value_dict = filters
_filters, _values = _filter_and_values_to_RList(filter_value_dict)
kwargs['filters'] = _filters
kwargs['values'] = _values
elif filters is None:
if values is not None:
raise ValueError("`filters` must be specified if `values` "
"is specified; alternatively use a dictionary "
" for `filters`")
elif filters and values:
# values needs to be a list of lists; convert it to one if it's not
# already
if not isinstance(values[0], (list, tuple)):
values = [values]
# If we got here, then assume filters is a list or tuple
if len(filters) != len(values):
raise ValueError('Length of `filters` and `values` must match')
filter_value_dict = dict(zip(filters, values))
_filters, _values = _filter_and_values_to_RList(filter_value_dict)
kwargs['filters'] = _filters
kwargs['values'] = _values
else:
raise ValueError('unhandled case')
results = r.getBM(**kwargs)
return rpy2_to_pandas(results, index_col=0)
