datasetsBM
Lists BioMart datasets.
datasetsBM(host=biomart_host)
hostaddress of the host server, default='http://www.ensembl.org/biomart'returnsnothing
>>> import AGEpy as age
>>> age.datasetsBM()
u'acarolinensis_gene_ensembl' Anole lizard genes (AnoCar2.0),
u'acarolinensis_genomic_sequence' Anole lizard sequences (AnoCar2.0),
u'amelanoleuca_gene_ensembl' Panda genes (ailMel1),
u'amelanoleuca_genomic_sequence' Panda sequences (ailMel1),
u'amexicanus_gene_ensembl' Cave fish genes (AstMex102),
u'amexicanus_genomic_sequence' Cave fish sequences (AstMex102),
u'anancymaae_gene_ensembl' Ma's night monkey genes (Anan_2.0),
u'anancymaae_genomic_sequence' Ma's night monkey sequences (Anan_2.0),
u'aplatyrhynchos_gene_ensembl' Duck genes (BGI_duck_1.0),
u'aplatyrhynchos_genomic_sequence' Duck sequences (BGI_duck_1.0),
u'btaurus_gene_ensembl' Cow genes (UMD3.1),
u'btaurus_genomic_sequence' Cow sequences (UMD3.1),
u'btaurus_marker_end' marker_feature_end,
u'btaurus_marker_start' marker_feature,
u'btaurus_qtl_feature' qtl_feature,
.
.
.
filtersBM
Lists BioMart filters for a specific dataset.
filtersBM(dataset,host=biomart_host)
datasetdataset to list filters of-
hostaddress of the host server, default='http://www.ensembl.org/biomart' -
returnsnothing
>>> import AGEpy as age
>>> age.filtersBM('hsapiens_gene_ensembl')
u'affy_hc_g110' 'AFFY HC G110 probe ID(s) [e.g. 266_s_at]' (type id_list, values []),
u'affy_hg_focus' 'AFFY HG Focus probe ID(s) [e.g. 212481_s_at]' (type id_list, values []),
u'affy_hg_u133_plus_2' 'AFFY HG U133 Plus 2 probe ID(s) [e.g. 1553551_s_at]' (type id_list, values []),
u'affy_hg_u133a' 'AFFY HG U133A probe ID(s) [e.g. 211600_at]' (type id_list, values []),
u'affy_hg_u133a_2' 'AFFY HG U133A 2 probe ID(s) [e.g. 211600_at]' (type id_list, values []),
u'affy_hg_u133b' 'AFFY HG U133B probe ID(s) [e.g. 224321_at]' (type id_list, values []),
u'affy_hg_u95a' 'AFFY HG U95A probe ID(s) [e.g. 33866_at]' (type id_list, values []),
u'affy_hg_u95av2' 'AFFY HG U95Av2 probe ID(s) [e.g. 33866_at]' (type id_list, values []),
u'affy_hg_u95b' 'AFFY HG U95B probe ID(s) [e.g. 48794_s_at]' (type id_list, values []),
u'affy_hg_u95c' 'AFFY HG U95C probe ID(s) [e.g. 66888_at]' (type id_list, values []),
u'affy_hg_u95d' 'AFFY HG U95D probe ID(s) [e.g. 70806_at]' (type id_list, values []),
u'affy_hg_u95e' 'AFFY HG U95E probe ID(s) [e.g. 88289_at]' (type id_list, values []),
u'affy_hta_2_0' 'AFFY HTA 2 0 probe ID(s) [e.g. TC04001102.hg]' (type id_list, values []),
u'affy_huex_1_0_st_v2' 'AFFY HuEx 1 0 st v2 probe ID(s) [e.g. 4037584]' (type id_list, values []),
u'affy_hugene_1_0_st_v1' 'AFFY HuGene 1 0 st v1 probe ID(s) [e.g. 8165644]' (type id_list, values []),
u'affy_hugene_2_0_st_v1' 'AFFY HuGene 2 0 st v1 probe ID(s) [e.g. 17100641]' (type id_list, values []),
u'affy_hugenefl' 'AFFY HuGeneFL probe ID(s) [e.g. Z70759_at]' (type id_list, values []),
u'affy_primeview' 'AFFY PrimeView probe ID(s) [e.g. 11761516_x_at]' (type id_list, values []),
.
.
.
attributesBM
Lists BioMart attributes for a specific dataset.
attributesBM(dataset,host=biomart_host)
datasetdataset to list attributes of-
hostaddress of the host server, default='http://www.ensembl.org/biomart' -
returnsnothing
>>> import AGEpy as age
>>> age.attributesBM('hsapiens_gene_ensembl')
u'3_utr_end' '3' UTR end' (default False),
u'3_utr_start' '3' UTR start' (default False),
u'3utr' '3' UTR' (default False),
u'5_utr_end' '5' UTR end' (default False),
u'5_utr_start' '5' UTR start' (default False),
u'5utr' '5' UTR' (default False),
u'acarolinensis_homolog_associated_gene_name' 'Anole lizard gene name' (default False),
u'acarolinensis_homolog_canonical_transcript_protein' 'Query protein or transcript ID' (default False),
u'acarolinensis_homolog_chrom_end' 'Anole lizard chromosome/scaffold end (bp)' (default False),
u'acarolinensis_homolog_chrom_start' 'Anole lizard chromosome/scaffold start (bp)' (default False),
u'acarolinensis_homolog_chromosome' 'Anole lizard chromosome/scaffold name' (default False),
u'acarolinensis_homolog_dn' 'dN with Anole lizard' (default False),
u'acarolinensis_homolog_ds' 'dS with Anole lizard' (default False),
u'acarolinensis_homolog_ensembl_gene' 'Anole lizard gene stable ID' (default False),
.
.
.
queryBM
Queries BioMart.
queryBM(query_attributes,query_dataset,query_filter=None,query_items=None,query_dic=None,host=biomart_host)
query_attributeslist of attributes to recover from BioMartquery_datasetdataset to queryquery_filterone BioMart filter associated with the items being queriedquery_itemslist of items to be queried (must assoiate with given filter)query_querydicfor complex queries this option should be used instead of 'filters' and 'items' and a dictionary of filters provided here eg. querydic={"filter1":["item1","item2"],"filter2":["item3","item4"]}. If using querydic, don't query more than 350 items at once.-
hostaddress of the host server, default='http://www.ensembl.org/biomart' -
returnsa Pandas dataframe of the queried attributes
>>> import AGEpy as age
>>> queryDf=queryBM(query_attributes=["ensembl_gene_id","external_gene_name", \
"go_id","name_1006","definition_1006"],\
query_dataset='hsapiens_gene_ensembl')
>>> print queryDf.head()
ensembl_gene_id external_gene_name go_id name_1006 \
0 ENSG00000283891 MIR628 GO:0005615 extracellular space
1 ENSG00000251931 RNU6-871P
2 ENSG00000207766 MIR626
3 ENSG00000275323 AC012314.7 GO:0003723 RNA binding
4 ENSG00000275323 AC012314.7 GO:0005634 nucleus
definition_1006
0 "That part of a multicellular organism outside..."
1
2
3 "Interacting selectively and non-covalently wi..."
4 "A membrane-bounded organelle of eukaryotic ce..."
FilterGOstring
Filters GO terms based on given strings using ENSEMBL's biomart homology mapping.
FilterGOstring(names_filter=["age-", "aging", "aged", 'aging', 'aging.', 'aging,'], exclude_names=["packaging","voltage","cleavage-", "stage-1","cage-like","message-specific", "damage-associated","stage-specific","foraging", "DNA-damaging","engaging","damaged","packaged"], defs_filter=[" age-", " aging", " aged", ' aging', ' aging.', ' aging,'], exclude_defs=["packaging","voltage","cleavage-", "stage-1","cage-like","message-specific", "damage-associated","stage-specific","foraging", "DNA-damaging","engaging","damaged","packaged"], host=biomart_host, HSA=None,MUS=None,CEL=None,DMEL=None)
names_filterlist of substrings to filter GO names on. Default=["age-", "aging", "aged", 'aging', 'aging.', 'aging,']exclude_nameslist of substrings to be used for exclusion of GO names. Default=["packaging","voltage","cleavage-", "stage-1","cage-like","message-specific", "damage-associated","stage-specific","foraging", "DNA-damaging","engaging","damaged","packaged"]defs_filterlist of substrings to filter GO defenitions on. Default=[" age-", " aging", " aged", ' aging', ' aging.', ' aging,']exclude_defslist of substrings to be used for exclustion of GO defenitions. Default=["packaging","voltage","cleavage-", "stage-1","cage-like","message-specific", "damage-associated","stage-specific","foraging", "DNA-damaging","engaging","damaged","packaged"]hostbiomart host server, default="http://www.ensembl.org/biomart"HSAretrieved hsa dataframeMUSretrieved mus dataframeCELretrieved cel dataframe-
DMELretrieved dmel dataframe -
returnshomology_df, HSA, MUS, CEL, DMEL
>>> import AGEpy as age
>>> homology_df, HSA, MUS, CEL, DMEL=age.FilterGOstring()
>>> print homology_df.head()
HSA_ensembl_gene_id HSA_external_gene_name \
0 ENSG00000000003 TSPAN6
1 ENSG00000000005 TNMD
2 ENSG00000000460 C1orf112
3 ENSG00000000971 CFH
4 ENSG00000002079 MYH16
HSA_go_id \
0 GO:0039532, , GO:0070062, GO:0016021, GO:00160...
1 GO:0005737, , GO:0016020, GO:0035990, GO:00717...
2 NaN
3 , GO:0030449, GO:0070062, GO:0045087, GO:00725...
4 NaN
HSA_name_1006 \
0 , negative regulation of NIK/NF-kappaB signali...
1 , nuclear envelope, cytoplasm, negative regula...
2 NaN
3 , innate immune response, heparan sulfate prot...
4 NaN
HSA_definition_1006 MUS_ensembl_gene_id \
0 "The component of a membrane consisting of the..." ENSMUSG00000067377
1 "The component of a membrane consisting of the..." ENSMUSG00000031250
2 NaN ENSMUSG00000041406
3 "Interacting selectively and non-covalently wi..." NaN
4 NaN NaN
CEL_ensembl_gene_id DMEL_ensembl_gene_id MUS_external_gene_name \
0 NaN NaN Tspan6
1 NaN NaN Tnmd
2 NaN NaN BC055324
3 NaN NaN None
4 NaN NaN None
MUS_go_id ... \
0 GO:0039532, , GO:0070062, GO:0016021, GO:00160... ...
1 GO:0016020, GO:0035990, GO:0071773, GO:0016021... ...
2 GO:0005575, GO:0008150, GO:0003674, ...
3 None ...
4 None ...
MUS_definition_1006 CEL_external_gene_name \
0 "The component of a membrane consisting of the..." None
1 "The component of a membrane consisting of the..." None
2 "Elemental activities, such as catalysis or bi..." None
3 None None
4 None None
CEL_go_id CEL_name_1006 CEL_definition_1006 DMEL_external_gene_name \
0 None None None None
1 None None None None
2 None None None None
3 None None None None
4 None None None None
DMEL_go_id DMEL_name_1006 DMEL_definition_1006 evidence
0 None None None NaN
1 None None None NaN
2 None None None NaN
3 None None None NaN
4 None None None NaN
evidence indicates from which organisms there is evidence of the intended string