getHomoloGene
Returns NBCI's Homolog Gene tables.
getHomoloGene(taxfile="build_inputs/taxid_taxname", genefile="homologene.data", proteinsfile="build_inputs/all_proteins.data", proteinsclusterfile="build_inputs/proteins_for_clustering.data", baseURL="http://ftp.ncbi.nih.gov/pub/HomoloGene/current/")
taxfilepath to local file or to baseURL/taxfile, default="build_inputs/taxid_taxname",genefilepath to local file or to baseURL/genefile, defult="homologene.data"proteinsfilepath to local file or to baseURL/proteinsfile, default="build_inputs/all_proteins.data"proteinsclusterfilepath to local file or to baseURL/proteinsclusterfile, default="build_inputs/proteins_for_clustering.data"baseURLbaseURL for downloading files, default="http://ftp.ncbi.nih.gov/pub/HomoloGene/current/"returns genedfHomolog gene Pandas dataframereturns protclusdfPandas dataframe. Lists one protein per gene that were used for homologene clustering. If a gene has multiple protein accessions derived from alternative splicing, only one protein isoform that give most protein alignment to proteins in other species was selected for clustering and it is listed in this file.returns proteinsdfPandas dataframe. Lists all proteins and their gene information. If a gene has multple protein accessions derived from alternative splicing event, each protein accession is list in a separate line.
>>> import AGEpy as age
>>> genedf, protclusdf, proteinsdf = age.getHomoloGene()
>>> print genedf.head()
HID Taxonomy ID Gene ID Gene Symbol Protein gi Protein accession \
0 3 9606 34 ACADM 4557231 NP_000007.1
1 3 9598 469356 ACADM 160961497 NP_001104286.1
2 3 9544 705168 ACADM 109008502 XP_001101274.1
3 3 9615 490207 ACADM 545503811 XP_005622188.1
4 3 9913 505968 ACADM 115497690 NP_001068703.1
organism
0 Homo sapiens
1 Pan troglodytes
2 Macaca mulatta
3 Canis lupus familiaris
4 Bos taurus
>>> print protclusdf.head()
taxid entrez GeneID gene symbol gene description protein accession.ver \
0 3702 10723019 AT1G27045 AT1G27045 NP_001185103.1
1 3702 10723020 AT2G41231 AT2G41231 NP_001189726.1
2 3702 10723023 AT1G24095 AT1G24095 NP_001185076.1
3 3702 10723026 AT1G12855 AT1G12855 NP_001184976.1
4 3702 10723027 AT4G22758 AT4G22758 NP_001190802.1
mrna accession.ver length of protein listed in column 5 \
0 NM_001198174.1 227
1 NM_001202797.1 99
2 NM_001198147.1 213
3 NM_001198047.1 462
4 NM_001203873.1 255
-11) contains data about gene location on the genome \
0 240254421
1 240254678
2 240254421
3 240254421
4 240256243
starting position of gene in 0-based coordinate \
0 9391608
1 17195291
2 8523246
3 4382159
4 11958309
end position of the gene in 0-based coordinate strand \
0 9393018 +
1 17195914 +
2 8524928 +
3 4383610 +
4 11960035 +
nucleotide gi of genomic sequence where this gene is annotated \
0 AT1G27045
1 AT2G41231
2 AT1G24095
3 AT1G12855
4 AT4G22758
organism
0 Arabidopsis thaliana
1 Arabidopsis thaliana
2 Arabidopsis thaliana
3 Arabidopsis thaliana
4 Arabidopsis thaliana
>>> print proteinsdf.head()
taxid entrez GeneID gene symbol gene description protein accession.ver \
0 3702 10723019 AT1G27045 AT1G27045 NP_001185103.1
1 3702 10723020 AT2G41231 AT2G41231 NP_001189725.1
2 3702 10723020 AT2G41231 AT2G41231 NP_001189726.1
3 3702 10723023 AT1G24095 AT1G24095 NP_001185076.1
4 3702 10723026 AT1G12855 AT1G12855 NP_001184976.1
mrna accession.ver length of protein listed in column 5 \
0 NM_001198174.1 227
1 NM_001202796.1 104
2 NM_001202797.1 99
3 NM_001198147.1 213
4 NM_001198047.1 462
-11) contains data about gene location on the genome \
0 240254421
1 240254678
2 240254678
3 240254421
4 240254421
starting position of gene in 0-based coordinate \
0 9391608
1 17195291
2 17195291
3 8523246
4 4382159
end position of the gene in 0-based coordinate strand \
0 9393018 +
1 17195914 +
2 17195914 +
3 8524928 +
4 4383610 +
nucleotide gi of genomic sequence where this gene is annotated \
0 AT1G27045
1 AT2G41231
2 AT2G41231
3 AT1G24095
4 AT1G12855
organism
0 Arabidopsis thaliana
1 Arabidopsis thaliana
2 Arabidopsis thaliana
3 Arabidopsis thaliana
4 Arabidopsis thaliana