updatedTaxonomy[taxid].add(org) del a orgName = obiTaxonomy.name(commonOrgs[org]) taxid = obiTaxonomy.taxname_to_taxid(orgName) print "Uploading", "gene_association." + org + ".tar.gz" sf_server.upload( "GO", "gene_association." + org + ".tar.gz", filename, title="GO Annotations for " + orgName, tags=["gene", "annotation", "ontology", "GO", orgName, "#uncompressed:%i" % uncompressedSize(filename), "#organism:" + orgName, "#version:%i" % obiGO.Annotations.version] + (["essential"] if org in essentialOrgs else []) + obiTaxonomy.shortname(taxid) ) sf_server.unprotect("GO", "gene_association." + org + ".tar.gz") try: tax = cPickle.load(open(sf_local.localpath_download("GO", "taxonomy.pickle"), "rb")) except Exception: tax = {} ## Upload taxonomy if any differences in the updated taxonomy if any(tax.get(key, set()) != updatedTaxonomy.get(key, set()) for key in set(updatedTaxonomy)): tax.update(updatedTaxonomy) cPickle.dump(tax, open(os.path.join(tmp_path, "taxonomy.pickle"), "wb")) print "Uploading", "taxonomy.pickle" sf_server.upload(
history[hi.split("\t", 1)[0]].append(hi.strip()) for taxid, genes in genes.items(): filename = os.path.join(tmpdir, "gene_info.%s.db" % taxid) f = open(filename, "wb") f.write("\n".join(genes)) f.flush() f.close() print "Uploading", filename sf_server.upload( "NCBI_geneinfo", "gene_info.%s.db" % taxid, filename, title="NCBI gene info for %s" % obiTaxonomy.name(taxid), tags=["NCBI", "gene info", "gene_names", obiTaxonomy.name(taxid)] + obiTaxonomy.shortname(taxid) + (["essential"] if taxid in essential else [])) sf_server.unprotect("NCBI_geneinfo", "gene_info.%s.db" % taxid) filename = os.path.join(tmpdir, "gene_history.%s.db" % taxid) f = open(filename, "wb") f.write("\n".join(history.get(taxid, ""))) f.flush() f.close() print "Uploading", filename sf_server.upload("NCBI_geneinfo", "gene_history.%s.db" % taxid, filename, title="NCBI gene history for %s" % obiTaxonomy.name(taxid), tags=[
for filename in end_files: print "Now reading %s..." % filename org = re.findall('/(\S{3,4})_\S{3}miRNA\.txt', filename)[0] type_file = re.findall(org + '_(\S*)miRNA\.txt', filename)[0] label = re.findall('/(\S{3,4}_\S{3}miRNA?)\.txt', filename)[0] org_taxid = str(toTaxo.get(org)) org = tax.name(str(toTaxo.get(org))) if type_file == 'mat': serverFiles.upload("miRNA", label, filename, title="miRNA: %s mature form" % org, tags=["miRNA"] + tax.shortname(org_taxid)) serverFiles.unprotect("miRNA", label) print '%s mat uploaded' % org for file_line in open(filename).readlines()[1:]: fastprint(miRNA_path, 'a', file_line) elif type_file == 'pre': serverFiles.upload("miRNA", label, filename, title="miRNA: %s pre-form" % org, tags=["miRNA"] + tax.shortname(org_taxid)) serverFiles.unprotect("miRNA", label) print '%s pre uploaded' % org
for fx in [l.rstrip() for l in open(file_org).readlines()]: if orgs_des[fx.split('_')[0]] in org_taxo: end_files = miRNA_info(path, fx,orgs_des[fx.split('_')[0]]) for filename in end_files: print "Now reading %s..." % filename org = re.findall('/(\S{3,4})_\S{3}miRNA\.txt',filename)[0] type_file = re.findall(org+'_(\S*)miRNA\.txt',filename)[0] label = re.findall('/(\S{3,4}_\S{3}miRNA?)\.txt',filename)[0] org_taxid = str(toTaxo.get(org)) org = tax.name(str(toTaxo.get(org))) if type_file == 'mat': serverFiles.upload("miRNA", label, filename, title="miRNA: %s mature form" % org, tags=["miRNA"] + tax.shortname(org_taxid)) serverFiles.unprotect("miRNA", label) print '%s mat uploaded' % org for file_line in open(filename).readlines()[1:]: fastprint(miRNA_path,'a',file_line) elif type_file == 'pre': serverFiles.upload("miRNA", label, filename, title="miRNA: %s pre-form" % org, tags=["miRNA"] + tax.shortname(org_taxid)) serverFiles.unprotect("miRNA", label) print '%s pre uploaded' % org for file_line in open(filename).readlines()[1:]: fastprint(premiRNA_path,'a',file_line) else:
if any(gi.startswith(id + "\t") for id in taxids): genes[gi.split("\t", 1)[0]].append(gi.strip()) history = dict([(taxid, []) for taxid in taxids]) for hi in hist: if any(hi.startswith(id + "\t") for id in taxids): history[hi.split("\t", 1)[0]].append(hi.strip()) for taxid, genes in genes.items(): filename = os.path.join(tmpdir, "gene_info.%s.db" % taxid) f = open(filename, "wb") f.write("\n".join(genes)) f.flush() f.close() print "Uploading", filename sf_server.upload("NCBI_geneinfo", "gene_info.%s.db" % taxid, filename, title = "NCBI gene info for %s" % obiTaxonomy.name(taxid), tags = ["NCBI", "gene info", "gene_names", obiTaxonomy.name(taxid)] + obiTaxonomy.shortname(taxid) + (["essential"] if taxid in essential else [])) sf_server.unprotect("NCBI_geneinfo", "gene_info.%s.db" % taxid) filename = os.path.join(tmpdir, "gene_history.%s.db" % taxid) f = open(filename, "wb") f.write("\n".join(history.get(taxid, ""))) f.flush() f.close() print "Uploading", filename sf_server.upload("NCBI_geneinfo", "gene_history.%s.db" % taxid, filename, title = "NCBI gene history for %s" % obiTaxonomy.name(taxid), tags = ["NCBI", "gene info", "history", "gene_names", obiTaxonomy.name(taxid)] + obiTaxonomy.shortname(taxid) + (["essential"] if taxid in essential else [])) sf_server.unprotect("NCBI_geneinfo", "gene_history.%s.db" % taxid)