def main():
taxtree_filename = "../taxonomy/nodes.dmp"
get_levels = False
taxtree = ncbi_taxonomy.parse_taxtree(taxtree_filename, get_levels)
species = sys.argv[1:]
for taxid in species:
lineage = ncbi_taxonomy.climb_tax_tree(taxid, taxtree)
print str(taxid) + "\t" + str(lineage)
def main():
taxtree_filename = "../taxonomy/nodes.dmp"
get_levels = True
taxtree, taxlevel = ncbi_taxonomy.parse_taxtree(taxtree_filename, get_levels)
species_file = sys.argv[1]
with open(species_file, 'r') as f:
for l in f:
taxid = l.rstrip('\n')
lineage = ncbi_taxonomy.climb_tax_tree_to_level(taxid, taxtree, taxlevel, "species")
print str(taxid) + "\t" + str(lineage)
def main():
taxtree_filename = "../taxonomy/nodes.dmp"
get_levels = True
taxtree, taxlevel = ncbi_taxonomy.parse_taxtree(taxtree_filename, get_levels)
stoplevel = "Family"
stopcriteria = [
944644, # marseille
549779, # mimi
10486, # irido
10501, # phycodna
43682, # asco
10240, # pox
137992, # asfar
]
species = sys.argv[1:]
for taxid in species:
family = ncbi_taxonomy.climb_tax_tree_to_level(taxid, taxtree, taxlevel, stoplevel)
print str(taxid) + "\t" + str(family)
def main():
filename_uniprot = "data_in/uniprotkb-viruses-reviewed-date-keywords-chain.txt"
taxfilename = "../taxonomy/viruses.categories.txt"
taxfilename_edit = "../taxonomy/dengue-edit"
ncbi_tax_file = "../taxonomy/names.dmp"
taxtree_filename = "../taxonomy/nodes.dmp"
simap_filename = "../SIMAP/virus_vs_all/homologs"
out_clades_file = "data_out/initial_clade_assignments"
# TODO read in the object output by uniprot_to_payload
# but for now, we do it this way
# read the tax and uniprot data
taxmap = parse_taxids(taxfilename,
taxfilename_edit) # mapping isolates to species
uniprot = parse_uniprot(filename_uniprot, taxmap)
# choose the isolates that will be in STRING
chosen = choose_isolates(uniprot)
# then get all the proteins that correspond to these isolates
chosen_proteins = get_chosen_proteins(uniprot, chosen)
# cleave any polyproteins based on the chain entries in uniprot
chosen_proteins = cleave_polyproteins(chosen_proteins)
# convert host name to taxid
ncbi_tax, taxid_to_name = ncbi_taxonomy.parse_ncbi_taxonomy_names(
ncbi_tax_file, True) # mapping name to taxids
chosen_proteins = convert_host_name_to_taxids(chosen_proteins, ncbi_tax)
get_levels = True
taxtree, taxlevel = ncbi_taxonomy.parse_taxtree(taxtree_filename,
get_levels)
# TODO all the above should be encapsulated
clades = generate_clades(chosen_proteins, taxtree, taxlevel, "Family")
print_clades(out_clades_file, clades)
def main():
pickle_file = "data_out/parsed-proteomes"
proteomes_list = "data_in/proteomes-all.tab"
mapfile_proteomes = "data_in/proteomes.entryids"
dirname_proteomes = "data_in/proteomes"
ncbi_tax_file = "../taxonomy/names.dmp"
taxtree_filename = "../taxonomy/nodes.dmp"
pogs_file = "data_in/pVOGs"
out_isolates = "data_out/isolates_amb"
out_isolates_all = "data_out/isolates_all"
out_fasta_dir = "data_out/fastafiles"
out_pfam_file = "data_out/pfam"
out_go_file = "data_out/goterms"
out_functions_file = "data_out/functions"
out_pdb_file = "data_out/pdb"
out_uniprot_file = "data_out/uniprot"
out_host_file = "data_out/hosts"
out_species_file = "data_out/string_v11.species.tsv"
out_synonyms_file = "data_out/synonyms"
out_best_synonyms_file = "data_out/synonyms_best"
out_functions_file = "data_out/functions"
out_pogs_file = "data_out/pogs"
if os.path.isfile(pickle_file):
chosen_proteins = pickle.load(open(pickle_file, "rb"))
else:
# read proteome to entry mapping
proteomes = parse_proteome_mapping(proteomes_list, mapfile_proteomes)
# generate taxmap based on all entries in ncbi taxonomy so that we can map isolate -> species
get_levels = True
taxtree, taxlevel = ncbi_taxonomy.parse_taxtree(
taxtree_filename, get_levels)
unused, taxnames = ncbi_taxonomy.parse_ncbi_taxonomy_names(
ncbi_tax_file, True)
taxmap = {}
for taxid in taxtree:
species = ncbi_taxonomy.climb_tax_tree_to_level(
taxid, taxtree, taxlevel, "species")
if species == -1:
next # above species
taxmap[taxid] = species
# read the tax and uniprot data
chosen_proteins = parse_uniprot_promeome_dir(
proteomes, dirname_proteomes, taxmap, True) # isolate_is_species
sys.stderr.write("parsed uniprot xml\n")
chosen_proteins = cleave_polyproteins(chosen_proteins)
chosen_proteins = dedup(chosen_proteins)
print "have " + str(len(chosen_proteins)) + " left"
chosen_proteins = remove_too_small_genomes(chosen_proteins)
pickle.dump(chosen_proteins, open(pickle_file, "wb"))
if False:
# run this when getting names for textmining
# takes a really long time because it blasts swiss-prot against (some of) tremble to find more synonyms
filename_uniprot_xml_all = "data_in/uniprot_viruses.xml"
allspecies = parse_uniprot_xml(filename_uniprot_xml_all, taxmap)
allspecies = cleave_polyproteins(allspecies)
else:
allspecies = []
# print simple derivatives of the uniprot data
print_fasta(
out_fasta_dir, chosen_proteins, False,
True) # False, True -> no name details, don't print polyproteins
print_pfam(out_pfam_file, chosen_proteins)
print_go(out_go_file, chosen_proteins)
print_pdb(out_pdb_file, chosen_proteins)
print_uniprot(out_uniprot_file, chosen_proteins)
print_hosts(out_host_file, chosen_proteins)
print_species(out_species_file, chosen_proteins)
print_synonyms(out_synonyms_file, out_best_synonyms_file, chosen_proteins,
allspecies)
print_functions(out_functions_file, chosen_proteins)
map_pogs(pogs_file, out_pogs_file, chosen_proteins)
# print output that is needed for text mining
#print_synonyms(out_synonyms_file, out_best_synonyms_file, chosen_proteins, chosen_proteins)
sys.stderr.write("done\n")
def main():
taxtree_filename = "../taxonomy/nodes.dmp"
get_levels = False
taxtree = ncbi_taxonomy.parse_taxtree(taxtree_filename, get_levels)
host_pathogen_list = sys.argv[1]
with open(host_pathogen_list, 'r') as f:
for l in f:
host, pathogen = l.rstrip('\n').split('\t')
lineage = ncbi_taxonomy.climb_tax_tree(host, taxtree)
host_domain = ''
if 2 in lineage:
host_domain = "bacteria"
elif 2157 in lineage:
host_domain = "archaea"
elif 9606 in lineage:
host_domain = "human"
elif 7742 in lineage:
host_domain = "vertebrates"
elif 33208 in lineage:
host_domain = "animals"
elif 3193 in lineage:
host_domain = "plants"
elif 6960 in lineage:
host_domain = "insects"
elif 4751 in lineage:
host_domain = "fungi"
elif 2759 in lineage:
host_domain = "eukaryota"
else:
host_domain = "none"
lineage = ncbi_taxonomy.climb_tax_tree(pathogen, taxtree)
pathogen_domain = ''
if 2 in lineage:
pathogen_domain = "bacteria"
elif 2157 in lineage:
pathogen_domain = "archaea"
elif 5794 in lineage:
pathogen_domain = "apicomplexa (protists)"
elif 5653 in lineage:
pathogen_domain = "kinetoplastida (protists)"
elif 554915 in lineage:
pathogen_domain = "amoebozoa"
elif 6340 in lineage:
pathogen_domain = "annelida (worms)"
elif 6157 in lineage:
pathogen_domain = "platyhelminthes (worms)"
elif 6231 in lineage:
pathogen_domain = "nematoda (worms)"
elif 10232 in lineage:
pathogen_domain = "acanthocephala (worms)"
elif 33340 in lineage:
pathogen_domain = "neoptera (fleas, louse)"
elif 4751 in lineage:
pathogen_domain = "fungi"
elif 7742 in lineage:
pathogen_domain = "vertebrates"
elif 2759 in lineage:
pathogen_domain = "eukaryota"
elif 10239 in lineage:
pathogen_domain = "viruses"
else:
pathogen_domain = "none"
print host + "\t" + host_domain + "\t" + pathogen + "\t" + pathogen_domain