def gi_list_to_taxa_pred(gi_list,gi_format,ncbi_taxonomy_dir,pred_out_taxa):
import re
re_gi = re.compile(r"[^\t]+\t[^\t]*\bgi\|([0-9]+\b)")
if ncbi_taxonomy_dir:
ncbi_taxonomy_dir = os.path.abspath(ncbi_taxonomy_dir)
giToTaxa = loadGiTaxBin(ncbiTaxaDumpDir=ncbi_taxonomy_dir)
inp = openCompressed(gi_list,"r")
if gi_format == "ncbi_pipes":
gi_extractor = lambda line: line.split("gi|")[1].split("|")[0].strip()
elif gi_format == "ncbi_pipes_blast_m8":
gi_extractor = lambda line: line.split("\t",2)[1].split("gi|")[1].split("|")[0].strip()
#gi_extractor = lambda line: re_gi.match(line).group(1)
else:
gi_extractor = lambda line: line.strip()
makeFilePath(pred_out_taxa)
pred = TaxaPred(pred_out_taxa,mode="w")
pred.initForAppend(idSampDtype=int,expectedrows=10**6)
data = pred.getData()
gi_rej = []
n_unresolved = 0
gi_rej_buf_size = 10**0
def _resolve_gi_to_taxid_entrez(gi_rej,predTaxid):
print ("Attempting to resolve taxids for {0} missing records by calling NCBI EUtils Web server. "+\
"This may fail or block with a potentially long time out depending on a quality of your Internet "+\
"connection or NCBI server load.").format(len(gi_rej))
from MGT.Entrez import EzRequest
id_rej = set( (g_r[1] for g_r in gi_rej) )
req = EzRequest(rettype="xml")
gi_rej_to_taxid = dict( (rec["Gi"],rec["TaxId"]) for rec in req.summary(ids=id_rej) )
print "DEBUG: gi_rej_to_taxid = ", gi_rej_to_taxid
n_unresolved = 0
for (i_samp,gi_samp) in gi_rej:
if gi_samp in gi_rej_to_taxid:
predTaxid[i_samp] = gi_rej_to_taxid[gi_samp]
print "DEBUG: predTaxid[{0}] = gi_rej_to_taxid[{1}]".format(i_samp,gi_samp)
else:
n_unresolved += 1
return n_unresolved
idSamp = []
lenSamp = []
predTaxid = []
predScore = []
i_samp_batch = 0
flush_buff_size = 10**5
for i_samp,line in enumerate(inp):
gi = int(gi_extractor(line))
taxid = rejTaxid
try:
taxid = giToTaxa[gi]
if not taxid:
taxid = rejTaxid
print "WARNING: GI corresponds to undefined taxid: {0}".format(gi)
except:
print "WARNING: GI is larger than the max GI in our taxonomy DB:{0}".format(gi)
if taxid == rejTaxid:
gi_rej.append((i_samp_batch,gi))
idSamp.append(i_samp)
lenSamp.append(1)
predTaxid.append(taxid)
predScore.append(1)
i_samp_batch += 1
if i_samp % flush_buff_size == 0:
if len(gi_rej):
n_unresolved += _resolve_gi_to_taxid_entrez(gi_rej=gi_rej,predTaxid = predTaxid)
gi_rej = []
print "Read {0} input records. Taxid not found for {1} records".format(i_samp,n_unresolved)
data.idSamp.append(idSamp)
data.lenSamp.append(lenSamp)
data.predTaxid.append(predTaxid)
data.predScore.append(predScore)
idSamp = []
lenSamp = []
predTaxid = []
predScore = []
i_samp_batch = 0
pred.flush()
if len(gi_rej):
n_unresolved += _resolve_gi_to_taxid_entrez(gi_rej=gi_rej,predTaxid = predTaxid)
gi_rej = []
data.idSamp.append(idSamp)
data.lenSamp.append(lenSamp)
data.predTaxid.append(predTaxid)
data.predScore.append(predScore)
idSamp = []
lenSamp = []
predTaxid = []
predScore = []
i_samp_batch = 0
pred.flush()
pred.close()
inp.close()
print "Read {0} input records. Taxid not found for {1} records".format(i_samp,n_unresolved)
def annot_cons_to_taxa_pred(annot_cons,rec_type,min_len_samp,pred_out_taxa):
makeFilePath(pred_out_taxa)
pred = TaxaPred(pred_out_taxa,mode="w")
pred.initForAppend(expectedrows=10**6)
data = pred.getData()
idSamp = []
lenSamp = []
predTaxid = []
predScore = []
i_samp_batch = 0
flush_buff_size = 10**5
inp = openCompressed(annot_cons,"r")
for i_samp,line in enumerate(inp):
words = line.rstrip("\n").split("\t")
rec = dict(it.izip(words[::2],words[1::2]))
rec_len_samp = int(rec.get("lenSamp",0))
if not ( rec_len_samp >= min_len_samp and \
rec.get("recType","") == rec_type ):
continue
taxid = rec["bott_taxid"]
if taxid:
taxid = int(taxid)
else:
taxid = rejTaxid
#print "DEBUG: empty taxid in rec: {0}".format(str(rec))
idSamp.append(rec["idSamp"])
lenSamp.append(rec_len_samp)
predTaxid.append(taxid)
predScore.append(float(rec.get("score",rec.get("conf_x",1.))))
i_samp_batch += 1
if i_samp % flush_buff_size == 0:
print "Read {0} input records.".format(i_samp)
data.idSamp.append(idSamp)
data.lenSamp.append(lenSamp)
data.predTaxid.append(predTaxid)
data.predScore.append(predScore)
idSamp = []
lenSamp = []
predTaxid = []
predScore = []
i_samp_batch = 0
pred.flush()
data.idSamp.append(idSamp)
data.lenSamp.append(lenSamp)
data.predTaxid.append(predTaxid)
data.predScore.append(predScore)
idSamp = []
lenSamp = []
predTaxid = []
predScore = []
i_samp_batch = 0
pred.flush()
pred.close()
inp.close()
print "Read {0} input records.".format(i_samp)