def buildOrganismsElement(h_annoT, h_ti_contig, hostTaxon, h_refRead,
h_refScore, h_gisPerTi, h_tiRef, reads,
h_readSequence, samFile, mySqlConf):
NAs = 'X'
useMysql = True
con = None
#(hostname,port,user,passwd,defaultDb)=range(5)
(_, _, _, passwd, _) = range(5)
if mySqlConf[passwd] == NAs: #then, we do not use mysql
useMysql = False
organismsObj = Organisms()
readCnt = len(reads)
hostScore = 0
if len(hostTaxon) > 0:
try:
hostScore = h_refScore[hostTaxon]
except:
hostScore = 0
numTargetReads = readCnt - hostScore
organismsObj.numAlignedReads = numTargetReads
organismsObj.numMappedGenomes = len(h_gisPerTi)
if useMysql:
con = dbUtils.init_mysql_innocentive(mySqlConf, 0)
for ti in h_gisPerTi:
refIdName = h_tiRef.get(ti, [ti, ti])
refId = refIdName[0]
score = h_refScore.get(refId, 0)
organismName = refIdName[1]
lineage = ''
#if taxonomyLevelF:
if useMysql:
organismName, lineage = dbUtils.findOrganismLineage(con, ti)
organism = Organism(organismName)
if useMysql:
words = organismName.split()
length = len(words)
if length > 0:
organism.genus = words[0]
if length > 1:
organism.species = words[1]
if length > 2:
organism.strain = words[2]
organism.relativeAmount = RelativeAmount(score)
organism.relativeAmount.count = len(h_refRead.get(refId, [-1]))
organism.taxonomy = Taxonomy(lineage)
organism.taxonomy.taxon_id = ti
genes = []
if h_annoT.get(ti, -1) != -1:
for giList in h_annoT[ti]:
gene = Gene(giList[1])
if giList[2] and giList[2] != NAs:
gene.locus_tag = giList[2]
if giList[3] and giList[3] != NAs:
gene.protein_id = giList[3]
if giList[4] and giList[4] != NAs:
gene.ref_name = giList[4]
if giList[5] and giList[5] != NAs:
gene.product = giList[5]
genes.append(gene)
organism.genes = genes
#add contig information
contigs = []
j = 0
ctgs = h_ti_contig.get(ti, [])
for c in ctgs:
ti_contig = ti + '_ctg_' + str(j)
contig2 = Contig(ti_contig)
contig2.ref_name = c[
0] #make sure that all string format only available in xml
contig2.length = str(c[1])
contig2.contig = c[2]
j += 1
contigs.append(contig2)
organism.contigs = contigs
#add read information
reads = []
readnames = h_refRead.get(refId, [])
for readname in readnames:
read = Read(readname)
read.readSequence = h_readSequence[readname]
reads.append(read)
organism.reads = reads
organismsObj.organisms.append(organism)
organismsObj.organisms = sorted(organismsObj.organisms,
key=lambda x: x.relativeAmount.value,
reverse=True)
organismsElement = organismsObj.buildElement()
if con:
dbUtils.mysql_close(con)
return organismsElement
def append_ti_into_fasta_mysql(con, nt, Ti2sel, enable_descF, enable_onlineF,
nt2, noTaxIdFa, invalSelFlag):
NOT_VALID=-1
GET_ALL_TAX=-2
TAXON_ID=1
#check if nt has ti tagged already
tiReadyF=False
if check_if_nt_has_ti(nt):
tiReadyF=True
get_all_taxF=False
if Ti2sel[0]==GET_ALL_TAX:
get_all_taxF=True
print 'selecting some reference genome sequences in [%s]' % nt
if (invalSelFlag):
fp1 = open(noTaxIdFa,'w')
with open(nt2,'w') as fp2:
with open(nt,'r') as fp:
for r in seqParse.parse(fp,'fasta'):
if tiReadyF:
mObj=re.search(r'ti\|(\d+)\|',r.id)
if not mObj:
continue
ti=int(mObj.group(1))
if ti!=NOT_VALID and (get_all_taxF or (ti in Ti2sel)):
if enable_descF and r.description:
fp2.write('>%s\n%s\n' % (r.description, r.seq))
else:
fp2.write('>%s\n%s\n' % (r.id, r.seq))
else:
mObj=re.search(r'gi\|(\d+)\|\S+\|(\S+)',r.id)
if not mObj:
continue
gi=int(mObj.group(1))
with con:
cur=con.cursor()
sqlcmd='select taxon from giAnnoT where gi=%d' %gi
cur.execute(sqlcmd)
entr = cur.fetchone()
if entr:
ti=int(entr[0])
elif enable_onlineF:
seqId=int(mObj.group(2))
ti=pathoUtilsA.ncbi_eutil(gi,seqId,TAXON_ID) #updated ti
else:
ti=NOT_VALID
if ti==NOT_VALID:
if (invalSelFlag):
fp1.write('>ti|-1|%s\n%s\n' % (r.description,r.seq))
else:
if get_all_taxF or (ti in Ti2sel):
organismName, _ = dbUtils.findOrganismLineage(con, ti)
organismName = re.sub('\s+', '_', organismName)
if enable_descF and r.description:
fp2.write('>ti|%d|org|%s|%s\n%s\n' % (ti, organismName,
r.description, r.seq))
else:
fp2.write('>ti|%d|org|%s|%s\n%s\n' % (ti, organismName,
r.id, r.seq))
print 'check %s' % nt2
if (invalSelFlag):
fp1.close()
print 'check %s' % noTaxIdFa
print 'done.'
def buildOrganismsElement(h_annoT, h_ti_contig, hostTaxon, h_refRead, h_refScore, h_gisPerTi, h_tiRef, reads, h_readSequence, samFile, mySqlConf): NAs = 'X' useMysql=True con = None #(hostname,port,user,passwd,defaultDb)=range(5) (_,_,_,passwd,_)=range(5) if mySqlConf[passwd]==NAs: #then, we do not use mysql useMysql=False organismsObj = Organisms() readCnt = len(reads) hostScore = 0 if len(hostTaxon)>0: try: hostScore = h_refScore[hostTaxon] except: hostScore = 0 numTargetReads = readCnt-hostScore organismsObj.numAlignedReads = numTargetReads organismsObj.numMappedGenomes = len(h_gisPerTi) if useMysql: con = dbUtils.init_mysql_innocentive(mySqlConf,0) for ti in h_gisPerTi: refIdName = h_tiRef.get(ti, [ti, ti]) refId = refIdName[0] score = h_refScore.get(refId,0) organismName=refIdName[1] lineage='' #if taxonomyLevelF: if useMysql: organismName, lineage = dbUtils.findOrganismLineage(con, ti) organism = Organism(organismName) if useMysql: words = organismName.split() length = len(words) if length>0 : organism.genus = words[0] if length>1 : organism.species = words[1] if length>2 : organism.strain = words[2] organism.relativeAmount = RelativeAmount(score) organism.relativeAmount.count = len(h_refRead.get(refId,[-1])) organism.taxonomy = Taxonomy(lineage) organism.taxonomy.taxon_id = ti genes = [] if h_annoT.get(ti,-1)!=-1: for giList in h_annoT[ti]: gene = Gene(giList[1]) if giList[2] and giList[2] != NAs: gene.locus_tag = giList[2] if giList[3] and giList[3] != NAs: gene.protein_id = giList[3] if giList[4] and giList[4] != NAs: gene.ref_name = giList[4] if giList[5] and giList[5] != NAs: gene.product = giList[5] genes.append(gene) organism.genes = genes #add contig information contigs = [] j= 0 ctgs = h_ti_contig.get(ti,[]) for c in ctgs: ti_contig = ti+'_ctg_'+str(j) contig2 = Contig(ti_contig) contig2.ref_name = c[0] #make sure that all string format only available in xml contig2.length = str(c[1]) contig2.contig = c[2] j+=1 contigs.append(contig2) organism.contigs = contigs #add read information reads = [] readnames = h_refRead.get(refId,[]) for readname in readnames: read = Read(readname) read.readSequence = h_readSequence[readname] reads.append(read) organism.reads = reads organismsObj.organisms.append(organism) organismsObj.organisms = sorted(organismsObj.organisms, key=lambda x: x.relativeAmount.value, reverse=True) organismsElement = organismsObj.buildElement() if con: dbUtils.mysql_close(con) return organismsElement