def getNodesDump_online(downloadD): if not os.path.exists(downloadD): os.makedirs(downloadD) downFbase='taxdump' downExt='tar.gz' phyloNodeFtp='ftp://ftp.ncbi.nih.gov/pub/taxonomy/%s.%s' % (downFbase,downExt) nodesDfn=pathoUtilsA.wget_download2(phyloNodeFtp,downFbase,downExt,downloadD,'select','nodes.dmp') return nodesDfn
def getGi2TaxDump_online(downloadD): if not os.path.exists(downloadD): os.makedirs(downloadD) downFbase='gi_taxid_nucl.dmp' downExt='gz' gi2taxFtp='ftp://ftp.ncbi.nih.gov/pub/taxonomy/%s.%s' % (downFbase,downExt) gi2taxDump=pathoUtilsA.wget_download2(gi2taxFtp,downFbase,downExt,downloadD,'select','gi_taxid_nucl.dmp') return gi2taxDump
def gb2prepare_load_data_file(MySqlConf,tiNtDfn,downloadD):
HOST_NAME,MYSQL_PORT,USER,PASSWORD,DEFAULT_DB = range(5)
#TODO[to develop to maintain pathoDB , differential updates]----------
#to clean up downloadD first
downloadD_gff = downloadD + '/gbff'
gbDnExt=['x','x','x']
gbDnExt[0] = 'seq.gz'
gbDnExt[1] = 'gbff.gz'
gbDnExt[2] = 'protein.gpff.gz'
if not os.path.exists(downloadD_gff):
os.makedirs(downloadD_gff)
else:
cmd = 'rm -rf %s/*.gbff.gz*\n' % (downloadD_gff)
cmd = '%srm -rf %s/*.gpff.gz*\n' % (cmd,downloadD_gff)
cmd = '%srm -rf %s/*.seq.gz*\n' % (cmd,downloadD_gff)
os.system(cmd)
#download genabank flat format files
downExt='gz'
downFbase='*.seq'
#downFbase='gbest?.seq' #debug
gbFlatFtpD='ftp://ftp.ncbi.nih.gov/genbank'
gbFlatFtp=gbFlatFtpD+'/'+downFbase+'.'+downExt
dummy=pathoUtilsA.wget_download2(gbFlatFtp,downFbase,downExt,downloadD_gff,'nothing','X')
#download refseq flat format files (genomic and rna)
downExt='gz'
downFbase='*.gbff'
#downFbase='complete.?.*.gbff' #debug
refSeqFlatFtpD='ftp://ftp.ncbi.nlm.nih.gov/refseq/release/complete'
refSeqFlatFtp=refSeqFlatFtpD+'/'+downFbase+'.'+downExt
dummy=pathoUtilsA.wget_download2(refSeqFlatFtp,downFbase,downExt,downloadD_gff,'nothing','X')
#download refseq flat format files (protein)
downExt='gz'
downFbase='*.gpff'
#downFbase='complete.?.protein.gpff' #debug
refSeqFlatFtpD='ftp://ftp.ncbi.nlm.nih.gov/refseq/release/complete'
refSeqFlatFtp=refSeqFlatFtpD+'/'+downFbase+'.'+downExt
dummy=pathoUtilsA.wget_download2(refSeqFlatFtp,downFbase,downExt,downloadD_gff,'nothing','X')
#download tsa flat format files
downExt='gz'
downFbase='*.gbff'
#downFbase='tsa.GAA?.1.gbff' #debug
refSeqFlatFtpD='ftp://ftp.ncbi.nih.gov/genbank/tsa'
refSeqFlatFtp=refSeqFlatFtpD+'/'+downFbase+'.'+downExt
dummy=pathoUtilsA.wget_download2(refSeqFlatFtp,downFbase,downExt,downloadD_gff,'nothing','X')
#except the following format files
cmd = 'rm -rf %s/*.mstr.gbff.gz' % downloadD_gff
os.system(cmd)
#the following two lines should be conistent with the one defined in parse_ncbi_entry()
GI,REF_NAME,TAXON_ID,ORGANISM,LINEAGE,PRODUCT,STBP,EDBP,SUB_GI=range(9)
GI_SUB,STRAND_SUB,STBP_SUB,EDBP_SUB,GENE_SUB,LOCUS_TAG_SUB,PRODUCT_SUB,PROTEIN_ID_SUB=range(8)
NAi=0
NAs='X'
##################################################################$
#processing genbank flat file and transfer all annotation to mysql
##################################################################$
ANNO_T,DELIM_T,TAX_T=range(3)
gi_annoT_fn=downloadD_gff+'/giAnnoT2load.csv'
delimT_fn=downloadD_gff+'/delimT2load.csv'
taxT_fn=downloadD_gff+'/tax2load.csv'
h_taxLookup = {}
#read tax2load to dictionary (debug) ------------>
if False:
fp=open(taxT_fn,'r')
for i in fp:
words = i.split('\t')
h_taxLookup[words[1]]=1
fp.close()
#<--------------------
fps=[-1,-1,-1]
fps[ANNO_T]=open(gi_annoT_fn,'w')
fps[DELIM_T]=open(delimT_fn,'w')
fps[TAX_T]=open(taxT_fn,'w')
print 'transferring gene bank report to mysql...'
gbFlatTmp = '%s/gb2process.tmp' % downloadD_gff
pkey_anno = 1
pkey_delim = 1
pkey_ti = 1
doneGbD = downloadD_gff+'/completed_gbff'
if not os.path.exists(doneGbD):
os.makedirs(doneGbD)
#count a total # of gz to process
F = len(os.listdir(downloadD_gff))
f = 0
for gbFlatFn in os.listdir(downloadD_gff):
tick=time()
if gbFlatFn.endswith(gbDnExt[0]) or gbFlatFn.endswith(gbDnExt[1]) or gbFlatFn.endswith(gbDnExt[2]):# or gbFlatFn!='gbcon208.seq.gz': #debug
cmd='gunzip -c %s/%s > %s\n' % (downloadD_gff,gbFlatFn,gbFlatTmp)
cmd='%smv %s/%s %s/%s\n' % (cmd,downloadD_gff,gbFlatFn,doneGbD,gbFlatFn)
os.system(cmd)
f+=1
else:
continue
print 'processing %s[%d/%d]...' % (gbFlatFn,f,F)
fp = open(gbFlatTmp,'r')
#skipping header
header=True
while header: # Dump the header in the file
tmp=fp.readline()
if len(tmp)>5:
header = (not tmp[:5] == "LOCUS")
entry = [tmp]
#only focus on the section between "LOCUS" ... "//"
ti=-1
for x in fp:
if re.search(r'^//', x): # Every time we get to a //\n line, we read the current entry and then start collecting a new one.
gB = parse_ncbi_entry(entry)
#print gB[0] #debug
entry=[]
#.............................................
#0) check if query gi has multiple sub gis
has_sub=0
if len(gB[SUB_GI])>0:
has_sub=1
#1) update query gi annotation
#mysql_update_anno_gi(con,gB[GI],gB[REF_NAME],gB[EDBP],gB[TAXON_ID],gB[PRODUCT],has_sub)
pkey_anno,fps[ANNO_T] = csv_update_anno_gi(fps[ANNO_T],gB[GI],gB[REF_NAME],gB[EDBP],gB[TAXON_ID],gB[PRODUCT],has_sub,pkey_anno)
#2) update query delimit
# mysql_update_delim(con,gB[GI],gB[GI],'+',gB[STBP],gB[EDBP])
for s in gB[SUB_GI]:
#3) update sub_gi annotation
#mysql_update_anno_sub_gi(con,s[GI],gB[REF_NAME],gB[TAXON_ID],s[PRODUCT_SUB],s[GENE_SUB],s[PROTEIN_ID_SUB])
#4) update sub_gi delimit
#mysql_update_delim(con,gB[GI],s[GI_SUB],s[GENE_SUB],s[PROTEIN_ID_SUB],s[STRAND_SUB],s[STBP_SUB],s[EDBP_SUB])
pkey_delim,fps[DELIM_T]=csv_update_delim(fps[DELIM_T],gB[GI],s[GI_SUB],s[GENE_SUB],s[LOCUS_TAG_SUB],s[PROTEIN_ID_SUB],s[STRAND_SUB],s[STBP_SUB],s[EDBP_SUB],pkey_delim)
#ti=mysql_update_ti(con,gB[TAXON_ID],gB[ORGANISM],gB[LINEAGE])
if h_taxLookup.get(gB[TAXON_ID],-1) == -1:
pkey_ti,fps[TAX_T] = csv_update_ti(fps[TAX_T],gB[TAXON_ID],gB[ORGANISM],gB[LINEAGE],pkey_ti)
h_taxLookup[gB[TAXON_ID]]=1
#.............................................
else:
entry.append(x)
#for loop end (x in fp)
fp.close()
tock=time()
elapsed=tock-tick
print 'elasped time:[%g]' % elapsed
fps[0].close()
fps[1].close()
fps[2].close()
#(gbFlatFn) finish for loop
con = dbUtils.init_mysql_innocentive(MySqlConf,0)
with con:
print 'loading %s...' % (gi_annoT_fn)
cur=con.cursor()
mysql_load_cmd = 'load data local infile \'%s\' into table giAnnoT fields terminated by \'\\t\'' % gi_annoT_fn
cur.execute(mysql_load_cmd)
cur=con.cursor()
mysql_idx_cmd = 'create unique index idx_gi on giAnnoT (gi)'
cur.execute(mysql_idx_cmd)
print 'done.'
print 'loading %s...' % (delimT_fn)
cur=con.cursor()
mysql_load_cmd = 'load data local infile \'%s\' into table giDelimT fields terminated by \'\\t\'' % delimT_fn
cur.execute(mysql_load_cmd)
cur=con.cursor()
mysql_idx_cmd = 'create index idx_subgi on giDelimT (gi,stbp,edbp)'
cur.execute(mysql_idx_cmd)
print 'done.'
print 'computing database size for each taxon id...'
if False:
#collect dbSize for each ti
h_ti_dbSz = get_ti_db_size(gi_annoT_fn)
update_taxT_fn(h_ti_dbSz,taxT_fn)
else:
add_dbsize2taxonT(tiNtDfn,taxT_fn)
print 'done.'
print 'loading %s...' % (taxT_fn)
cur=con.cursor()
mysql_load_cmd = 'load data local infile \'%s\' into table cj_taxonT fields terminated by \'\\t\'' % taxT_fn
cur.execute(mysql_load_cmd)
cur=con.cursor()
mysql_idx_cmd = 'create unique index idx_taxon on cj_taxonT (taxon)'
cur.execute(mysql_idx_cmd)
print 'done.'
dbUtils.mysql_close(con)
print 'done'
