testminintervalbetweengenes_basesperfaline.readline().strip())
print(minintervalbetweengenes_basesperfaline)
#gtffile = open(options.gtffile, 'r')
vcffile = open(options.variants, 'r')
#covfile = open(options.genomedepth, 'r')
cns_string = ">"
aa_string = ""
cdscns_string = ""
outcns = open(options.outfileprename + "_cns.fa", 'w')
outaa = open(options.outfileprename + "_aa.fa", 'w')
outcdscns = open(options.outfileprename + "_cdscns.fa", 'w')
cdsmap = {}
if __name__ == '__main__':
if options.genomedepth != None:
depthfile = Util.GATK_depthfile(options.genomedepth,
options.genomedepth + ".index")
species_idx = depthfile.title.index("Depth_for_" + options.species)
Considerdepth = True
else:
Considerdepth = False
depthfile = None
species_idx = -1
vcfpop = VCFutil.VCF_Data(options.variants) # new a class
RefSeqMap, currentChromNO, nextChromNO = Util.getRefSeqMap(
refFastafilehander=reffa)
print(currentChromNO, nextChromNO)
cns_string += currentChromNO + "\n"
gtfMap = Util.getGtfMap(options.gtffile)
lastposofdepthfp = 0 #because this time RefSeqMap[0] is 0
vcfchrom = "begin"
def filldata(self,
vcfFileName,
depthfileName,
tablename="derived_alle_ref",
posUniq=True,
continuechrom=None,
continuepos=None):
depthfile = Util.GATK_depthfile(depthfileName,
depthfileName + ".index")
depth_linelist = None
vcffile = open(vcfFileName, 'r')
vcfline = vcffile.readline()
while re.search(r'^##', vcfline) != None:
vcfline = vcffile.readline()
if re.search(r'^#', vcfline) != None:
poptitlelist = re.split(r'\s+', vcfline.strip())[9:]
print(poptitlelist)
else:
print(
"need title'#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT'"
)
exit(-1)
for pop in poptitlelist:
self.dbtools.operateDB("callproc",
"mysql_sp_add_column",
data=("life_pilot", tablename, pop,
"varchar(128)", "default null"))
popsdata = [] #depth for ref or alt
if continuechrom != None and continuepos != None:
print("filldata", continuechrom, continuepos)
vcfpossearcher = VCFutil.VCF_Data(vcfFileName)
vcffile.seek(vcfpossearcher.VcfIndexMap[continuechrom])
vcfline = vcffile.readline()
while vcfline:
vcflist = re.split(r'\s+', vcfline.strip())
chrom = vcflist[0].strip()
pos = int(vcflist[1].strip())
print(chrom, pos)
if chrom == continuechrom and pos == continuepos:
break
vcfline = vcffile.readline()
else:
justiceGATKorSamtools = vcffile.readline()
vcflist = re.split(r'\s+', justiceGATKorSamtools.strip())
dp4 = re.search(r"DP4=(\d*),(\d*),(\d*),(\d*)", vcflist[7])
refdep = 0
altalleledep = 0
if dp4 != None: #vcf from samtools
print("function for samtools vcf is still need to be finish")
exit(-1)
else:
chrom = vcflist[0].strip()
pos = int(vcflist[1].strip())
snpID = vcflist[2].strip()
REF = vcflist[3].strip()
ALT = vcflist[4].strip()
AD_idx = (re.split(":", vcflist[8])).index(
"AD") #gatk GT:AD:DP:GQ:PL
sample_idx_in_vcf = 0
for sample in vcflist[9:]:
samplename = poptitlelist[sample_idx_in_vcf]
sample_idx_in_vcf += 1
species_idx = depthfile.title.index("Depth_for_" +
samplename)
if len(re.split(":", sample)) != len(
re.split(":", vcflist[8])
) and depth_linelist == None: # ./. when lack of variantion information,then consider the depthfile
depth_linelist = depthfile.getdepthByPos(chrom, pos)
if int(depth_linelist[species_idx]) <= 1:
popsdata.append('no covered')
else:
popsdata.append(depth_linelist[species_idx] + ",0")
continue
elif len(re.split(":", sample)) != len(
re.split(":",
vcflist[8])) and depth_linelist != None:
if int(depth_linelist[species_idx]) <= 1:
popsdata.append('no covered')
else:
popsdata.append(depth_linelist[species_idx] + ",0")
continue
popsdata.append(re.split(":", sample)[AD_idx])
depth_linelist = None
print(
"insert into " + tablename +
"(chrID,snp_pos,snpID,ref_base,alt_base," +
"".join([e + ","
for e in poptitlelist[:-1]] + poptitlelist[-1:]) +
") select %s,%s,%s,%s,%s," + "%s," *
(len(poptitlelist) - 1) +
"%s from dual where not exists( select * from " +
tablename + " where " + tablename + ".chrID='" + chrom +
"' and " + tablename + ".snp_pos=" + str(pos) + ")",
(chrom, pos, snpID, REF, ALT) + tuple(popsdata))
self.dbtools.operateDB(
"insert",
"insert into " + tablename +
"(chrID,snp_pos,snpID,ref_base,alt_base," +
"".join([e + ","
for e in poptitlelist[:-1]] + poptitlelist[-1:]) +
") select %s,%s,%s,%s,%s," + "%s," *
(len(poptitlelist) - 1) +
"%s from dual where not exists( select * from " +
tablename + " where " + tablename + ".chrID='" + chrom +
"' and " + tablename + ".snp_pos=" + str(pos) + ")",
data=(chrom, pos, snpID, REF, ALT) + tuple(popsdata))
for vcfline in vcffile:
vcflist = re.split(r'\s+', vcfline.strip())
print(vcfline)
if posUniq and pos == int(vcflist[1].strip()):
continue
chrom = vcflist[0].strip()
pos = int(vcflist[1].strip())
snpID = vcflist[2].strip()
REF = vcflist[3].strip()
ALT = vcflist[4].strip()
AD_idx = (re.split(":",
vcflist[8])).index("AD") #gatk GT:AD:DP:GQ:PL
sample_idx_in_vcf = 0
popsdata = []
for sample in vcflist[9:]:
samplename = poptitlelist[sample_idx_in_vcf]
sample_idx_in_vcf += 1
species_idx = depthfile.title.index("Depth_for_" + samplename)
if len(re.split(":", sample)) != len(re.split(
":", vcflist[8])) and depth_linelist == None: # ./.
depth_linelist = depthfile.getdepthByPos(chrom, pos)
if int(depth_linelist[species_idx]) <= 1:
popsdata.append('no covered')
else:
popsdata.append(depth_linelist[species_idx] + ",0")
continue
elif len(re.split(":", sample)) != len(
re.split(":", vcflist[8])) and depth_linelist != None:
if int(depth_linelist[species_idx]) <= 1:
popsdata.append('no covered')
else:
popsdata.append(depth_linelist[species_idx] + ",0")
continue
# AD_depth = re.split(",", re.split(":", sample)[AD_idx])
popsdata.append(re.split(":", sample)[AD_idx])
depth_linelist = None
print(
"insert into " + tablename +
"(chrID,snp_pos,snpID,ref_base,alt_base," +
"".join([e + ","
for e in poptitlelist[:-1]] + poptitlelist[-1:]) +
") select %s,%s,%s,%s,%s," + "%s," * (len(poptitlelist) - 1) +
"%s from dual where not exists( select * from " + tablename +
" where " + tablename + ".chrID='" + chrom + "' and " +
tablename + ".snp_pos=" + str(pos) + ")",
(chrom, pos, snpID, REF, ALT) + tuple(popsdata))
self.dbtools.operateDB(
"insert",
"insert into " + tablename +
"(chrID,snp_pos,snpID,ref_base,alt_base," +
"".join([e + ","
for e in poptitlelist[:-1]] + poptitlelist[-1:]) +
") select %s,%s,%s,%s,%s," + "%s," * (len(poptitlelist) - 1) +
"%s from dual where not exists( select * from " + tablename +
" where " + tablename + ".chrID='" + chrom + "' and " +
tablename + ".snp_pos=" + str(pos) + ")",
data=(chrom, pos, snpID, REF, ALT) + tuple(popsdata))
depthfile.closedepthfile()
vcffile.close()
def fillarchicpop(self,
archicpopVcfFile,
depthFile,
chromtable,
archicpopNameindepthFile,
tablename="derived_alle_ref",
archicpopfieldNameintable="archicpop"):
"""
abandon the snps which exist in archicpopVcfFile but absence in all others pop snp sets
"""
depthfile = Util.GATK_depthfile(depthFile, depthFile + ".index")
species_idx = depthfile.title.index("Depth_for_" +
archicpopNameindepthFile)
archicpop = VCFutil.VCF_Data(archicpopVcfFile)
totalChroms = self.dbtools.operateDB(
"select", "select count(*) from " + chromtable)[0][0]
for i in range(0, totalChroms, 20):
currentsql = "select * from " + chromtable + " order by chrlength desc limit " + str(
i) + ",20"
result = self.dbtools.operateDB("select", currentsql)
for row in result:
currentchrID = row[0]
print(currentchrID + ":", end="")
currentchrLen = int(row[2])
archicpopSeqOfAChr = {}
archicpopSeqOfAChr[currentchrID] = archicpop.getVcfListByChrom(
archicpopVcfFile, currentchrID)
allsnpsInAchr = self.dbtools.operateDB(
"select", "select snp_pos,alt_base from " + tablename +
" where chrID='" + currentchrID + "'")
for snp in allsnpsInAchr:
snp_pos = int(snp[0])
ALT = snp[1]
low = 0
high = len(archicpopSeqOfAChr[currentchrID]) - 1
while low <= high:
mid = (low + high) >> 1
if archicpopSeqOfAChr[currentchrID][mid][0] < snp_pos:
low = mid + 1
elif archicpopSeqOfAChr[currentchrID][mid][0] > snp_pos:
high = mid - 1
else: #find the pos
pos, REF, ALT, INFO, FORMAT, samples = archicpopSeqOfAChr[
currentchrID][mid]
dp4 = re.search(r"DP4=(\d*),(\d*),(\d*),(\d*)",
INFO)
refdep = 0
altalleledep = 0
if dp4 != None: #vcf from samtools
refdep = int(dp4.group(1)) + int(dp4.group(2))
altalleledep = int(dp4.group(3)) + int(
dp4.group(4))
else:
AD_idx = (re.split(":", FORMAT)).index(
"AD") #gatk GT:AD:DP:GQ:PL
for sample in samples:
if len(re.split(":", sample)) == 1: # ./.
continue
AD_depth = re.split(
",",
re.split(":", sample)[AD_idx])
try:
refdep += int(AD_depth[0])
altalleledep += int(AD_depth[1])
except ValueError:
print(sample, end="")
popsdata = ALT + ":" + str(refdep) + "," + str(
altalleledep)
break
else:
depth_linelist = depthfile.getdepthByPos(
currentchrID, snp_pos)
if int(depth_linelist[species_idx]) <= 1:
popsdata = "no covered"
else:
popsdata = ALT + ":" + depth_linelist[
species_idx] + ",0"
# print(snp[0],end="\t")
self.dbtools.operateDB(
"update", "update " + tablename + " set " +
archicpopfieldNameintable + " = '" + popsdata +
"' where chrID=" + "'" + currentchrID +
"' and snp_pos=" + str(snp[0]))
help="ancenstral(a) or derived(d)")
(options, args) = parser.parse_args()
mindeptojudgefix = 15
#####################
VCFobj = {}
vcfnameKEY_depthfilename_titlenameVALUE_tojudgeancestrall = {}
vcfnameKEY_depthobjVALUE_tojudgeancestral = {}
VCFobj["wigeon"] = VCFutil.VCF_Data(
"/home/bioinfo/liurui/data/vcffiles/uniqmap/taihudomesticgoose/taihudomesticgoose.pool.withindel.vcf"
)
VCFobj["fanya"] = VCFutil.VCF_Data(
"/home/bioinfo/liurui/data/vcffiles/uniqmap/fanya/fanya._pool.withindel.vcf"
)
vcfnameKEY_depthfilename_titlenameVALUE_tojudgeancestrall[
"wigeon"] = Util.GATK_depthfile(
"/home/bioinfo/liurui/data/depth/g_j_sm_k_l_y_f_w_pool/gjsmklyfw_gatk.depth",
"/home/bioinfo/liurui/data/depth/g_j_sm_k_l_y_f_w_pool/gjsmklyfw_gatk.depth.index"
) #here is a temp trick not a error
vcfnameKEY_depthfilename_titlenameVALUE_tojudgeancestrall[
"fanya"] = Util.GATK_depthfile(
"/home/bioinfo/liurui/data/depth/g_j_sm_k_l_y_f_w_pool/gjsmklyfw_gatk.depth",
"/home/bioinfo/liurui/data/depth/g_j_sm_k_l_y_f_w_pool/gjsmklyfw_gatk.depth.index"
)
vcfnameKEY_depthobjVALUE_tojudgeancestral["wigeon"] = [
"/home/bioinfo/liurui/data/depth/g_j_sm_k_l_y_f_w_pool/gjsmklyfw_gatk.depth",
9
]
vcfnameKEY_depthobjVALUE_tojudgeancestral["fanya"] = [
"/home/bioinfo/liurui/data/depth/g_j_sm_k_l_y_f_w_pool/gjsmklyfw_gatk.depth",
3
]
####################################