import sys
from vcfDict import vcfDict
if __name__ == "__main__":
vcfLoc,bpFile,bpOut = sys.argv[1],sys.argv[2],sys.argv[3]
outFile = open(bpOut,"w")
vcf = vcfDict(vcfLoc)
vcf.loadDict()
with open(bpFile) as f:
for line in f:
if line[0] == "p":
sline = line.split(",")
windowID = sline[0]
if vcf.getLine(windowID) != "":
#Site is present
outFile.write(line)
else:
outFile.write(line)
outFile.close()
def isDataLine(line):
"""
Determines in line contains site data
"""
if len(line) > 1:
return line[0] != "#"
return False
if __name__ == "__main__":
"""
"""
anc_loc, desc_loc, merge_loc = sys.argv[1], sys.argv[2], sys.argv[3]
desc = vcfDict(desc_loc)
desc.loadDict()
merge_file = open(merge_loc, "w")
#Write header information to merge file
with open(desc_loc) as desc_file:
for desc_line in desc_file:
if not isDataLine(desc_line):
merge_file.write(desc_line)
else:
#data lines start
break
with open(anc_loc) as anc_file:
for anc_line in anc_file:
if isDataLine(anc_line):
def isDataLine(line):
"""
Determines in line contains site data
"""
if len(line) > 1:
return line[0] != "#"
return False
if __name__ == "__main__":
"""
Given a .txt file of locations("CHROM:POS") and a vcf file,
creates a new vcf file of sites that match the given locations.
"""
locations_dir, vcf_dir, out_loc = sys.argv[1], sys.argv[2], sys.argv[3]
vcf_dict = vcfDict(vcf_dir)
vcf_dict.loadDict()
out_file = open(out_loc, "w")
#Write header information to merge file
with open(vcf_dir) as vcf_file:
for vcf_line in vcf_file:
if not isDataLine(vcf_line):
out_file.write(vcf_line)
else:
#data lines start
break
with open(locations_dir) as loc_file:
for loc in loc_file:
loc = loc.replace(" ", "")
def isDataLine(line):
"""
Determines in line contains site data
"""
if len(line) > 1:
return line[0] != "#"
return False
if __name__ == "__main__":
"""
"""
CC3_loc,GP2_loc,common_sites_loc = sys.argv[1],sys.argv[2],sys.argv[3]
desc = vcfDict(GP2_loc)
desc.loadDict()
merge_file = open(common_sites_loc,"w")
with open(CC3_loc) as anc_file:
for anc_line in anc_file:
if isDataLine(anc_line):
anc_line_col = str.split(anc_line)
anc_line_key = anc_line_col[0] + ":" + anc_line_col[1]
desc_line = desc.getLine(anc_line_key)
if desc_line != "":
merge_file.write(desc_line)
pass
def sameAltBase(line_a, line_b):
"""
Returns whether the sites have the same alternate base
"""
altIdx = 4
sline_a = str.split(line_a)
sline_b = str.split(line_b)
return sline_a[altIdx] == sline_b[altIdx]
if __name__ == "__main__":
#Get location of both .vcf files and load vcfDicts for each
file_a, file_b = sys.argv[1], sys.argv[2]
dict_a = vcfDict(file_a)
dict_b = vcfDict(file_b)
dict_a.loadDict()
dict_b.loadDict()
#size information for each file before processing
aSize = dict_a.getSize()
bSize = dict_b.getSize()
a_keys = dict_a.getKeys()
bAnda = 0
same_alt = 0
#Check every key in dict_a against dict_b
#if a site is present .getLine() removes the site after
for key in a_keys:
"""
Determines in line contains site data
"""
if len(line) > 1:
return line[0] != "#"
return False
if __name__ == "__main__":
"""
"""
known_sites,ccm = sys.argv[1],sys.argv[2]
sites = vcfDict(known_sites)
sites.loadDict()
with open(ccm) as ccm_vcf:
for line in ccm_vcf:
if isDataLine(line):
key = str.split(line)[0] + ":"+ str.split(line)[1]
siteLine = sites.getLine(key)
if siteLine != "":
print siteLine
else:
pass
# print key
import sys
import traceback
from vcfDict import vcfDict
from vcfLine import vcfLine
from vcfSample import vcfSample
from mpileLine import mpileLine
if __name__ == "__main__":
mpile_in,vcf_in,csv_out = sys.argv[1],sys.argv[2],sys.argv[3]
#Load dictionary of sites in vcf_in file
vcfSites = vcfDict(vcf_in)
vcfSites.loadDict()
#Create output file for csv_out
outFile = open(csv_out,"w")
with open(mpile_in) as pileFile:
for line in pileFile:
try:
pile_line = mpileLine(line)
print pile_line.repr()
if vcfSites.siteExists(pile_line.siteID):
vcf_line = vcfLine(vcfSites.getLine(pile_line.siteID))
except Exception, e:
print sys.exc_info()[0]
print traceback.format_exc()
print line
outFile.close()
def isDataLine(line):
"""
Determines in line contains site data
"""
if len(line) > 1:
return line[0] != "#"
return False
if __name__ == "__main__":
"""
"""
common_sites_loc,target_file,output_file = sys.argv[1],sys.argv[2],sys.argv[3]
desc = vcfDict(common_sites_loc)
desc.loadDict()
outFile = open(output_file,"w")
with open(target_file) as t_file:
for t_line in t_file:
if isDataLine(t_line):
t_line_col = str.split(t_line)
t_line_key = t_line_col[0] + ":" + t_line_col[1]
desc_line = desc.getLine(t_line_key)
if desc_line != "":
#outFile.write(desc_line)
#do not write line
from vcfDict import vcfDict
import sys
if __name__ == "__main__":
mpile_in,vcf_sites_loc,mpile_out_loc = sys.argv[1],sys.argv[2],sys.argv[3]
vcfSites = vcfDict(vcf_sites_loc)
vcfSites.loadDict()
mpile_out = open(mpile_out_loc,"w")
with open(mpile_in) as mpile_file:
for line in mpile_file:
sline = line.split("\t")
lineID = sline[0] + ":" + sline[1]
if vcfSites.siteExists(lineID):
mpile_out.write(line)
mpile_out.close()
mpile_file.close()
import sys
from vcfDict import vcfDict
if __name__ == "__main__":
vcfFile, bpFile, outFile_loc = sys.argv[1], sys.argv[2], sys.argv[3]
vcfSites = vcfDict(vcfFile)
vcfSites.loadDict()
outFile = open(outFile_loc, "w")
with open(vcfFile) as vcf_f:
for line in vcf_f:
if line[0] == "#":
outFile.write(line)
with open(bpFile) as bp:
for line in bp:
if line[0] != '""':
sline = line.split(",")
id = sline[1][1:-1]
resp = vcfSites.getLine(id)
if resp != "":
outFile.write(resp)
outFile.close()
vcf_f.close()
bp.close()
#Removes sites from intAB present in other samples except for sample B and sample A
for i in range(0, len(samples)):
if i != bSetIdx and (samples[i].getFileName() !=
targetDict.getFileName()):
for ele in samples[i].getKeys():
try:
intAB.remove(ele)
except:
pass
return intAB
if __name__ == "__main__":
"""
"""
GPB = vcfDict("../data/compareSNPs/tmp/GP2-3_B_m0.vcf")
GPC = vcfDict("../data/compareSNPs/tmp/GP2-3_C_m0.vcf")
GPD = vcfDict("../data/compareSNPs/tmp/GP2-3_D_m0.vcf")
GPE = vcfDict("../data/compareSNPs/tmp/GP2-3_E_m0.vcf")
GPF = vcfDict("../data/compareSNPs/tmp/GP2-3_F_m0.vcf")
GPG = vcfDict("../data/compareSNPs/tmp/GP2-3_G_m0.vcf")
GPH = vcfDict("../data/compareSNPs/tmp/GP2-3_H_m0.vcf")
GPI = vcfDict("../data/compareSNPs/tmp/GP2-3_I_m0.vcf")
GPJ = vcfDict("../data/compareSNPs/tmp/GP2-3_J_m0.vcf")
GPK = vcfDict("../data/compareSNPs/tmp/GP2-3_K_m0.vcf")
GPL = vcfDict("../data/compareSNPs/tmp/GP2-3_L_m0.vcf")
GPM = vcfDict("../data/compareSNPs/tmp/GP2-3_M_m0.vcf")
GPN = vcfDict("../data/compareSNPs/tmp/GP2-3_N_m0.vcf")
GPO = vcfDict("../data/compareSNPs/tmp/GP2-3_O_m0.vcf")
CCB = vcfDict("../data/compareSNPs/tmp/CC_B_m0.vcf")
Return whether the given site is one of the target sites
"""
lineID = lineVcf.chrom + ":" + lineVcf.pos
return targetSitesDict.getLine(lineID) != ""
if __name__ == "__main__":
vcf_unfilt, vcf_targetSites, out_loc = sys.argv[1], sys.argv[2], sys.argv[
3]
outFile = open(out_loc, "w")
outFile.write(
"siteID,start_chrom,start_pos,stop_chrom,stop_pos,altSiteCount,refSiteCount,avgDepth,avgRefReads,avgAltReads,avgOtherReads"
+ "\n")
targetSitesDict = vcfDict(vcf_targetSites)
targetSitesDict.loadDict()
window = []
with open(vcf_unfilt) as unfilt:
for line in unfilt:
lineVcf = vcfLine(line)
if lineVcf.isDataLine: #Add data lines from unfiltered file to window
window.append(lineVcf)
if len(
window
) == WINDOW_SIZE + 1: #Remove oldest site seen keep size == WINDOW_SIZE
window.pop(0)