help='name of the phylip output file',
type=str,
required=False)
parser.add_argument('-s',
'--samples',
help='column names of the samples to process (optional)',
type=str,
required=False)
args = parser.parse_args()
# check if any option was specified:
if not (args.fasta or args.phylip):
raise IOError('Either -f or -p options need to be specified.')
# check if samples names are given and if all sample names are present in a header
sampleNames = calls.checkSampleNames(args.samples, args.input)
############################# program #############################
callsDF = calls.callsParser(args.input, sampleNames)
if args.fasta and args.phylip:
outputFasta = open(args.fasta, 'w')
outputPhy = open(args.phylip, 'w')
NumberPos = len(callsDF.positions)
NumberSamp = len(sampleNames)
outputPhy.write(' %s %s\n' % (NumberSamp, NumberPos)) # make .phy header
# write sample name into file
for s in callsDF.names:
help=
'Specify the populations in the format "pop1[sample1,sample2];pop2[sample5,sample6]"',
type=str,
required=True)
#parser.add_argument('-p', '--parental', help = 'Specify a parental groups', type=str, required=True)
args = parser.parse_args()
# check and append population names and samples
popNames = args.pop
pops = []
for popi in popNames.strip("\"").split(";"):
popName = popi.split("[")[0]
popSample = re.split("\[|\]", popi)[1]
pops.append(popName)
vars()[popName + "samples"] = calls.checkSampleNames(popSample, args.input)
############################## program #############################
counter = 0
print('Opening the file...')
with open(args.input) as datafile:
header_words = datafile.readline().split()
# make output header
print('Creating the output file...')
fileoutput = open(args.output, 'w')
popsP = '\t'.join(str(w) for w in pops)
fileoutput.write("%s\n" % popsP)
#import collections
import calls # my custom module
############################# options #############################
parser = calls.CommandLineParser()
parser.add_argument('-i', '--input', help = 'name of the input file', type=str, required=True)
parser.add_argument('-o', '--output', help = 'name of the output file', type=str, required=True)
parser.add_argument('-m', '--missing', help = 'missing data threshold to remove sites', type=int, required=True)
parser.add_argument('-s', '--samples', help = 'column names of the samples to process (optional)', type=str, required=False)
args = parser.parse_args()
# check if samples names are given and if all sample names are present in a header
sampleNames = calls.checkSampleNames(args.samples, args.input)
############################# program #############################
counter = 0
siteNumber = 1
chrPrev = str(1)
print('Opening the file...')
with open(args.input) as datafile:
header_line = datafile.readline()
header_words = header_line.split()
# index samples
sampCol = calls.indexSamples(sampleNames, header_words)
'--family',
help='Specify the family list in the format \
"family1[sample1,sample2];family2[sample5,sample6]"',
type=str,
required=True)
args = parser.parse_args()
# check Family list
familyNames = args.family
Fsamples = []
famDict = {}
for i in familyNames.strip("\"").split(";"):
famName = i.split("[")[0]
famSample = re.split("\[|\]|", i)[1]
Fsamples.append(famSample.split(","))
famDict[famName] = calls.checkSampleNames(famSample, args.input)
Fsamples = calls.flattenList(Fsamples)
############################# program #############################
callsDF = calls.callsParser(args.input, Fsamples)
outputPED = open(args.output + '.ped', 'w')
outputMAP = open(args.output + '.map', 'w')
for i in range(len(callsDF.positions)):
# make map file
snpsID = str(callsDF.chrmosomes[i]) + "_" + str(callsDF.positions[i])
cM = float(callsDF.positions[i]) * 0.000001
outputMAP.write("%s %s %s %s\n" %
(callsDF.chrmosomes[i], snpsID, cM, callsDF.positions[i]))
############################# modules #############################
import calls # my custom module
############################# options #############################
parser = calls.CommandLineParser()
parser.add_argument('-a', '--annotation', help = 'name of the SIFT annotation file', type=str, required=True)
parser.add_argument('-t', '--tab', help = 'tab delimited genotype file', type=str, required=True)
parser.add_argument('-o', '--output', help = 'name of the output file', type=str, required=True)
parser.add_argument('-f', '--fields', help = 'annotation fields to extract. Possible options: CHROM, POS, REF_ALLELE, ALT_ALLELE, TRANSCRIPT_ID, GENE_ID, GENE_NAME, REGION, VARIANT_TYPE, REF_AMINO, ALT_AMINO, AMINO_POS, SIFT_SCORE, SIFT_MEDIAN, NUM_SEQS, dbSNP, SIFT_PREDICTION', type=str, required=True)
parser.add_argument('-s', '--samples', help = 'column names of the samples to process (optional)', type=str, required=False)
args = parser.parse_args()
# check if samples names are given and if all sample names are present in a header
sampleNames = calls.checkSampleNames(args.samples, args.tab)
############################# program #############################
print('Opening the file...')
counter = 0
siftFile = open(args.annotation, 'r')
annotOptions = siftFile.readline().split()
fieldsNames = args.fields.split(',')
fieldsIndex = calls.indexSamples(fieldsNames, annotOptions)
sift_words = siftFile.readline().split()
sift_chr = int(sift_words[0].split('_')[1])
sift_pos = int(sift_words[1])
'-s',
'--samples',
help=
'column names of the samples to make a reference for. Specify in the format "group1[sample1,sample2];group2[sample3,sample4,sample5]"',
type=str,
required=True)
args = parser.parse_args()
# check and append group names and samples
groupNames = args.samples
groups = []
for groupi in groupNames.strip("\"").split(";"):
groupNames = groupi.split("[")[0]
groupSample = re.split("\[|\]", groupi)[1]
groups.append(groupNames)
vars()[groupNames + "samples"] = calls.checkSampleNames(
groupSample, args.callsFile)
############################ script ##############################
fileoutput = open(args.output, 'w')
fastaRef = FastaParser(args.fastaReference)
# to track lines in the input files
fastaNum = 0
CHRprev = 0
CHRnum = 0
fastaNumAdd = 0
print('Opening the file...')
with open(args.callsFile) as callsFile:
import calls # my custom module
import re
############################# options #############################
parser = calls.CommandLineParser()
parser.add_argument('-i', '--input', help = 'name of the input file', type=str, required=True)
parser.add_argument('-o', '--output', help = 'name of the output file', type=str, required=True)
parser.add_argument('-s', '--sample', help = 'Specify the sample group', type=str, required=True)
parser.add_argument('-p', '--parental', help = 'Specify a parental groups', type=str, required=True)
args = parser.parse_args()
# check if samples names are given and if all sample names are present in a header
sNames = calls.checkSampleNames(args.sample, args.input)
pNames = calls.checkSampleNames(args.parental, args.input)
############################# program #############################
counter = 0
print('Opening the file...')
with open(args.input) as datafile:
header_words = datafile.readline().split()
# index samples
sIndex = calls.indexSamples(sNames, header_words)
pIndex = calls.indexSamples(pNames, header_words)
'--family',
help='Specify the family list in the format \
"family1[sample1,sample2];family2[sample5,sample6]"',
type=str,
required=True)
args = parser.parse_args()
print "Checking sample names ..."
familyNames = args.family
Fsamples = []
familySamples = {}
for i in familyNames.strip("\"").split(";"):
famName = i.split("[")[0]
famSample = re.split("\[|\]|", i)[1]
Fsamples.append(famSample.split(","))
familySamples[famName] = calls.checkSampleNames(famSample, args.input)
samples = calls.flattenList(Fsamples)
calls.checkSampleNames('ANC', args.input)
calls.checkSampleNames('DER', args.input)
############################# program #############################
outputSNPs = open(args.output + '.snps', 'w')
with open(args.input) as datafile:
header_words = datafile.readline().split()
sampleIndex = calls.indexSamples(samples, header_words)
ANCindex = calls.indexSamples(['ANC'], header_words)
DERindex = calls.indexSamples(['DER'], header_words)
FamilyIndex = {}
