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phylo_analysis.py
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#!/usr/bin/env python3
""" Perform phylogenetic analysis with FreeTree """
import os
import sys
import argparse
from funpipe.phylo import phylo #vcf_snp_to_fasta, fasttree
from funpipe.legacy import filter_variants
from funpipe.utils import cd
def phylo_analysis(input, prefix, max_amb):
outvcf = filter_variants(input, prefix+'.vcf')
temp_phylo = phylo( outvcf )
temp_phylo.vcf_snp_to_fasta(max_amb)
temp_phylo.fasttree()
return 1
if __name__ == '__main__':
parser = argparse.ArgumentParser(description=__doc__)
# required arguments
required = parser.add_argument_group('required arguments')
required.add_argument(
'-v', '--vcf', required=True, help='Input vcf', nargs='+')
required.add_argument(
'-r', '--fasta', required=True, help='input reference fasta file')
# optional arguments
parser.add_argument(
'--max_amb', default=10,
help='maximum number of samples with ambiguous calls for a site to be'
+ ' included, recommended number of samples 10%')
parser.add_argument('--ram', help='RAM usage for GATK')
parser.add_argument(
'-d', '--outdir', default='.', help='Output Directory')
parser.add_argument(
'-p', '--prefix', default='Output', help='Prefix of output file')
args = parser.parse_args()
with cd(args.outdir):
# if args.input > 1:
# if fa is None:
# raise ValueError('Please specify fasta file.\n')
# else:
# (gatk(fa, RAM=args.ram)
# .combineVar())
phylo_analysis(args.input, args.prefix, args.max_amb)
#!/usr/bin/env python3
""" Perform phylogenetic analysis with FreeTree """
import os
import sys
import argparse
from funpipe.phylo import phylo #vcf_snp_to_fasta, fasttree
from funpipe.legacy import filter_variants
from funpipe.utils import cd
def phylo_analysis(input, prefix, max_amb):
outvcf = filter_variants(input, prefix+'.vcf')
temp_phylo = phylo( outvcf )
temp_phylo.vcf_snp_to_fasta(max_amb)
temp_phylo.fasttree()
return 1
if __name__ == '__main__':
parser = argparse.ArgumentParser(description=__doc__)
# required arguments
required = parser.add_argument_group('required arguments')
required.add_argument(
'-v', '--vcf', required=True, help='Input vcf', nargs='+')
required.add_argument(
'-r', '--fasta', required=True, help='input reference fasta file')
# optional arguments
parser.add_argument(
'--max_amb', default=10,
help='maximum number of samples with ambiguous calls for a site to be'
+ ' included, recommended number of samples 10%')
parser.add_argument('--ram', help='RAM usage for GATK')
parser.add_argument(
'-d', '--outdir', default='.', help='Output Directory')
parser.add_argument(
'-p', '--prefix', default='Output', help='Prefix of output file')
args = parser.parse_args()
with cd(args.outdir):
# if args.input > 1:
# if fa is None:
# raise ValueError('Please specify fasta file.\n')
# else:
# (gatk(fa, RAM=args.ram)
# .combineVar())
phylo_analysis(args.input, args.prefix, args.max_amb)