def main(): # test script p = PyPhy() from seqUtils import convert_fasta with open('test/shankarappa-p1.fa', 'rU') as f: fasta = convert_fasta(f) out = p.read_data(fasta, is_codon=True) print out t = '((A:1,B:2):0.5,C:0.2):0;' out = p.read_tree(t) print out p.set_model(is_codon=True)
def main(): # test script p = PyPhy() from seqUtils import convert_fasta with open("test/shankarappa-p1.fa", "rU") as f: fasta = convert_fasta(f) out = p.read_data(fasta, is_codon=True) print out t = "((A:1,B:2):0.5,C:0.2):0;" out = p.read_tree(t) print out p.set_model(is_codon=True)
""" Use project file to punch out genes from FDA amino acid refs """ import os import HyPhy import hyphyAlign import json from seqUtils import convert_fasta hyphy = HyPhy._THyPhy (os.getcwd(), 1) # instance of HyPhy hyphyAlign.change_settings(hyphy) # default settings handle = open('fda_hcv_polyprotein.fa', 'rU') fasta = convert_fasta(handle) handle.close() handle = open('/Users/art/git/MiseqPipeline/projects.json', 'rU') proj = json.load(handle) handle.close() h77 = {} for key in proj['regions'].iterkeys(): if 'H77' in key and not key.endswith('seed'): aa = ''.join(proj['regions'][key]['reference']) h77.update({str(key): str(aa)}) outfile = open('fda_hcv_coords.fa', 'w') for h, s in fasta: for gene, refseq in h77.iteritems(): aquery, aref, ascore = hyphyAlign.pair_align(hyphy, refseq, s)
""" Use project file to punch out genes from FDA amino acid refs """ import os import HyPhy import hyphyAlign import json from seqUtils import convert_fasta hyphy = HyPhy._THyPhy(os.getcwd(), 1) # instance of HyPhy hyphyAlign.change_settings(hyphy) # default settings handle = open('fda_hcv_polyprotein.fa', 'rU') fasta = convert_fasta(handle) handle.close() handle = open('/Users/art/git/MiseqPipeline/projects.json', 'rU') proj = json.load(handle) handle.close() h77 = {} for key in proj['regions'].iterkeys(): if 'H77' in key and not key.endswith('seed'): aa = ''.join(proj['regions'][key]['reference']) h77.update({str(key): str(aa)}) outfile = open('fda_hcv_coords.fa', 'w') for h, s in fasta: for gene, refseq in h77.iteritems(): aquery, aref, ascore = hyphyAlign.pair_align(hyphy, refseq, s)
""" Prune terminal branches on phylogeny given minimum distance cutoff. """ from Bio import Phylo import sys from seqUtils import convert_fasta try: fasta = convert_fasta(open(sys.argv[1], 'rU').readlines()) t = Phylo.read(sys.argv[2], 'newick') cutoff = float(sys.argv[3]) outfile = open(sys.argv[4], 'w') except: print 'Prune terminal branches on phylogeny given minimum distance cutoff.' print 'Filter the original sequence alignment based on the pruned tree.' print 'python prune_newick.py [fasta] [newick] [cutoff] [outfile]' raise # make sure that tip names match sequence names in FASTA seq_names = [h for h, s in fasta] seq_names.sort() tip_names = [tip.name for tip in t.get_terminals()] tip_names.sort() # actually this won't work because tip names got truncated :-P while True: tips = t.get_terminals() pruned = False for tip in tips: if tip.branch_length < cutoff: