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choco_postprocess_viruses.py
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#!/usr/bin/env python
import sys
import collections
import utils
import pyphlan as ppa
try:
import argparse as ap
import bz2
except ImportError:
sys.stderr.write( "argparse not found" )
sys.exit(-1)
def read_params( args ):
p = ap.ArgumentParser(description='Profile ChocoPhlAn genes\n')
p.add_argument( '--markers', required = True, default=None, type=str )
p.add_argument( '--vir_taxonomy', required = True, default=None, type=str )
p.add_argument( '--mic_taxonomy', required = True, default=None, type=str )
p.add_argument('out', nargs='?', default=None, type=str,
help= "the output summary file\n"
"[stdout if not present]")
return vars( p.parse_args() )
if __name__ == "__main__":
args = read_params( sys.argv )
cen2data = {}
vtree = ppa.PpaTree( args['vir_taxonomy'] )
mtree = ppa.PpaTree( args['mic_taxonomy'] )
vall = set([a.name for a in vtree.tree.get_terminals()])
#mall = set([int(a.name[3:]) for a in mtree.tree.get_terminals()])
mall = set([a.name for a in mtree.tree.get_terminals()])
lin = (l.split('\t') for l in open(args['markers']))
for d1,cen,taxa,tax,d2,d3,coreness,d4,d5,d6,d7,tin,tout,d8,tsin,tsout in lin:
tsin,tsout = set(["t__"+a for a in tsin.strip().split(":") if a]),set(["t__"+b for b in tsout.strip().split(":") if b])
#tsin,tsout = set([int(a) for a in tsin.strip().split(":") if a]),set([int(b) for b in tsout.strip().split(":") if b])
cen2data[int(cen)] = {'taxa':int(taxa),'tax':tax,'coreness':float(coreness),'tsin':tsin,'tsout':tsout}
tax2cen = collections.defaultdict( set )
for k,v in cen2data.items():
tax2cen[v['tax']].add( k )
for t,cs in tax2cen.items():
q0 = sorted([c for c in cs if not cen2data[c]['tsout']],key=lambda x:-cen2data[x]['coreness'])
ok,err = [],[]
for c in cs:
if c in q0:
continue
#print "======================",list(vall)[:3], list(cen2data[c]['tsout'])[:3]
vext = vall & cen2data[c]['tsout']
if vext:
#print "ERRRRRRRRRRRRRRRRRRRR"
err.append( c )
else:
#print "OOOOOOOOOOOOOOOOOR"
ok.append( c )
q10,q20 = {},{}
for c in ok:
q10[c] = mtree.lca( [str(tt) for tt in cen2data[c]['tsout'] if str(tt) in mall] ).full_name.split(".t__")[0]
#print ["t__"+str(tt) for tt in cen2data[c]['tsout']]
#print list(vall)[:3]
#print ["t__"+str(tt) for tt in cen2data[c]['tsout'] if "t__"+str(tt) in mall]
#print "q1000000000000",q10[c], [str(tt) for tt in cen2data[c]['tsout']]
for c in err:
q20[c] = mtree.lca( [str(tt) for tt in cen2data[c]['tsout'] if str(tt) in mall] ).full_name.split(".t__")[0]
#print ["t__"+str(tt) for tt in cen2data[c]['tsout']]
#print "q2000000000000", q20[c], ["t__"+str(tt) for tt in cen2data[c]['tsout']]
def maxn(x,y): return x > 50 or ( x > 10 and y > 15 )
#print q0,q10,q20
n = 0
for o in q0:
sys.stdout.write( "\t".join([ str(o),str(t),""]) + "\n" )
n += 1
if n > 50:
break
if maxn( n, len(cs) ):
continue
##print "============"
added = set()
for taxlev in "sgfoc":
##print "a"
for c in ok:
##print "q",taxlev+"__", q10[c]
if True: # taxlev+"__" in q10[c]:
##print taxlev+"__" in q10[c]
if c not in added:
sys.stdout.write( "\t".join([str(c),str(t),str(q10[c])]) + "\n" )
added.add(c)
n += 1
if maxn( n, len(cs) ):
break
##print "b"
for c in err:
#print c,q20[c]
if True: # taxlev+"__" in q20[c]:
if c not in added:
sys.stdout.write( "\t".join([str(c),str(t),str(q20[c])]) + "\n" )
added.add(c)
n += 1
if maxn( n, len(cs) ):
break
if maxn( n, len(cs) ):
break
##print "+++++++++++++++++++++"
##print t,len(cs),len(q0),err
"""
cscores = collections.defaultdict( set )
fwmarkers = {}
maps = collections.defaultdict( set )
tree = ppa.PpaTree( args['taxonomy'] )
clades2terms = ppa.clades2terms( tree.tree )
clades2taxa = dict([(clade.full_name,set([-int(taxon.name[4:]) for taxon in taxa])) for clade,taxa in clades2terms.items()])
ntaxa = 0
for v in clades2terms.values():
ntaxa += len(v)
for l in open( args['cscores'] ):
gene_seed, clade, n, n_tot, coreness = l.strip().split('\t')
gene_seed, clade, n, n_tot, coreness = int(gene_seed), clade, int(n), int(n_tot), float(coreness)
cscores[gene_seed].add( (clade, n, n_tot, coreness) )
for i,l in enumerate(open( args['fwmarkers'] )):
taxa_id, gene_seed, clade, n, n_tot, coreness, n_ext_seeds, n_ext_taxa, uniqueness, ext_taxa = l.strip().split('\t')
taxa_id, gene_seed, n, n_tot, coreness, n_ext_seeds, n_ext_taxa, uniqueness = int(taxa_id), int(gene_seed), int(n), int(n_tot), float(coreness), int(n_ext_seeds), int(n_ext_taxa), float(uniqueness)
fwmarkers[gene_seed] = (taxa_id, clade, n, n_tot, coreness, n_ext_seeds, n_ext_taxa, uniqueness)
for l in open( args['maps'] ):
line = l.strip().split('\t')
if len(line) < 2:
continue
fr,to = line
fr,to = int(fr.split("_")[0]), to # can be improved!!!!
maps[fr].add( to )
g2t,g2c,c2g = {},{},{}
if args['g2t']:
with open( args['g2t'] ) as inp:
g2t = dict(([int(a) for a in l.strip().split('\t')] for l in inp))
elif args['t2g']:
with open( args['t2g'] ) as inp:
for ll in (l.strip().split('\t') for l in inp):
for g in ll[1:]:
g2t[int(g)] = int(ll[0])
genomes = set([g2t[g] for g in cscores])
with open( args['g2c'] ) as inp:
for l in inp:
line = list(l.strip().split('\t'))
#if int(line[0]) not in genomes:
# continue
#vals = [int(a) for a in line if utils.is_number(a)]
vals = [a for a in line]
if len(vals) > 1:
g2c[int(vals[0])] = vals[1:]
for g,c in g2c.items():
for cc in c:
c2g[cc] = g
with utils.openw( args['out'] ) as out:
for gene_seed,cscores_t in cscores.items():
taxa = g2t[gene_seed]
for clade, n, n_tot, coreness in cscores_t:
out.write( "\t".join(["CSCORE",str(gene_seed),str(taxa),clade,str(n), str(n_tot), str(coreness)]) +"\n" )
# anche sotto ???
if gene_seed in fwmarkers:
taxa_id, clade, n, n_tot, coreness, n_ext_seeds, n_ext_taxa, uniqueness = fwmarkers[gene_seed]
if uniqueness < 0.01:
out.write( "\t".join(["FWMARKER",str(gene_seed),str(taxa),clade,str(n), str(n_tot), str(coreness),
str(n_ext_seeds), str(n_ext_taxa), str(1.0-uniqueness)]) +"\n" )
if gene_seed in maps:
ext_tax = set([(c2g[s] if s in c2g else 0) for s in maps[gene_seed]])
ext_tax_ok = ext_tax & clades2taxa[clade]
ext_tax_ko = ext_tax - clades2taxa[clade]
ext_tax_okl = ":".join([str(s) for s in ext_tax_ok])
ext_tax_kol = ":".join([str(s) for s in ext_tax_ko])
muniq = 1.0 - float(len(ext_tax_kol)) / float(ntaxa)
out.write( "\t".join(["MARKER",str(gene_seed),str(taxa),clade,str(n), str(n_tot), str(coreness),
str(n_ext_seeds), str(n_ext_taxa), str(1.0-uniqueness),
str(len(ext_tax)), str(len(ext_tax_ok)), str(len(ext_tax_ko)),
str(muniq), ext_tax_okl, ext_tax_kol]) +"\n" )
"""