def unzip(args):
if not args.graph[0].endswith(".gfa") and not args.graph[0].endswith(
".gfa.gz"):
logging.fatal("Invalid gfa file.")
return
# G=nx.MultiDiGraph()
G = nx.DiGraph()
utils.read_gfa(args.graph[0], None, None, G, remap=False)
if args.source == None and args.sink == None:
unzip_graph(G, args, minunzip=args.minunzip)
else:
b = bubbles.Bubble(G, args.source, args.sink)
unzip_bubble(G,
b,
minunzip=args.minunzip,
idoffset=max([n
for n in G.nodes() if type(n) == int]) + 1)
if args.output == None:
of = os.path.splitext(args.graph[0])[0] + ".unzipped.gfa"
else:
of = args.output + ".gfa"
utils.write_gfa(G, None, outputfile=of)
def chop_cmd(args):
if not args.graph[0].endswith(".gfa"):
logging.fatal("Invalid gfa file.")
return
G=nx.DiGraph()
utils.read_gfa(args.graph[0], None, None, G, remap=False)
# assert(len(G.edges())==0)
if args.output==None:
fof=os.path.splitext(args.graph[0])[0]+".chopped.fasta"
gof=os.path.splitext(args.graph[0])[0]+".chopped.gfa"
else:
fof=args.output+".fasta"
gof=args.output+".gfa"
if args.check:
Gorg=G.copy()
chop(G,k=args.k,extend=args.extend)
logging.debug("Merging node sequence...")
for node in G.nodes():
if type(node)==str: #skip start/end nodes
continue
G.node[node]['seq']=G.node[node]['prefix']+G.node[node]['seq']+G.node[node]['suffix']
logging.debug("Done.")
logging.debug("Write overlap graph...")
utils.write_gfa(G,None,outputfile=gof,remap=False)
logging.debug("Done.")
if args.fasta:
logging.debug("Write corresponding fasta file...")
with open(fof,'w') as ff:
for node in G.nodes():
if type(node)==str: #skip start/end nodes
continue
name=">"+str(node)+"\n"
seq=G.node[node]['seq']
ff.write(name)
for i in range( (len(seq)/args.lw)+(len(seq) % args.lw > 0)):
ff.write(seq[i*args.lw:(i+1)*args.lw]+"\n")
logging.debug("Done.")
if args.check:
logging.debug("Validate if all k-mers from the original graph are contained in overlap graph...")
import extract
r="$".join([G.node[node]['seq'] for node in G])
for path in Gorg.graph['paths']:
logging.debug("Check: %s"%path)
s=extract.extract(Gorg,path)
for i in xrange(len(s)-args.k):
if r.find(s[i:i+args.k])==-1:
logging.error("Flat representation does not cover all k-length substrings for %s, could not find: %s!"%(path,s[i:i+args.k]))
sys.exit(1)
logging.debug("Done.")
def comp_cmd(args):
g = nx.DiGraph()
g.graph['paths'] = []
utils.read_gfa(args.graph[0], None, None, g, targetsample=None)
g = comp(g)
utils.write_gfa(g,
"",
outputfile=args.graph[0].replace('.gfa', '.rc.gfa'),
nometa=False)
def chop_cmd(args):
if not args.graph[0].endswith(".gfa"):
logging.fatal("Invalid gfa file.")
return
G=nx.DiGraph()
utils.read_gfa(args.graph[0], None, None, G, remap=False)
# assert(len(G.edges())==0)
if args.output==None:
fof=os.path.splitext(args.graph[0])[0]+".chopped.fasta"
gof=os.path.splitext(args.graph[0])[0]+".chopped.gfa"
else:
fof=args.output+".fasta"
gof=args.output+".gfa"
if args.check:
Gorg=G.copy()
chop(G,k=args.k,extend=args.extend)
logging.debug("Merging node sequence...")
for node in G.nodes():
G.node[node]['seq']=G.node[node]['prefix']+G.node[node]['seq']+G.node[node]['suffix']
logging.debug("Done.")
logging.debug("Write overlap graph...")
utils.write_gfa(G,None,outputfile=gof,remap=False)
logging.debug("Done.")
if args.fasta:
logging.debug("Write corresponding fasta file...")
with open(fof,'w') as ff:
for node in G.nodes():
name=">"+str(node)+"\n"
seq=G.node[node]['seq']
ff.write(name)
for i in range( (len(seq)/args.lw)+(len(seq) % args.lw > 0)):
ff.write(seq[i*args.lw:(i+1)*args.lw]+"\n")
logging.debug("Done.")
if args.check:
logging.debug("Validate if all k-mers from the original graph are contained in overlap graph...")
import extract
r="$".join([G.node[node]['seq'] for node in G])
for path in Gorg.graph['paths']:
logging.debug("Check: %s"%path)
s=extract.extract(Gorg,path)
for i in xrange(len(s)-args.k):
if r.find(s[i:i+args.k])==-1:
logging.error("Flat representation does not cover all k-length substrings for %s, could not find: %s!"%(path,s[i:i+args.k]))
sys.exit(1)
logging.debug("Done.")
def unzip(args):
if not args.graph[0].endswith(".gfa"):
logging.fatal("Invalid gfa file.")
return
G=nx.MultiDiGraph()
utils.read_gfa(args.graph[0], None, None, G, remap=False)
if args.source==None and args.sink==None:
unzip_graph(G,minunzip=args.minunzip)
else:
b=bubbles.Bubble(G,args.source,args.sink)
unzip_bubble(G,b,minunzip=args.minunzip,idoffset=max([n for n in G.nodes() if type(n)==int])+1)
if args.output==None:
of=os.path.splitext(args.graph[0])[0]+".unzipped.gfa"
else:
of=args.output+".gfa"
utils.write_gfa(G,None,outputfile=of)
def convert(args):
for graph in args.graphs:
if args.nocycles:
g=nx.DiGraph()
else:
g=nx.MultiDiGraph()
g.graph['paths']=[]
g.graph['path2id']=dict()
g.graph['id2path']=dict()
if graph.endswith(".gfa"): #gfa to gml/gfa
utils.read_gfa(graph,None,None,g,minsamples=args.minsamples,
maxsamples=args.maxsamples,
targetsample=args.targetsample)
if args.type=="gfa":
fn=graph.replace(".gfa",".rewrite.gfa")
graph=utils.write_gfa(g,"", outputfile=fn)
logging.info("gfa graph written to: %s"%fn)
elif args.type=="gml":
fn=utils.write_gml(g,"", hwm=args.hwm, outputfile=graph.replace(".gfa",""), partition=args.partition)
logging.info("gml graph written to: %s"%fn)
elif args.type=="maf":
logging.info("Converting graph to maf..")
graph2maf(g,graph.replace(".gfa",".maf"))
elif graph.endswith(".fa") or graph.endswith(".fasta") or graph.endswith(".fna"): #assume fasta to gfa
i=0
for name,seq in utils.fasta_reader(graph):
g.graph['paths'].append(os.path.basename(graph))
g.graph['path2id'][os.path.basename(graph)]=0
g.graph['id2path'][0]=os.path.basename(graph)
g.add_node(i,offsets={0:0},seq=seq)
i+=1
filename=graph[:graph.rfind(".")]+".gfa"
utils.write_gfa(g,"", outputfile=filename)
logging.info("gfa graph written to: %s"%filename)
else:
logging.fatal("Unknown filetype, need gfa or fasta extension.")
return
def comp_cmd(args):
g=nx.DiGraph()
g.graph['paths']=[]
utils.read_gfa(args.graph[0],None,None,g,targetsample=None)
g=comp(g)
utils.write_gfa(g,"",outputfile=args.graph[0].replace('.gfa','.rc.gfa'), nometa=False)
def convert(args):
for graph in args.graphs:
if args.nocycles:
g = nx.DiGraph()
else:
g = nx.MultiDiGraph()
g.graph['paths'] = []
g.graph['path2id'] = dict()
g.graph['id2path'] = dict()
if graph.endswith(".gfa"): #gfa to gml/gfa
utils.read_gfa(graph,
None,
None,
g,
minsamples=args.minsamples,
maxsamples=args.maxsamples,
targetsample=args.targetsample,
remap=False)
if args.type == "gfa":
fn = graph.replace(".gfa", ".rewrite.gfa")
graph = utils.write_gfa(g, "", outputfile=fn)
logging.info("gfa graph written to: %s" % fn)
elif args.type == "gml":
fn = utils.write_gml(g,
"",
hwm=args.hwm,
outputfile=graph.replace(".gfa", ""),
partition=args.partition)
logging.info("gml graph written to: %s" % fn)
elif args.type == "maf":
logging.info("Converting graph to maf..")
graph2maf(g, graph.replace(".gfa", ".maf"))
elif graph.endswith(
".maf"): #multiple alignment format, convert to graph
g = maf2graph(graph)
filename = graph[:graph.rfind(".")] + ".gml"
utils.write_gml(g, "", outputfile=filename)
filename = graph[:graph.rfind(".")] + ".gfa"
utils.write_gfa(g, "", outputfile=filename)
logging.debug("gfa graph written to: %s" % filename)
elif graph.endswith(".fa") or graph.endswith(
".fasta") or graph.endswith(".fna"): #assume fasta to gfa
if args.aligned:
seqs = []
names = []
for name, seq in utils.fasta_reader(graph, keepdash=True):
seqs.append(seq)
names.append(name)
g, nid = utils.aln2graph(seqs, names)
else:
i = 0
start = uuid.uuid4().hex
end = uuid.uuid4().hex
g.graph['startnodes'] = [start]
g.graph['endnodes'] = [end]
g.add_node(start, offsets=dict())
g.add_node(end, offsets=dict())
for i, v in enumerate(utils.fasta_reader(graph)):
name, seq = v
g.graph['paths'].append(name)
g.graph['path2id'][name] = i
g.graph['id2path'][i] = name
g.node[start]['offsets'][i] = 0
g.node[end]['offsets'][i] = len(seq)
g.add_node(i, offsets={i: 0}, seq=seq)
g.add_edge(start, i, paths=set([i]))
g.add_edge(i, end, paths=set([i]))
filename = graph[:graph.rfind(".")] + ".gfa"
utils.write_gfa(g, "", outputfile=filename)
logging.debug("gfa graph written to: %s" % filename)
else:
logging.fatal("Unknown filetype, need gfa or fasta extension.")
return