def load_from_alignment_file(self, filename):
'''
Loads the sequences from the given sequence file (does not need to be an aligned file)
'''
self.seq_file = filename
self.sequences = Sequence.readSequences(filename)
def load_scores(self, gene_family):
dealignedfile = gene_family.seq_file + ".dealigned.fa"
Sequence.outputSequencesToFasta(gene_family.sequences, dealignedfile)
fsafile = gene_family.seq_file + ".fsa.fa"
cmd = "fsa " + dealignedfile + " > " + fsafile
print("EXEC " + cmd)
if not os.path.isfile(
fsafile
) or not "use_cache" in self.other_args or os.path.getsize(
fsafile) <= 10:
os.system(cmd)
else:
print("Actually, file exists and we'll use it.")
seqs = Sequence.readSequences(fsafile)
gene_family.scores = Distances.getPairwisePctID(sequences=seqs,
verbose=False,
run_nw_algorithm=False)
#here's an annoying problem: when having multiple input files, some (distinct) genes will have the same name
#(this happens with simphy)
#so here we copy the alginment files, but rename the genes with its file index
newinfiles = ""
files_list = infiles.split(",")
newfile_to_old_file = {}
if rename_genes:
print("Copying alignment files, ensuring gene name uniqueness...")
for i in range(len(files_list)):
f = files_list[i]
filename, ext = os.path.splitext(f)
newfile = join(workdir,
os.path.basename(f).replace(ext, "_" + str(i) + ".fa"))
sequences = Sequence.readSequences(f)
Sequence.outputSequencesToFasta(sequences, newfile, str(i), True)
if newinfiles != "":
newinfiles += ","
newinfiles += newfile
newfile_to_old_file[newfile] = f
infiles = newinfiles
else:
for i in range(len(files_list)):
f = files_list[i]
newfile_to_old_file[f] = f
#############################################################################################
def predict_orthologs(self, files, workdir, speciestree_file):
workdir_seqs = join(workdir, "in")
workdir_out = join(workdir, "out")
allseqs = []
for f in files:
seqs = Sequence.readSequences(f)
for s in seqs:
allseqs.append(s)
#one file per species, see OMA comments above
if len(self.cached_clusters) == 0:
seqs_by_species = Sequence.combineSequenceFilesBySpecies(
files, self.other_args["species_separator"],
int(self.other_args["species_index"]))
isdna = True
if "seqtype" in self.other_args and self.other_args[
"seqtype"] == "AA":
print("Input type set to AA")
isdna = False
if not os.path.exists(workdir_seqs):
os.mkdir(workdir_seqs)
for key in seqs_by_species:
outfile = join(workdir_seqs, key + ".fasta")
Sequence.outputSequencesToFasta(sequences=seqs_by_species[key],
filename=outfile,
name_suffix="",
aligned=False,
convertToAA=isdna,
name_prefix="")
cmd = "/u/lafonman/src/orthomcl-pipeline/bin/orthomcl-pipeline -i " + workdir_seqs + " -o " + workdir_out + " -m /u/lafonman/src/orthomcl-pipeline/orthomcl.conf --nocompliant --yes"
print("EXEC " + cmd)
os.system(cmd)
seen_genes = set()
clusters = []
clfile = join(workdir_out, "groups/groups.txt")
f = open(clfile, 'r')
for line in f:
line = line.replace("\n", "")
if line != "":
gz = line.split(":")[1].split()
cluster = set()
for g in gz:
gname = g.split("|")[1]
cluster.add(gname)
seen_genes.add(gname)
clusters.append(cluster)
f.close()
for s in allseqs:
name = s.name
if not name in seen_genes:
cl = set()
cl.add(name)
clusters.append(cl)
self.cached_clusters = clusters
else:
print("USING CACHED CLUSTERS")
clusters = self.cached_clusters
#restrict clusters to current family
#f_set = set()
#for s in gene_family.sequences:
# f_set.add(s.name)
#f_clusters = []
#for cl in clusters:
# inter = f_set.intersection(cl)
# if len(inter) > 0:
# f_clusters.append(inter)
self.clusters_filenames = [join(workdir, "orthomcl.clusters")]
self.relations_filenames = [join(workdir, "orthomcl.relations")]
write_clusters(self.clusters_filenames[0], clusters)
#output relations
relstr = ""
seen_keys = {}
for c in clusters:
for c1 in c:
for c2 in c:
if c1 != c2:
key1 = c1 + ";;" + c2
key2 = c2 + ";;" + c1
if key1 not in seen_keys and key2 not in seen_keys:
seen_keys[key1] = 1
seen_keys[key2] = 1
relstr += c1 + "\t" + c2 + "\t"
sp1 = c1.split(
self.other_args["species_separator"])[int(
self.other_args["species_index"])]
sp2 = c2.split(
self.other_args["species_separator"])[int(
self.other_args["species_index"])]
if sp1 != sp2:
relstr += "Orthologs"
else:
relstr += "Paralogs"
relstr += ";;"
relstr = relstr[0:-2] #extra ;; at end
for i in range(len(allseqs)):
for j in range(i + 1, len(allseqs)):
n1 = allseqs[i].name
n2 = allseqs[j].name
key = n1 + ";;" + n2
if not key in seen_keys:
relstr += n1 + "\t" + n2 + "\t" + "Paralogs" + ";;"
f = open(self.relations_filenames[0], 'w')
f.write(relstr)
f.close()