def make_alns_dict(self):
"""Makes dendropy aln out of dict self.comb_seq for all genes.
"""
physcraper.debug("make_alns_dict")
firstelement = True
count = 0
for gene in self.comb_seq.keys():
if count == 0:
len1 = len(self.comb_seq[gene].keys())
len2 = len1
count = 1
else:
len2 = len(self.comb_seq[gene].keys())
assert len1 == len2
for gene in self.comb_seq.keys():
if firstelement:
aln1 = DnaCharacterMatrix.from_dict(self.comb_seq[gene])
firstelement = False
self.aln_all[count] = aln1
aln1.write(path="{}/aln_0.fas".format(self.workdir),
schema="fasta")
else:
aln = DnaCharacterMatrix.from_dict(
self.comb_seq[gene], taxon_namespace=aln1.taxon_namespace)
self.aln_all[count] = aln
aln.write(path="{}/aln_{}.fas".format(self.workdir, count),
schema="fasta")
count += 1
def create_sub_files(
alignment_file,
dates_file,
subtree_file,
subtree_dates_file,
subfasta_file,
new_dates_file,
):
dates_dic = read_dates(dates_file)
# clean up comments and add dates to end of taxon names
with open(subtree_file, "r") as fp:
content = fp.read().replace("None", "")
content = re.sub("NODE_\d+", "", content)
for taxon, date in dates_dic.items():
content = content.replace(taxon, taxon + "_" + date)
with open(subtree_dates_file, "w") as fp:
fp.write(content)
# add dates to end of sequence names
sub_aln_dic = {}
dna = DnaCharacterMatrix.get(path=alignment_file, schema="fasta")
for taxon, date in dates_dic.items():
t = dna.taxon_namespace.get_taxon(label=taxon)
new_taxon_name = taxon + "_" + date
sub_aln_dic[new_taxon_name] = str(dna[t])
sub_dna = DnaCharacterMatrix.from_dict(sub_aln_dic)
sub_dna.write(path=subfasta_file, schema="fasta")
with open(new_dates_file, "w") as fp:
fp.write(str(len(dates_dic)))
for taxon, date in dates_dic.items():
fp.write("\n" + taxon + "_" + date + "\t" + date)
query_seq = DnaCharacterMatrix.get(path="ascomycota.fasta",schema="fasta")
def seq_dict_build(seq, label, seq_dict):
new_seq = seq.symbols_as_string().replace("-","")
for tax in seq_dict.keys():
inc_seq = seq_dict[tax].symbols_as_string().replace("-","")
if len(inc_seq) > len(new_seq):
if inc_seq.find(new_seq) != -1:
sys.stdout.write("seq {} is subsequence of {}, not added\n".format(label, tax))
return
else:
if new_seq.find(inc_seq) != -1:
del d[tax]
d[label] = seq
sys.stdout.write("seq {} is supersequence of {}, {} added and {} removed\n".format(label, tax, label, tax))
return
print (".")
d[label] = seq
return
for taxon, seq in query_seq.items():
if len(seq.values()) > 800:
seq_dict_build(seq, taxon.label, d)
else:
sys.stdout.write("*")
cull = DnaCharacterMatrix.from_dict(d)
cull.write(path="query_cull.fas", schema="fasta")
taxon.label = "ncbi_id_{}".format(gi_ncbi_map[gi].strip())
except:
taxon.label = "gi_{}".format(gi)
sys.stderr.write("no taxon id found for gi_{}".format(gi))
stops.append(len(seq.values()))
stops.sort()
stop = stops[int(len(stops)/2)]
d = {}
for taxon, seq in orig_seq.items():
d[str(taxon.label)] = seq.values()[:stop]
dna_orig = DnaCharacterMatrix.from_dict(d)
dna_taxa = [i for i in dna_orig.taxon_namespace]
tre_orig = Tree.get(path = "{}_random_resolve.tre".format("ascomycota"), schema = "newick",taxon_namespace=dna_orig.taxon_namespace)
""
treed_taxa = [i.taxon for i in tre_orig.leaf_nodes()]
tre_orig.prune_taxa(set(treed_taxa) - set(dna_taxa))
for taxon in set(dna_taxa) - set(treed_taxa):
del d[taxon.label]
#####NEXT STEPS!!!
#make a function that doe sthis dumb shit in orig as well
taxon.label = ncbi_to_ott[int(gi_ncbi_map[gi])]
except:
taxon.label = "ncbi_id_{}".format(gi_ncbi_map[gi].strip())
except:
taxon.label = "gi_{}".format(gi)
sys.stderr.write("no taxon id found for gi_{}".format(gi))
stops.append(len(seq.values()))
stops.sort()
stop = stops[int(len(stops) / 2)]
d = {}
for taxon, seq in orig_seq.items():
d[str(taxon.label)] = seq.values()[:stop]
dna_orig = DnaCharacterMatrix.from_dict(d)
dna_taxa = [i for i in dna_orig.taxon_namespace]
tre_orig = Tree.get(path="{}_random_resolve.tre".format("ascomycota"),
schema="newick",
taxon_namespace=dna_orig.taxon_namespace)
""
treed_taxa = [i.taxon for i in tre_orig.leaf_nodes()]
tre_orig.prune_taxa(set(treed_taxa) - set(dna_taxa))
for taxon in set(dna_taxa) - set(treed_taxa):
del d[taxon.label]
#####NEXT STEPS!!!
import sys
from dendropy import DnaCharacterMatrix
infi = sys.argv[1]
outstub = sys.argv[2]
start = int(sys.argv[3])
stop = int(sys.argv[4])
orig = DnaCharacterMatrix.get(path=infi, schema="nexus")
d = {}
for taxon, seq in orig.items():
d[taxon.label] = seq.values()[start:stop]
dna = DnaCharacterMatrix.from_dict(d)
dna.write(path="{}.fas".format(outstub), schema="fasta")
"""prunes to 1 seq per spp, and fills in missing data for missing spp,
in preparation for concanteneation, return dict to be made in char matrix"""
aln_dict = {}
tmp_dict = {}
for taxon, seq in physcraper_obj.aln.items():
aln_dict[taxon.label] = seq
seqlen = len(seq) #should all be same bc aligned
for spp_name in spp_dict.keys():
try:
otu = random.choice(spp_dict[spp_name])
tmp_dict[spp_name] = aln_dict[otu]
except KeyError:
tmp_dict[spp_name] = "-" * seqlen
return tmp_dict
aln1 = DnaCharacterMatrix.from_dict(arbitrary_prune_fill(spp_to_otu1, gene1))
aln2 = DnaCharacterMatrix.from_dict(arbitrary_prune_fill(spp_to_otu2, gene2), taxon_namespace = aln1.taxon_namespace)
concat = DnaCharacterMatrix.concatenate([aln1,aln2])
concat.write(path="concat.fas",
schema="fasta")
#Open the two pyscraper objects
#Merge the alignements on OTT_ID?
#How to force/missing data ...
