def get_data(self, data):
if data == "cteno_panxs":
return Sb.make_copy(self._cteno_panxs)
elif data == "cteno_panxs_aln":
return Alb.make_copy(self._cteno_panxs_aln)
elif data == "cteno_ids":
return deepcopy(self._cteno_ids)
elif data == "cteno_sim_scores":
return deepcopy(self._cteno_sim_scores)
elif data == "ss2_dfs":
psi_pred_ss2_dfs = Sb.OrderedDict()
for rec in cteno_panxs.records:
path = os.path.join(self.resource_path, "psi_pred",
"%s.ss2" % rec.id)
psi_pred_ss2_dfs[rec.id] = pd.read_csv(path,
comment="#",
header=None,
delim_whitespace=True)
psi_pred_ss2_dfs[rec.id].columns = [
"indx", "aa", "ss", "coil_prob", "helix_prob", "sheet_prob"
]
return psi_pred_ss2_dfs
elif data == "ss2_paths":
psi_pred_ss2 = Sb.OrderedDict()
for rec in cteno_panxs.records:
psi_pred_ss2[rec.id] = os.path.join(self.resource_path,
"psi_pred",
"%s.ss2" % rec.id)
return psi_pred_ss2
else:
raise AttributeError("Unknown data type: %s" % data)
def make_msa(seqbuddy, aligner, trimal=()):
"""
Create a multiple sequence alignment
:param seqbuddy: SeqBuddy object
:param aligner: path to alignment program
:param trimal: List of TrimAl thresholds to try
:return: AlignBuddy object
"""
trimal = trimal if trimal else ["clean"]
if len(seqbuddy) == 1:
alignment = Alb.AlignBuddy(str(seqbuddy))
else:
alignment = Alb.generate_msa(Sb.make_copy(seqbuddy), aligner, quiet=True)
ave_seq_length = Sb.ave_seq_length(seqbuddy)
for threshold in trimal:
align_copy = Alb.trimal(Alb.make_copy(alignment), threshold=threshold)
cleaned_seqs = Sb.clean_seq(Sb.SeqBuddy(str(align_copy)))
cleaned_seqs = Sb.delete_small(cleaned_seqs, 1)
# Structured this way for unit test purposes
if len(alignment.records()) != len(cleaned_seqs):
continue
elif Sb.ave_seq_length(cleaned_seqs) / ave_seq_length < 0.5:
continue
else:
alignment = align_copy
break
return alignment
if not os.path.isfile("%s%s_pep.gb" % (ref_dir, ref_name)):
sb_pep = Sb.translate_cds(Sb.make_copy(seqbuddy))
sb_pep.write("%s%s_pep.gb" % (ref_dir, ref_name))
if not os.path.isfile("%s%s_rna.gb" % (ref_dir, ref_name)):
sb_rna = Sb.dna2rna(Sb.make_copy(seqbuddy))
sb_rna.write("%s%s_rna.gb" % (ref_dir, ref_name))
if not os.path.isfile("%s%s_aln.gb" % (ref_dir, ref_name)):
alignbuddy = Alb.generate_msa(Sb.make_copy(seqbuddy), "mafft")
alignbuddy.write("%s%s_aln.gb" % (ref_dir, ref_name))
else:
alignbuddy = Alb.AlignBuddy("%s%s_aln.gb" % (ref_dir, ref_name))
if not os.path.isfile("%s%s_pep_aln.gb" % (ref_dir, ref_name)):
alb_pep = Alb.translate_cds(Alb.make_copy(alignbuddy))
alb_pep.write("%s%s_pep_aln.gb" % (ref_dir, ref_name))
if not os.path.isfile("%s%s_rna_aln.gb" % (ref_dir, ref_name)):
alb_rna = Alb.dna2rna(Alb.make_copy(alignbuddy))
alb_rna.write("%s%s_rna_aln.gb" % (ref_dir, ref_name))
if not os.path.isfile("%s%s_tree.nwk" % (ref_dir, ref_name)):
phylobuddy = Pb.generate_tree(Alb.make_copy(alignbuddy), "fasttree")
phylobuddy.write("%s%s_tree.nwk" % (ref_dir, ref_name))
else:
phylobuddy = Pb.PhyloBuddy("%s%s_tree.nwk" % (ref_dir, ref_name))
tmp_dir = TempDir()
# Create all of the Tool objects for processing
def test_make_msa(hf, monkeypatch):
seqbuddy = hf.get_data("cteno_panxs")
seqbuddy.records = seqbuddy.records[:2]
alb_obj = group_by_cluster.make_msa(seqbuddy, "clustalo")
assert type(alb_obj) == Alb.AlignBuddy
assert str(alb_obj) == """\
>Bab-PanxαA Be_abyssicola|m.8 and m.21|ML036514|937+ 2.
MLLLGSLGTIKNLSIFKDLSLDDWLDQMNRTFMFLLLCFMGTIVAVSQYTGKNISCNGFE
KFSDDFSQDYCWTQGLYTIKEAYDLPESQIPYPGIIPENVPACREHSLKNGGKIICPPPE
EIKPLTRARHLWYQWIPFYFWVIAPVFYLPYMFVKRMGLDRMKPLLKIMSDYYHCTTETP
SEEIIVKCADWVYNSIVDRLSEGSSWTSWRNRHGLGLAVLFSKLMYLGGSILVMMVTTLM
FQVGDFKTYGIEWLKQFPSDENYTTSVKHKLFPKMVACEIKRWGPSGLEEENGMCVLAPN
VIYQYIFLIMWFALAITICTNFFNIFFWVFKLTATRYTYSKLVATGHFSHKHPGWKFMYY
RIGTSGRVLLNIVAQNTNPIIFGAIMEKLTPSVIKHLRIGHVPGEYLTDPA
>Bab-PanxαB Be_abyssicola|m.19|ML47742|1063 2.
--MLDILSKFKGVTPFKGITIDDGWDQLNRSFMFVLLVVMGTTVTVRQYTGSVISCDGFK
KFGSTFAEDYCWTQGLYTVLEGYDQPSYNIPYPGLLPDELPACTPVKLKDGTRLKCPDAD
QLMSPTRISHLWYQWVPFYFWLAAAAFFMPYLLYKNFGMGDIKPLVRLLHNPVESDQ--E
LKKMTDKAATWLFYKFDLYMSEQSLVASLTRKHGLGLSMVFVKILYAAVSFCCFILTAEM
FSIGDFKTYGSKWIKKMRYEDTLATEEKDKLFPKMVACEVKRWGASGIEEEQGMCVLAPN
VINQYLFLILWFCLVFVMICNIVSIFVSLIKLLFTYGSYRRLLST-AFLRDDSAIKHMYF
NVGSSGRLILHVLANNTAPRVFEDILLTLAPKLIQRKLRGNGKAV------
"""
seqbuddy.records = [seqbuddy.records[0]]
alb_obj = group_by_cluster.make_msa(seqbuddy, "clustalo")
assert type(alb_obj) == Alb.AlignBuddy
assert str(alb_obj) == """\
>Bab-PanxαA Be_abyssicola|m.8 and m.21|ML036514|937+ 2.
MLLLGSLGTIKNLSIFKDLSLDDWLDQMNRTFMFLLLCFMGTIVAVSQYTGKNISCNGFE
KFSDDFSQDYCWTQGLYTIKEAYDLPESQIPYPGIIPENVPACREHSLKNGGKIICPPPE
EIKPLTRARHLWYQWIPFYFWVIAPVFYLPYMFVKRMGLDRMKPLLKIMSDYYHCTTETP
SEEIIVKCADWVYNSIVDRLSEGSSWTSWRNRHGLGLAVLFSKLMYLGGSILVMMVTTLM
FQVGDFKTYGIEWLKQFPSDENYTTSVKHKLFPKMVACEIKRWGPSGLEEENGMCVLAPN
VIYQYIFLIMWFALAITICTNFFNIFFWVFKLTATRYTYSKLVATGHFSHKHPGWKFMYY
RIGTSGRVLLNIVAQNTNPIIFGAIMEKLTPSVIKHLRIGHVPGEYLTDPA
"""
# Don't modify if any sequence is reduced to nothing
align = Alb.AlignBuddy("""\
>A
MSTGTC-------
>B
M---TC-------
>C
M---TC---AILP
>D
-STP---YWAILP
""", in_format="fasta")
seqbuddy = Sb.SeqBuddy(Alb.make_copy(align).records(), in_format="fasta")
seqbuddy = Sb.clean_seq(seqbuddy)
monkeypatch.setattr(Alb, "generate_msa", lambda *_, **__: align)
alb_obj = group_by_cluster.make_msa(seqbuddy, "clustalo", trimal=[0.3])
assert str(alb_obj) == str(align)
# Don't modify if average sequence length is reduced by more than half
align = Alb.AlignBuddy("""\
>A
MSTGTC-------
>B
M---TC-------
>C
M---TC---AILP
>D
-STPTC-YWAILP
""", in_format="fasta")
seqbuddy = Sb.SeqBuddy(Alb.make_copy(align).records(), in_format="fasta")
seqbuddy = Sb.clean_seq(seqbuddy)
monkeypatch.setattr(Alb, "generate_msa", lambda *_, **__: align)
alb_obj = group_by_cluster.make_msa(seqbuddy, "clustalo", trimal=[0.3])
assert str(alb_obj) == str(align)
# Remove some gaps
alb_obj = group_by_cluster.make_msa(seqbuddy, "clustalo", trimal=[0.3, 0.55])
assert str(alb_obj) == """\
def test_make_msa(hf, monkeypatch):
seqbuddy = hf.get_data("cteno_panxs")
seqbuddy.records = seqbuddy.records[:2]
alb_obj = group_by_cluster.make_msa(seqbuddy, "clustalo")
assert type(alb_obj) == Alb.AlignBuddy
assert str(alb_obj) == """\
>Bab-PanxαA Be_abyssicola|m.8 and m.21|ML036514|937+ 2.
MLLLGSLGTIKNLSIFKDLSLDDWLDQMNRTFMFLLLCFMGTIVAVSQYTGKNISCNGFE
KFSDDFSQDYCWTQGLYTIKEAYDLPESQIPYPGIIPENVPACREHSLKNGGKIICPPPE
EIKPLTRARHLWYQWIPFYFWVIAPVFYLPYMFVKRMGLDRMKPLLKIMSDYYHCTTETP
SEEIIVKCADWVYNSIVDRLSEGSSWTSWRNRHGLGLAVLFSKLMYLGGSILVMMVTTLM
FQVGDFKTYGIEWLKQFPSDENYTTSVKHKLFPKMVACEIKRWGPSGLEEENGMCVLAPN
VIYQYIFLIMWFALAITICTNFFNIFFWVFKLTATRYTYSKLVATGHFSHKHPGWKFMYY
RIGTSGRVLLNIVAQNTNPIIFGAIMEKLTPSVIKHLRIGHVPGEYLTDPA
>Bab-PanxαB Be_abyssicola|m.19|ML47742|1063 2.
--MLDILSKFKGVTPFKGITIDDGWDQLNRSFMFVLLVVMGTTVTVRQYTGSVISCDGFK
KFGSTFAEDYCWTQGLYTVLEGYDQPSYNIPYPGLLPDELPACTPVKLKDGTRLKCPDAD
QLMSPTRISHLWYQWVPFYFWLAAAAFFMPYLLYKNFGMGDIKPLVRLLHNPVESDQ--E
LKKMTDKAATWLFYKFDLYMSEQSLVASLTRKHGLGLSMVFVKILYAAVSFCCFILTAEM
FSIGDFKTYGSKWIKKMRYEDTLATEEKDKLFPKMVACEVKRWGASGIEEEQGMCVLAPN
VINQYLFLILWFCLVFVMICNIVSIFVSLIKLLFTYGSYRRLLST-AFLRDDSAIKHMYF
NVGSSGRLILHVLANNTAPRVFEDILLTLAPKLIQRKLRGNGKAV------
"""
seqbuddy.records = [seqbuddy.records[0]]
alb_obj = group_by_cluster.make_msa(seqbuddy, "clustalo")
assert type(alb_obj) == Alb.AlignBuddy
assert str(alb_obj) == """\
>Bab-PanxαA Be_abyssicola|m.8 and m.21|ML036514|937+ 2.
MLLLGSLGTIKNLSIFKDLSLDDWLDQMNRTFMFLLLCFMGTIVAVSQYTGKNISCNGFE
KFSDDFSQDYCWTQGLYTIKEAYDLPESQIPYPGIIPENVPACREHSLKNGGKIICPPPE
EIKPLTRARHLWYQWIPFYFWVIAPVFYLPYMFVKRMGLDRMKPLLKIMSDYYHCTTETP
SEEIIVKCADWVYNSIVDRLSEGSSWTSWRNRHGLGLAVLFSKLMYLGGSILVMMVTTLM
FQVGDFKTYGIEWLKQFPSDENYTTSVKHKLFPKMVACEIKRWGPSGLEEENGMCVLAPN
VIYQYIFLIMWFALAITICTNFFNIFFWVFKLTATRYTYSKLVATGHFSHKHPGWKFMYY
RIGTSGRVLLNIVAQNTNPIIFGAIMEKLTPSVIKHLRIGHVPGEYLTDPA
"""
# Don't modify if any sequence is reduced to nothing
align = Alb.AlignBuddy("""\
>A
MSTGTC-------
>B
M---TC-------
>C
M---TC---AILP
>D
-STP---YWAILP
""",
in_format="fasta")
seqbuddy = Sb.SeqBuddy(Alb.make_copy(align).records(), in_format="fasta")
seqbuddy = Sb.clean_seq(seqbuddy)
monkeypatch.setattr(Alb, "generate_msa", lambda *_, **__: align)
alb_obj = group_by_cluster.make_msa(seqbuddy, "clustalo", trimal=[0.3])
assert str(alb_obj) == str(align)
# Don't modify if average sequence length is reduced by more than half
align = Alb.AlignBuddy("""\
>A
MSTGTC-------
>B
M---TC-------
>C
M---TC---AILP
>D
-STPTC-YWAILP
""",
in_format="fasta")
seqbuddy = Sb.SeqBuddy(Alb.make_copy(align).records(), in_format="fasta")
seqbuddy = Sb.clean_seq(seqbuddy)
monkeypatch.setattr(Alb, "generate_msa", lambda *_, **__: align)
alb_obj = group_by_cluster.make_msa(seqbuddy, "clustalo", trimal=[0.3])
assert str(alb_obj) == str(align)
# Remove some gaps
alb_obj = group_by_cluster.make_msa(seqbuddy,
"clustalo",
trimal=[0.3, 0.55])
assert str(alb_obj) == """\
print(" -> Creating alignment file")
alignbuddy = Alb.faux_alignment(Sb.make_copy(seqbuddy), r_seed=12345)
alignbuddy.write("%s%s_aln.gb" % (ref_dir, ref_name))
else:
alignbuddy = Alb.AlignBuddy("%s%s_aln.gb" % (ref_dir, ref_name))
if not os.path.isfile("%s%s_pep_aln.gb" % (ref_dir, ref_name)):
print(" -> Creating protein alignment file")
alb_pep = Alb.faux_alignment(
Sb.SeqBuddy("%s%s_pep.gb" % (ref_dir, ref_name)))
alb_pep.write("%s%s_pep_aln.gb" % (ref_dir, ref_name))
del alb_pep
if not os.path.isfile("%s%s_rna_aln.gb" % (ref_dir, ref_name)):
print(" -> Creating RNA alignment file")
alb_rna = Alb.dna2rna(Alb.make_copy(alignbuddy))
alb_rna.write("%s%s_rna_aln.gb" % (ref_dir, ref_name))
del alb_rna
if not os.path.isfile("%s%s_tree.nwk" % (ref_dir, ref_name)):
print(" -> Creating tree file")
from dendropy.simulate import treesim
tree = treesim.birth_death_tree(birth_rate=1.0,
death_rate=0.5,
ntax=len(seqbuddy))
tree = tree.as_string("newick")
for indx, rec in enumerate(seqbuddy.records):
tree = re.sub("T%s:" % indx, "%s:" % rec.id, tree)
phylobuddy = Pb.PhyloBuddy(tree)
phylobuddy.write("%s%s_tree.nwk" % (ref_dir, ref_name))
del tree