def main(argv):
print "AnnotateTreeCmd v1.0"
if len(argv) == 2 and argv[1] == '-t':
conduct_tests()
exit(0)
elif len(argv) != 7:
print 'usage python AnnotateTreeCmd.py seqnumfile seqfile treefile cdrfile tag wd.'
sys.exit(0)
for file in argv[1:4]:
check_file(file)
(seqnumfile, seqfile, treefile, cdrfile, tag, wdir) = argv[1:7]
if len(cdrfile) > 0:
check_file(cdrfile)
else:
cdrfile = None
try:
if not os.path.exists(wdir):
os.makedirs(wdir)
except:
print "Error creating directory %s." % wdir
sys.exit(0)
try:
msa = Alignment()
msa.read_nt(seqfile) # Check that the sequence comprises a valid set of codons
for seq in msa:
if '*' in seq:
print "Stop codon found in sequence %s." % seq.id
sys.exit(0)
except:
print "Error parsing %s: %s." % (seqfile, sys.exc_info()[1])
sys.exit(0)
try:
seq_pos = msa.read_position_numbers(seqnumfile)
except:
print "Error parsing %s: %s." % (seqnumfile, sys.exc_info()[1])
sys.exit(0)
if cdrfile is not None:
try:
acdr = AnalyseCDR(msa, file_name=cdrfile)
except:
print "Error parsing %s: %s." % (cdrfile, sys.exc_info()[1])
sys.exit(0)
try:
seq_align = AlignIO.read(seqfile, "fasta")
except:
try:
seq_align = AlignIO.read(seqfile, "phylip")
except:
print "Error parsing %s: %s." % (seqfile, sys.exc_info()[1])
sys.exit(0)
try:
tree = Phylo.read(treefile, "newick")
except:
print "Error parsing %s: %s." % (treefile, sys.exc_info()[1])
sys.exit(0)
dnaml = Dnaml()
int_aas = dnaml.run_dnaml(seq_align, tree, seq_pos, cdrfile, wdir, report, tag)
if int_aas is not None:
try:
if cdrfile is not None:
acdr = AnalyseCDR(int_aas, file_name=cdrfile)
cdr_output = acdr.analyse()
fo = open(wdir + "/" + tag + "cdr_analysis.html", "w")
fo.write(cdr_output)
fo.close()
except:
print "Warning: CDRs were not analysed: " + str(sys.exc_info()[1])
try:
gc.collect()
RenderTree.render_annotate(wdir + "/" + tag + "annotated_treefile.new", wdir + "/" + tag + "annotated_treefile.png")
gc.collect()
RenderTree.render_annotate(wdir + "/" + tag + "annotated_treefile.new", wdir + "/" + tag + "annotated_treefile.svg")
gc.collect()
if cdrfile is not None:
RenderTree.render_annotate(wdir + "/" + tag + "annotated_treefile_sum.new", wdir + "/" + tag + "annotated_treefile_sum.png")
gc.collect()
RenderTree.render_annotate(wdir + "/" + tag + "annotated_treefile_sum.new", wdir + "/" + tag + "annotated_treefile_sum.svg")
gc.collect()
RenderTree.render_annotate(wdir + "/" + tag + "annotated_treefile_tot.new", wdir + "/" + tag + "annotated_treefile_tot.png")
gc.collect()
RenderTree.render_annotate(wdir + "/" + tag + "annotated_treefile_tot.new", wdir + "/" + tag + "annotated_treefile_tot.svg")
gc.collect()
RenderTree.render_annotate(wdir + "/" + tag + "intermediates_treefile.new", wdir + "/" + tag + "intermediates_treefile.png")
gc.collect()
RenderTree.render_annotate(wdir + "/" + tag + "intermediates_treefile.new", wdir + "/" + tag + "intermediates_treefile.svg")
gc.collect()
except:
print "Error rendering trees: " + str(sys.exc_info()[1])
first = True
orig_recs = []
for rec in SeqIO.parse(wdir + "/" + tag + "aa_alignment.fa", "fasta"):
if not first and "node_" not in rec.id:
orig_recs.append(rec)
first = False
logo_alignment_file = wdir + "/" + tag + "alignment_for_logo.fa"
SeqIO.write(orig_recs, wdir + "/" + tag + "alignment_for_logo.fa", "fasta")
with open(wdir + "/" + tag + "weblogo_status.txt", "w") as fo:
retcode = subprocess.call("seqlogo -f %salignment_for_logo.fa -F PNG -o aa_logo -h 2 -w 20 -acS" % tag, cwd=wdir, shell=True, stdout=fo, stderr=subprocess.STDOUT)
if retcode == 1:
fo.write("Trying seqlogo.pl instead.\n")
retcode = subprocess.call("seqlogo.pl -f %salignment_for_logo.fa -F PNG -o aa_logo -h 2 -w 20 -acS" % tag, cwd=wdir, shell=True, stdout=fo, stderr=subprocess.STDOUT)
if retcode == 1:
print "Weblogo not installed: logo plot will not be generated."
def main(argv):
print "AnnotateTreeCmd v1.0"
if len(argv) == 2 and argv[1] == '-t':
conduct_tests()
exit(0)
elif len(argv) != 7:
print 'usage python AnnotateTreeCmd.py seqnumfile seqfile treefile cdrfile tag wd.'
sys.exit(0)
for file in argv[1:4]:
check_file(file)
(seqnumfile, seqfile, treefile, cdrfile, tag, wdir) = argv[1:7]
if len(cdrfile) > 0:
check_file(cdrfile)
else:
cdrfile = None
try:
if not os.path.exists(wdir):
os.makedirs(wdir)
except:
print "Error creating directory %s." % wdir
sys.exit(0)
try:
msa = Alignment()
msa.read_nt(
seqfile) # Check that the sequence comprises a valid set of codons
for seq in msa:
if '*' in seq:
print "Stop codon found in sequence %s." % seq.id
sys.exit(0)
except:
print "Error parsing %s: %s." % (seqfile, sys.exc_info()[1])
sys.exit(0)
try:
seq_pos = msa.read_position_numbers(seqnumfile)
except:
print "Error parsing %s: %s." % (seqnumfile, sys.exc_info()[1])
sys.exit(0)
if cdrfile is not None:
try:
acdr = AnalyseCDR(msa, file_name=cdrfile)
except:
print "Error parsing %s: %s." % (cdrfile, sys.exc_info()[1])
sys.exit(0)
try:
seq_align = AlignIO.read(seqfile, "fasta")
except:
try:
seq_align = AlignIO.read(seqfile, "phylip")
except:
print "Error parsing %s: %s." % (seqfile, sys.exc_info()[1])
sys.exit(0)
try:
tree = Phylo.read(treefile, "newick")
except:
print "Error parsing %s: %s." % (treefile, sys.exc_info()[1])
sys.exit(0)
dnaml = Dnaml()
int_aas = dnaml.run_dnaml(seq_align, tree, seq_pos, cdrfile, wdir, report,
tag)
if int_aas is not None:
try:
if cdrfile is not None:
acdr = AnalyseCDR(int_aas, file_name=cdrfile)
cdr_output = acdr.analyse()
fo = open(wdir + "/" + tag + "cdr_analysis.html", "w")
fo.write(cdr_output)
fo.close()
except:
print "Warning: CDRs were not analysed: " + str(sys.exc_info()[1])
try:
gc.collect()
RenderTree.render_annotate(
wdir + "/" + tag + "annotated_treefile.new",
wdir + "/" + tag + "annotated_treefile.png")
gc.collect()
RenderTree.render_annotate(
wdir + "/" + tag + "annotated_treefile.new",
wdir + "/" + tag + "annotated_treefile.svg")
gc.collect()
if cdrfile is not None:
RenderTree.render_annotate(
wdir + "/" + tag + "annotated_treefile_sum.new",
wdir + "/" + tag + "annotated_treefile_sum.png")
gc.collect()
RenderTree.render_annotate(
wdir + "/" + tag + "annotated_treefile_sum.new",
wdir + "/" + tag + "annotated_treefile_sum.svg")
gc.collect()
RenderTree.render_annotate(
wdir + "/" + tag + "annotated_treefile_tot.new",
wdir + "/" + tag + "annotated_treefile_tot.png")
gc.collect()
RenderTree.render_annotate(
wdir + "/" + tag + "annotated_treefile_tot.new",
wdir + "/" + tag + "annotated_treefile_tot.svg")
gc.collect()
RenderTree.render_annotate(
wdir + "/" + tag + "intermediates_treefile.new",
wdir + "/" + tag + "intermediates_treefile.png")
gc.collect()
RenderTree.render_annotate(
wdir + "/" + tag + "intermediates_treefile.new",
wdir + "/" + tag + "intermediates_treefile.svg")
gc.collect()
except:
print "Error rendering trees: " + str(sys.exc_info()[1])
first = True
orig_recs = []
for rec in SeqIO.parse(wdir + "/" + tag + "aa_alignment.fa", "fasta"):
if not first and "node_" not in rec.id:
orig_recs.append(rec)
first = False
logo_alignment_file = wdir + "/" + tag + "alignment_for_logo.fa"
SeqIO.write(orig_recs, wdir + "/" + tag + "alignment_for_logo.fa",
"fasta")
with open(wdir + "/" + tag + "weblogo_status.txt", "w") as fo:
retcode = subprocess.call(
"seqlogo -f %salignment_for_logo.fa -F PNG -o aa_logo -h 2 -w 20 -acS"
% tag,
cwd=wdir,
shell=True,
stdout=fo,
stderr=subprocess.STDOUT)
if retcode == 1:
fo.write("Trying seqlogo.pl instead.\n")
retcode = subprocess.call(
"seqlogo.pl -f %salignment_for_logo.fa -F PNG -o aa_logo -h 2 -w 20 -acS"
% tag,
cwd=wdir,
shell=True,
stdout=fo,
stderr=subprocess.STDOUT)
if retcode == 1:
print "Weblogo not installed: logo plot will not be generated."
