def make_xml(start_pos, stop_pos, nsamples):
"""
@return: location of xml file, location of log file
"""
out = StringIO()
print >> out, g_xml_pre_alignment
print >> out, """
<!-- The sequence alignment (each sequence refers to a taxon above). -->
<alignment id="alignment" dataType="nucleotide">
"""
lines = g_fasta_string.splitlines()
for header, seq in Fasta.gen_header_sequence_pairs(lines):
print >> out, '<sequence>'
print >> out, '<taxon idref="%s"/>' % header
print >> out, seq
print >> out, '</sequence>'
print >> out, '</alignment>'
print >> out, """
<patterns id="firsthalf.patterns" from="%d" to="%d">
<alignment idref="alignment"/>
</patterns>
""" % (start_pos, stop_pos)
print >> out, get_xml_post_alignment(nsamples)
log_loc = Util.get_tmp_filename(prefix='beast', suffix='.log')
print >> out, get_log_xml(log_loc)
xml_loc = Util.create_tmp_file(out.getvalue(),
prefix='beast',
suffix='.xml')
return xml_loc, log_loc
def make_xml(start_pos, stop_pos, nsamples):
"""
@return: location of xml file, location of log file
"""
out = StringIO()
print >> out, g_xml_pre_alignment
print >> out, """
<!-- The sequence alignment (each sequence refers to a taxon above). -->
<alignment id="alignment" dataType="nucleotide">
"""
lines = g_fasta_string.splitlines()
for header, seq in Fasta.gen_header_sequence_pairs(lines):
print >> out, '<sequence>'
print >> out, '<taxon idref="%s"/>' % header
print >> out, seq
print >> out, '</sequence>'
print >> out, '</alignment>'
print >> out, """
<patterns id="firsthalf.patterns" from="%d" to="%d">
<alignment idref="alignment"/>
</patterns>
""" % (start_pos, stop_pos)
print >> out, get_xml_post_alignment(nsamples)
log_loc = Util.get_tmp_filename(prefix='beast', suffix='.log')
print >> out, get_log_xml(log_loc)
xml_loc = Util.create_tmp_file(
out.getvalue(), prefix='beast', suffix='.xml')
return xml_loc, log_loc
def get_response_content(fs):
out = StringIO()
try:
alignment = Fasta.Alignment(fs.fasta.splitlines())
print >> out, 'This is a valid alignment.'
except Fasta.AlignmentError as e:
alignment = None
print >> out, 'This is not a valid alignment:', e
if alignment:
try:
old_column_count = len(alignment.columns)
alignment.force_nucleotide()
removed_column_count = old_column_count - len(alignment.columns)
if removed_column_count:
print >> out, ('After removing %d' % removed_column_count),
print >> out, 'columns this is a valid nucleotide alignment.'
else:
print >> out, 'This is a valid nucleotide alignment.'
except Fasta.AlignmentError as e:
print >> out, 'This is not a valid nucleotide alignment:', e
for header, seq in Fasta.gen_header_sequence_pairs(StringIO(fs.fasta)):
print >> out, '%s: %d' % (header, len(seq))
return out.getvalue()
def get_response_content(fs):
out = StringIO()
try:
alignment = Fasta.Alignment(fs.fasta.splitlines())
print >> out, 'This is a valid alignment.'
except Fasta.AlignmentError as e:
alignment = None
print >> out, 'This is not a valid alignment:', e
if alignment:
try:
old_column_count = len(alignment.columns)
alignment.force_nucleotide()
removed_column_count = old_column_count - len(alignment.columns)
if removed_column_count:
print >> out, ('After removing %d' % removed_column_count),
print >> out, 'columns this is a valid nucleotide alignment.'
else:
print >> out, 'This is a valid nucleotide alignment.'
except Fasta.AlignmentError as e:
print >> out, 'This is not a valid nucleotide alignment:', e
for header, seq in Fasta.gen_header_sequence_pairs(StringIO(fs.fasta)):
print >> out, '%s: %d' % (header, len(seq))
return out.getvalue()
def get_header_seq_pairs():
lines = g_fasta_string.splitlines()
return list(Fasta.gen_header_sequence_pairs(lines))
def get_header_seq_pairs():
lines = g_fasta_string.splitlines()
return list(Fasta.gen_header_sequence_pairs(lines))