def clustal_from_alignment(aln, interleave_len=None):
"""Returns a string in Clustal format.
- aln: can be an Alignment object or a dict.
- interleave_len: sequence line width. Only available if sequences are
aligned.
"""
if not aln:
return ''
# get seq output order
try:
order = aln.RowOrder
except:
order = aln.keys()
order.sort()
seqs = SequenceCollection(aln)
clustal_list = ["CLUSTAL\n"]
if seqs.isRagged():
raise ValueError,\
"Sequences in alignment are not all the same length." +\
"Cannot generate Clustal format."
aln_len = seqs.SeqLen
#Get all labels
labels = copy(seqs.Names)
#Find all label lengths in order to get padding.
label_lengths = [len(l) for l in labels]
label_max = max(label_lengths)
max_spaces = label_max+4
#Get ordered seqs
ordered_seqs = [seqs.NamedSeqs[label] for label in order]
if interleave_len is not None:
curr_ix = 0
while curr_ix < aln_len:
clustal_list.extend(["%s%s%s"%(x,' '*(max_spaces-len(x)),\
y[curr_ix:curr_ix+ \
interleave_len]) for x,y in zip(order,ordered_seqs)])
clustal_list.append("")
curr_ix += interleave_len
else:
clustal_list.extend(["%s%s%s"%(x,' '*(max_spaces-len(x)),y) \
for x,y in zip(order,ordered_seqs)])
clustal_list.append("")
return '\n'.join(clustal_list)
def clustal_from_alignment(aln, interleave_len=None):
"""Returns a string in Clustal format.
- aln: can be an Alignment object or a dict.
- interleave_len: sequence line width. Only available if sequences are
aligned.
"""
if not aln:
return ''
# get seq output order
try:
order = aln.RowOrder
except:
order = aln.keys()
order.sort()
seqs = SequenceCollection(aln)
clustal_list = ["CLUSTAL\n"]
if seqs.isRagged():
raise ValueError,\
"Sequences in alignment are not all the same length." +\
"Cannot generate Clustal format."
aln_len = seqs.SeqLen
#Get all labels
labels = copy(seqs.Names)
#Find all label lengths in order to get padding.
label_lengths = [len(l) for l in labels]
label_max = max(label_lengths)
max_spaces = label_max+4
#Get ordered seqs
ordered_seqs = [seqs.NamedSeqs[label] for label in order]
if interleave_len is not None:
curr_ix = 0
while curr_ix < aln_len:
clustal_list.extend(["%s%s%s"%(x,' '*(max_spaces-len(x)),\
y[curr_ix:curr_ix+ \
interleave_len]) for x,y in zip(order,ordered_seqs)])
clustal_list.append("")
curr_ix += interleave_len
else:
clustal_list.extend(["%s%s%s"%(x,' '*(max_spaces-len(x)),y) \
for x,y in zip(order,ordered_seqs)])
clustal_list.append("")
return '\n'.join(clustal_list)
def stockholm_from_alignment(aln, interleave_len=None, GC_annotation=None):
"""Returns a string in Stockholm format.
- aln: can be an Alignment object or a dict.
- interleave_len: sequence line width. Only available if sequences are
aligned.
- GC_annotation: dict containing Per-column annotation {<tag>:<s>},
added to Stockholm file in the following format: #=GC <tag> <s>
- <s> is an aligned text line of annotation type <tag>.
- #=GC lines are associated with a sequence alignment block;
- <s> is aligned to the residues in the alignment block, and has the
same length as the rest of the block. #=GC lines are
placed at the end of each block.
"""
if not aln:
return ""
# get seq output order
try:
order = aln.RowOrder
except:
order = aln.keys()
order.sort()
seqs = SequenceCollection(aln)
stockholm_list = ["# STOCKHOLM 1.0\n"]
if seqs.isRagged():
raise ValueError, "Sequences in alignment are not all the same length." + "Cannot generate Stockholm format."
aln_len = seqs.SeqLen
# Get all labels
labels = copy(seqs.Names)
# Get ordered seqs
ordered_seqs = [seqs.NamedSeqs[label] for label in order]
if GC_annotation is not None:
GC_annotation_list = [(k, GC_annotation[k]) for k in sorted(GC_annotation.keys())]
# Add GC_annotation to list of labels.
labels.extend(["#=GC " + k for k in GC_annotation.keys()])
for k, v in GC_annotation.items():
if len(v) != aln_len:
raise ValueError, """GC annotation %s is not same length as alignment. Cannot generate Stockholm format.""" % (
k
)
# Find all label lengths in order to get padding.
label_lengths = [len(l) for l in labels]
label_max = max(label_lengths)
max_spaces = label_max + 4
if interleave_len is not None:
curr_ix = 0
while curr_ix < aln_len:
stockholm_list.extend(
[
"%s%s%s" % (x, " " * (max_spaces - len(x)), y[curr_ix : curr_ix + interleave_len])
for x, y in zip(order, ordered_seqs)
]
)
if GC_annotation is not None:
stockholm_list.extend(
[
"#=GC %s%s%s" % (x, " " * (max_spaces - len(x) - 5), y[curr_ix : curr_ix + interleave_len])
for x, y in GC_annotation_list
]
)
stockholm_list.append("")
curr_ix += interleave_len
else:
stockholm_list.extend(["%s%s%s" % (x, " " * (max_spaces - len(x)), y) for x, y in zip(order, ordered_seqs)])
if GC_annotation is not None:
stockholm_list.extend(
["#=GC %s%s%s" % (x, " " * (max_spaces - len(x) - 5), y) for x, y in GC_annotation_list]
)
stockholm_list.append("")
return "\n".join(stockholm_list) + "//"
def stockholm_from_alignment(aln, interleave_len=None, GC_annotation=None):
"""Returns a string in Stockholm format.
- aln: can be an Alignment object or a dict.
- interleave_len: sequence line width. Only available if sequences are
aligned.
- GC_annotation: dict containing Per-column annotation {<tag>:<s>},
added to Stockholm file in the following format: #=GC <tag> <s>
- <s> is an aligned text line of annotation type <tag>.
- #=GC lines are associated with a sequence alignment block;
- <s> is aligned to the residues in the alignment block, and has the
same length as the rest of the block. #=GC lines are
placed at the end of each block.
"""
if not aln:
return ''
# get seq output order
try:
order = aln.RowOrder
except:
order = aln.keys()
order.sort()
seqs = SequenceCollection(aln)
stockholm_list = ["# STOCKHOLM 1.0\n"]
if seqs.isRagged():
raise ValueError,\
"Sequences in alignment are not all the same length." +\
"Cannot generate Stockholm format."
aln_len = seqs.SeqLen
#Get all labels
labels = copy(seqs.Names)
#Get ordered seqs
ordered_seqs = [seqs.NamedSeqs[label] for label in order]
if GC_annotation is not None:
GC_annotation_list = \
[(k,GC_annotation[k]) for k in sorted(GC_annotation.keys())]
#Add GC_annotation to list of labels.
labels.extend(['#=GC ' + k for k in GC_annotation.keys()])
for k, v in GC_annotation.items():
if len(v) != aln_len:
raise ValueError, """GC annotation %s is not same length as alignment. Cannot generate Stockholm format.""" % (
k)
#Find all label lengths in order to get padding.
label_lengths = [len(l) for l in labels]
label_max = max(label_lengths)
max_spaces = label_max + 4
if interleave_len is not None:
curr_ix = 0
while curr_ix < aln_len:
stockholm_list.extend(["%s%s%s"%(x,' '*(max_spaces-len(x)),\
y[curr_ix:curr_ix+ \
interleave_len]) for x,y in zip(order, ordered_seqs)])
if GC_annotation is not None:
stockholm_list.extend(["#=GC %s%s%s"%(x,\
' '*(max_spaces-len(x)-5),\
y[curr_ix:curr_ix + interleave_len]) for x,y in\
GC_annotation_list])
stockholm_list.append("")
curr_ix += interleave_len
else:
stockholm_list.extend(["%s%s%s"%(x,' '*(max_spaces-len(x)),y) \
for x,y in zip(order, ordered_seqs)])
if GC_annotation is not None:
stockholm_list.extend(["#=GC %s%s%s"%(x,' '*(max_spaces-len(x)-5),\
y) for x,y in GC_annotation_list])
stockholm_list.append("")
return '\n'.join(stockholm_list) + '//'
