def new_nexus_without_sites(nexus_obj, sites_to_remove):
"""
Returns a new NexusReader instance with the sites in
`sites_to_remove` removed.
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param sites_to_remove: A list of site numbers
:type sites_to_remove: List
:return: A NexusWriter instance
:raises AssertionError: if nexus_obj is not a nexus
:raises NexusFormatException: if nexus_obj does not have a `data` block
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
# make new nexus
nexout = NexusWriter()
nexout.add_comment(
"Removed %d sites: %s" %
(len(sites_to_remove), ",".join(["%s" % s for s in sites_to_remove])))
new_sitepos = 0
for sitepos in range(nexus_obj.data.nchar):
if sitepos in sites_to_remove:
continue # skip!
for taxon, data in nexus_obj.data:
nexout.add(taxon, new_sitepos, data[sitepos])
new_sitepos += 1
return nexout
def combine_nexuses(*nexuslist):
"""
Combines a list of NexusReader instances into a single nexus
:param nexuslist: A list of NexusReader instances
:return: A NexusWriter instance
"""
if len(nexuslist) == 1 and isinstance(nexuslist[0], (list, tuple)):
nexuslist = nexuslist[0]
nexuslist = [get_nexus_reader(nex) for nex in nexuslist]
out = NexusWriter()
# check they're all nexus instances and get all block types
blocks = set()
for nex in nexuslist:
blocks.update(list(nex.blocks))
for block in blocks:
if block == 'data':
out = combine_datablocks(out, nexuslist)
elif block == 'trees':
out = combine_treeblocks(out, nexuslist)
else: # pragma: no cover
raise ValueError("Don't know how to combine %s blocks" % block)
return out
def snpMatrixGenerator(sourceFile,
destFile,
recordAll=False,
recordRandomSample=True):
if recordAll == recordRandomSample:
print "Invalid Options"
exit()
destNexus = NexusWriter()
block = ""
snpCol = 0
for line in sourceFile:
if all(x in line.lower() for x in {"begin", "data"}):
sourceNexus = NexusReader()
sourceNexus.read_string(block)
if "data" in sourceNexus.blocks:
snpCol = _findDifferences(sourceNexus, destNexus, snpCol,
recordAll, recordRandomSample)
block = line
else:
block += line
sourceNexus = NexusReader()
sourceNexus.read_string(block)
if "data" in sourceNexus.blocks:
snpCol = _findDifferences(sourceNexus, destNexus, snpCol, recordAll,
recordRandomSample)
destFile.write(destNexus.make_nexus() + '\n')
destFile.close()
sourceFile.close()
def test_regression_format_string_has_quoted_symbols(self):
"""Regression: Symbols in the format string should be quoted"""
nex = NexusWriter()
for char, b in data.items():
for taxon, value in b.items():
nex.add(taxon, char, value)
out = nex.make_nexus()
assert 'SYMBOLS="123456"' in out
def test_regression_format_string_has_datatype_first(self):
"""Regression: Format string should contain 'datatype' as the first element"""
# SplitsTree complains otherwise.
nex = NexusWriter()
for char, b in data.items():
for taxon, value in b.items():
nex.add(taxon, char, value)
out = nex.make_nexus()
assert "FORMAT DATATYPE=STANDARD" in out
def binarise(nexus_obj, one_nexus_per_block=False):
"""
Returns a binary variant of the given `nexus_obj`.
If `one_nexus_per_block` then we return a list of NexusWriter instances.
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param one_nexus_per_block: Whether to return a single NexusWriter, or a
list of NexusWriter's (one per character)
:type one_nexus_per_block: Boolean
:return: A NexusWriter instance or a list of NexusWriter instances.
:raises AssertionError: if nexus_obj is not a nexus
:raises NexusFormatException: if nexus_obj does not have a `data` block
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
nexuslist = []
n = NexusWriter()
for i in sorted(nexus_obj.data.charlabels):
label = nexus_obj.data.charlabels[i] # character label
char = nexus_obj.data.characters[
label] # character dict (taxon->state)
recoding = _recode_to_binary(char) # recode
new_char_length = len(recoding[recoding.keys()[0]])
# loop over recoded data
for j in range(new_char_length):
for taxon, state in recoding.items():
# make new label
new_label = "%s_%d" % (str(label), j)
# add to nexus
n.add(taxon, new_label, state[j])
if one_nexus_per_block:
nexuslist.append(n)
n = NexusWriter()
if one_nexus_per_block:
return nexuslist
else:
return n
def nexus(args): # pragma: no cover
usage = """
Convert a lexibank dataset to nexus.
lexibank nexus <DATASET> --output=...
"""
get_dataset(args)
parser = argparse.ArgumentParser(prog='nexus', usage=usage)
parser.add_argument('--output', help='Nexus output file', default=None)
xargs = parser.parse_args(args.args[1:])
writer = NexusWriter()
if not xargs.output:
print(writer.write())
else:
writer.write_to_file(filename=xargs.output)
def shufflenexus(nexus_obj, resample=False):
"""
Shuffles the characters between each taxon to create a new nexus
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param resample: The number of characters to resample. If set to False, then
the number of characters will equal the number of characters in the
original data file.
:type resample: Integer
:return: A shuffled NexusReader instance
:raises AssertionError: if nexus_obj is not a nexus
:raises ValueError: if resample is not False or a positive Integer
:raises NexusFormatException: if nexus_obj does not have a `data` block
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
if resample is False:
resample = nexus_obj.data.nchar
try:
resample = int(resample)
except ValueError:
raise ValueError('resample must be a positive integer or False!')
if resample < 1:
raise ValueError('resample must be a positive integer or False!')
newnexus = NexusWriter()
newnexus.add_comment("Randomised Nexus generated from %s" %
nexus_obj.filename)
for i in range(resample):
# pick existing character
character = randrange(0, nexus_obj.data.nchar)
chars = nexus_obj.data.characters[character]
site_values = [chars[taxon] for taxon in nexus_obj.data.taxa]
shuffle(site_values)
for taxon in nexus_obj.data.taxa:
newnexus.add(taxon, i, site_values.pop(0))
return newnexus
def create_nexus(bt_matrix, sample_list):
'''
create NexusWriter object from BedTool matrix
BedTool object apparently can contain empty lines, a simple length-check skips these
requires pybedtools, nexus
'''
n = NexusWriter()
if isinstance(bt_matrix, BedTool):
matrix_lines = str(bt_matrix).split(
"\n") # create lines from BedTool object
else:
matrix_lines = bt_matrix
i = 0
current_chromosome = ""
for line in matrix_lines:
line = line.split("\t")
if len(line) < 4: #check for empty line, why 4? it works
print "skipping: line empty: %s" % ",".join(line)
continue
chrom, start, end, samples_present = line[0], line[1], line[2], line[
3].split(",") # create locus and presnt_ssample objects
locus = "%s:%i - %i" % (chrom, int(start), int(end)) # define locus
i += 1
if chrom != current_chromosome:
print chrom
current_chromosome = chrom
else:
pass
for taxon in sample_list: # iterate over taxons
presence = 1 if taxon in samples_present else 0
n.add(taxon, locus, presence)
return n
def make_nexus(model_dict):
sequence = []
n = NexusWriter()
dictline = {}
for dictline in model_dict:
lang = dictline.get('Language')
isocode = dictline.get('ISOCODE')
kvec = ""
for k in sorted(dictline):
#print(k)
if (k == 'Language' or k == 'ISOCODE'):
continue
else:
k = repr(dictline.get(k))
krem = k.replace("'", "")
kmod = krem[2:36]
kvec = kvec + kmod.zfill(35)
# label is number of elements in vector, number of taxa and a random 1
label = "%s_%s_%d" % ("756", "51", 1)
n.add(lang, label, kvec)
return n
def combine_nexuses(nexuslist):
"""
Combines a list of NexusReader instances into a single nexus
:param nexuslist: A list of NexusReader instances
:type nexuslist: List
:return: A NexusWriter instance
:raises TypeError: if nexuslist is not a list of NexusReader instances
:raises IOError: if unable to read an file in nexuslist
:raises NexusFormatException: if a nexus file does not have a `data` block
"""
out = NexusWriter()
charpos = 0
for nex_id, nex in enumerate(nexuslist, 1):
check_for_valid_NexusReader(nex, required_blocks=['data'])
if hasattr(nex, 'short_filename'):
nexus_label = os.path.splitext(nex.short_filename)[0]
elif hasattr(nex, 'label'):
nexus_label = nex.label
else:
nexus_label = str(nex_id)
out.add_comment("%d - %d: %s" %
(charpos, charpos + nex.data.nchar - 1, nexus_label))
for site_idx, site in enumerate(sorted(nex.data.characters), 0):
data = nex.data.characters.get(site)
charpos += 1
# work out character label
charlabel = nex.data.charlabels.get(site_idx, site_idx + 1)
label = '%s.%s' % (nexus_label, charlabel)
for taxon, value in data.items():
out.add(taxon, label, value)
return out
def read_file(self):
with open( self.input_file, 'r') as f:
self.first_line = f.readline()
# TODO: Needs work xread / tnt file format is loose
# xread has some other potential clues
xread_filename = f.readline().strip().replace("'", "")
xread_matrix_dimensions = f.readline()
lines = f.readlines()
f.close
if "#NEXUS" == self.first_line.strip():
print "text file is nexus"
# move to nexus folder
filename, file_extension = os.path.splitext(self.input_file)
os.rename(self.input_file, filename + ".nex")
# send to correct matrix handler
# TODO: A little dirty, probably should
# change mediator's handler param so this flows cleaner
matrixHandler = NexusHandler( filename + ".nex" )
return matrixHandler.read_file()
elif "xread" == self.first_line.strip():
print "xread format found"
dimensions = str(xread_matrix_dimensions).split(' ')
self.ncols = int(dimensions[0])
self.nrows = int(dimensions[1])
custom_block = "\n\nBEGIN VERIFIED_TAXA;\n"
custom_block += "Dimensions ntax=" + str(self.nrows) + " nchar=4;\n"
matrix = ""
matrix_arr = []
line_buffer = ""
row_taxa = []
for l in lines:
if ";proc/;" != l.strip():
if line_buffer:
line_row = line_buffer + " " + l.strip()
else:
line_row = l.strip()
if len(line_row) >= self.ncols:
# reconstitute broken rows, then remove space/tabbing
line_parts = line_row.split(' ')
line_parts = list(filter(None, line_parts))
taxon_name = line_parts[0]
taxon_chars = line_parts[1]
#taxon_chars = line_parts[1].replace("[", "(")
#taxon_chars = taxon_chars.replace("]", ")")
# verify taxa
verified_taxa = verifyTaxa(taxon_name)
verified_name = None
if verified_taxa:
for taxa in verified_taxa:
# We split here to exclude the odd citation on the taxon name ( maybe regex what looks like name & name, year would be better )
verified_name = taxa['name_string'].lower().split(' ')
row_taxa.append( verified_name[0] )
custom_block += taxon_name + " " + taxa['name_string'] + " " + taxa['match_value'] + " " + taxa['datasource'] + "\n"
matrix += " " + verified_name[0] + " " + taxon_chars.strip() + "\n"
matrix_arr.append(taxon_chars.strip())
else:
row_taxa.append( taxon_name )
custom_block += taxon_name + "\n"
matrix += " " + taxon_name + " " + taxon_chars.strip() + "\n"
matrix_arr.append(taxon_chars.strip())
line_buffer = ""
else:
line_buffer += l.strip()
custom_block += ";\n"
custom_block += "END;\n"
self.custom_block = custom_block
print "matrix array"
marr = []
for row in matrix_arr:
items = list(row)
marr.append(items)
m = numpy.matrix(marr)
nw = NexusWriter()
nw.add_comment("Morphobank generated Nexus from xread .txt file ")
for rx in range(self.nrows):
taxon_name = row_taxa[rx]
cell_value = m.item(rx)
for cindex, cv in enumerate(cell_value):
char_no = cindex + 1
nw.add(taxon_name, char_no, cv)
# keep the upload path and filename, but change extension
file_parts = self.input_file.split('.')
output_file = file_parts[0] + '.nex'
nw.write_to_file(filename=output_file, interleave=False, charblock=True)
# move to nexus folder
#os.rename(xread_filename + ".nex", "./nexus/" + xread_filename + ".nex")
# wait for file to move before open and append
#while not os.path.exists('./nexus/' + xread_filename + '.nex'):
# time.sleep(1)
#if os.path.isfile('./nexus/' + xread_filename + '.nex'):
# Custom Block Section
nexus_file = codecs.open(output_file, 'a', 'utf-8')
nexus_file.write(custom_block)
nexus_file.close()
return output_file
else:
print "do not know how to process this .txt file"
def create_nexus(bt_matrix, sample_list, absence_code=0, has_missing=False):
'''
create NexusWriter object from BedTool matrix
BedTool object apparently can contain empty lines, a simple length-check skips these
:param has_missing indicate whether input BED file should be parsed for uncertainly called loci, that will be coded as "?"
requires pybedtools, nexus
'''
from nexus import NexusWriter
n = NexusWriter()
# if isinstance(bt_matrix, BedTool):
# matrix_lines = str(bt_matrix).split("\n") # create lines from BedTool object
# else:
# matrix_lines = str(bt_matrix).split("\n")
matrix_lines = str(bt_matrix).split("\n")
current_chrom = ""
if has_missing:
print u"[ {} ] adding missing characters".format(modulename)
for line in matrix_lines:
line = line.split("\t")
if len(line) < 4: # check for incomplete line
print u"[ {} ]".format(modulename),
print u"skipping incomplete or empty line: %s" % ",".join(line)
continue
if not has_missing:
chrom, start, end, samples_present = line[0], line[1], line[
2], line[3].split(
",") # create locus and present_sample objects
locus = "%s_%i_%i" % (chrom, int(start), int(end)) # define locus
if current_chrom != chrom:
print u"[ {} ] Operating on".format(modulename),
print chrom
current_chrom = chrom
# add locus to nexus object
for taxon in sample_list: # iterate over taxons
char = 1 if taxon in samples_present else absence_code
n.add(taxon, locus, char)
elif has_missing:
chrom, start, end, samples_present, type, samples_missing = line[
0], line[1], line[2], line[3].split(
","), line[4], line[5].split(
",") # create locus and present_sample objects
locus = "%s_%i_%i" % (chrom, int(start), int(end)) # define locus
if current_chrom != chrom:
print u"[ {} ] Operating on".format(modulename),
print chrom
current_chrom = chrom
# add locus to nexus object
for taxon in sample_list: # iterate over taxons
if taxon in samples_present:
char = 1
elif taxon in samples_missing:
char = "?"
else:
char = absence_code
n.add(taxon, locus, char)
return n
def setUp(self):
self.nex = NexusWriter()
for char, b in data.items():
for taxon, value in b.items():
self.nex.add(taxon, char, value)
def setUp(self):
self.nex = NexusWriter()
def read_file(self):
book = xlrd.open_workbook(self.input_file)
sh = book.sheet_by_index(0)
nw = NexusWriter()
self.nrows = sh.nrows
self.ncols = sh.ncols
nw.add_comment("Morphobank generated Nexus File")
custom_block = "\n\nBEGIN VERIFIED_TAXA;\n"
custom_block += "Dimensions ntax=" + str(self.nrows) + " nchar=4;\n"
# Species List Taxa
for rx in range(self.nrows):
if rx:
taxon_name = str(sh.cell_value(rowx=rx, colx=0)).strip()
verified_taxa = verifyTaxa(taxon_name)
verified_name = None
if verified_taxa:
for taxa in verified_taxa:
verified_name = taxa['name_string'].lower()
custom_block += taxon_name + " " + taxa['name_string'] + " " + taxa['match_value'] + " " + taxa['datasource'] + "\n"
else:
custom_block += taxon_name + "\n"
for cx in range(self.ncols):
if cx:
if is_number( sh.cell_value(rowx=rx, colx=cx)):
cell_value = int(sh.cell_value(rowx=rx, colx=cx))
else:
cell_value = sh.cell_value(rowx=rx, colx=cx)
cell_value = cell_value.replace("{", "(")
cell_value = cell_value.replace("}", ")")
if verified_name:
nw.add(verified_name, cx, cell_value)
else:
nw.add(taxon_name, cx, cell_value)
custom_block += ";\n"
custom_block += "END;\n"
self.custom_block = custom_block
# keep the upload path and filename, but change extension
file_parts = self.input_file.split('.')
output_file = file_parts[0] + '.nex'
nw.write_to_file(filename=file_parts[0] + '.nex', interleave=False, charblock=True)
## quick append Custom Block
nexus_file = open(output_file, 'a')
nexus_file.write(custom_block)
nexus_file.close()
return output_file
