def check_tree_subset(fasta_labels, tree_fp):
""" Returns a list of all fasta labels that are not a subset of the tree
fasta_labels: list of fasta labels
tree_fp: tree filepath
"""
# Need to get modified fasta labels with underscore stripped
raw_fasta_labels = set([label.split('_')[0] for label in fasta_labels])
tree_f = open(tree_fp, "U")
tree = DndParser(tree_f)
# Get a set of tree tip names
tree_tips = set(tree.getTipNames())
labels_not_in_tips = []
for curr_label in raw_fasta_labels:
if curr_label not in tree_tips:
labels_not_in_tips.append(curr_label)
# Return True if all found in tree tips
if len(labels_not_in_tips) == 0:
labels_not_in_tips = True
return labels_not_in_tips
def check_tree_subset(fasta_labels,
tree_fp):
""" Returns a list of all fasta labels that are not a subset of the tree
fasta_labels: list of fasta labels
tree_fp: tree filepath
"""
# Need to get modified fasta labels with underscore stripped
raw_fasta_labels = set([label.split('_')[0] for label in fasta_labels])
tree_f = open(tree_fp, "U")
tree = DndParser(tree_f)
# Get a set of tree tip names
tree_tips = set(tree.getTipNames())
labels_not_in_tips = []
for curr_label in raw_fasta_labels:
if curr_label not in tree_tips:
labels_not_in_tips.append(curr_label)
# Return True if all found in tree tips
if len(labels_not_in_tips) == 0:
labels_not_in_tips = True
return labels_not_in_tips
def check_tree_exact_match(fasta_labels,
tree_fp):
"""Checks fasta labels to exact match to tree tips
Returns a list of two lists, the fasta labels not in tips, and tips not
in fasta labels.
fasta_labels: list of fasta labels
tree_fp: tree filepath
"""
# Need to get modified fasta labels with underscore stripped
raw_fasta_labels = set([label.split('_')[0] for label in fasta_labels])
tree_f = open(tree_fp, "U")
tree = DndParser(tree_f)
# Get a set of tree tip names
tree_tips = set(tree.getTipNames())
labels_not_in_tips = []
for curr_label in raw_fasta_labels:
if curr_label not in tree_tips:
labels_not_in_tips.append(curr_label)
# Return True if all found in tree tips
if len(labels_not_in_tips) == 0:
labels_not_in_tips = True
tips_not_in_labels = []
for curr_tip in tree_tips:
if curr_tip not in raw_fasta_labels:
tips_not_in_labels.append(curr_tip)
if len(tips_not_in_labels) == 0:
tips_not_in_labels = True
return [labels_not_in_tips, tips_not_in_labels]
def check_tree_exact_match(fasta_labels,
tree_fp):
"""Checks fasta labels to exact match to tree tips
Returns a list of two lists, the fasta labels not in tips, and tips not
in fasta labels.
fasta_labels: list of fasta labels
tree_fp: tree filepath
"""
# Need to get modified fasta labels with underscore stripped
raw_fasta_labels = set([label.split('_')[0] for label in fasta_labels])
tree_f = open(tree_fp, "U")
tree = DndParser(tree_f)
# Get a set of tree tip names
tree_tips = set(tree.getTipNames())
labels_not_in_tips = []
for curr_label in raw_fasta_labels:
if curr_label not in tree_tips:
labels_not_in_tips.append(curr_label)
# Return True if all found in tree tips
if len(labels_not_in_tips) == 0:
labels_not_in_tips = True
tips_not_in_labels = []
for curr_tip in tree_tips:
if curr_tip not in raw_fasta_labels:
tips_not_in_labels.append(curr_tip)
if len(tips_not_in_labels) == 0:
tips_not_in_labels = True
return [labels_not_in_tips, tips_not_in_labels]
