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class EMBLConverter(CustomVisitor): |
def __init__(self, locus_tag=None, translation_table=11): |
CustomVisitor.__init__(self) |
self.contigs = {} |
self.locus_tag = locus_tag |
self.translation_table = translation_table |
def visit_feature_node(self, feature_node): |
sequence_id = feature_node.get_seqid() |
contig = self.contigs.get(sequence_id) |
if contig: # contig already exists, just try and update it |
contig.add_feature(sequence_id = sequence_id, feature_type = feature_node.get_type(), start = feature_node.get_start(), |
end = feature_node.get_end(), strand = feature_node.get_strand(), |
feature_attributes = feature_node.attribs, |
locus_tag = self.locus_tag, translation_table = self.translation_table) |
else: |
contig = EMBLContig() |
successfully_added_feature = contig.add_feature(sequence_id = sequence_id, feature_type = feature_node.get_type(), start = feature_node.get_start(), |
end = feature_node.get_end(), strand = feature_node.get_strand(), |
feature_attributes = feature_node.attribs, |
locus_tag = self.locus_tag, translation_table = self.translation_table) |
if successfully_added_feature: |
self.contigs[sequence_id] = contig |
else: |
pass # discard the contig because we didn't add a feature so it is empty |
def visit_region_node(self, region_node): |
pass # for now |
def visit_comment_node(self, comment_node): |
pass # for now |
def visit_sequence_node(self, sequence_node): |
sequence_id = sequence_node.get_description() |
contig = self.contigs.setdefault(sequence_id, EMBLContig()) |
contig.add_sequence(sequence_node.get_sequence()) |
# This file is part of GridCal. |
# |
# GridCal is free software: you can redistribute it and/or modify |
# it under the terms of the GNU General Public License as published by |
# the Free Software Foundation, either version 3 of the License, or |
# (at your option) any later version. |
# |
# GridCal is distributed in the hope that it will be useful, |
# but WITHOUT ANY WARRANTY; without even the implied warranty of |
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
# GNU General Public License for more details. |
# |
# You should have received a copy of the GNU General Public License |
# along with GridCal. If not, see <http://www.gnu.org/licenses/>. |
import numpy as np |
def slice_to_range(sl: slice, n): |
""" |
Turn a slice into a range |
:param sl: slice object |
:param n: total number of items |
:return: range object, if the slice is not supported an exception is raised |
""" |
if sl.start is None and sl.step is None and sl.start is None: # (:) |
return range(n) |
elif sl.start is not None and sl.step is None and sl.start is None: # (a:) |
return range(sl.start, n) |
elif sl.start is not None and sl.step is not None and sl.start is None: # (?) |
raise Exception('Invalid slice') |
elif sl.start is not None and sl.step is None and sl.start is not None: # (a:b) |
return range(sl.start, sl.stop) |
elif sl.start is not None and sl.step is not None and sl.start is not None: # (a:s:b) |
return range(sl.start, sl.stop, sl.step) |
elif sl.start is None and sl.step is None and sl.start is not None: # (:b) |
return range(sl.stop) |
else: |
raise Exception('Invalid slice') |
def dense_to_str(mat: np.ndarray): |
""" |
Turn dense 2D numpy array into a string |
:param mat: 2D numpy array |
:return: string |
""" |
rows, cols = mat.shape |
val = "Matrix (" + ("%d" % rows) + " x " + ("%d" % cols) + ")\n" |
val += str(mat).replace('. ', ' ').replace('[', ' ').replace(']', '').replace('0 ', '_ ').replace('0.', '_ ') |
# for i in range(0, rows): |
# for j in range(0, cols): |
# x = mat[i, j] |
# if x is not None: |
# if x == 0: |
# val += '{:<4}'.format(0) |
# else: |