def save_selection_dialog(self, mode="selection"):
"""
Save selection in a single file.
"""
# Builds the selection.
if mode == "selection":
selection = self.get_selected_sequences()
elif mode == "all":
selection = self.get_all_sequences()
else:
raise KeyError("Unknown 'mode': %s" % mode)
# Ask users if they want to include indels in the sequences to save.
remove_indels_choice = False
for e in selection:
if "-" in e.my_sequence:
remove_indels_choice = self.ask_to_remove_indels()
break
# Ask users to choose a directory where to save the file.
filepath = asksaveasfile_qt("Save FASTA file", name_filter="*.fasta", parent=self.get_qt_parent())
if not filepath:
return None
dirpath = os.path.dirname(filepath)
filename = os.path.basename(filepath)
self.build_sequence_file(selection, filename, file_format="fasta",
remove_indels=remove_indels_choice, same_length=remove_indels_choice,
new_directory=dirpath, add_extension=False)
def save_session_from_main_menu(self):
save_project_full_path = asksaveasfile_qt("Save PyMod Session file",
name_filter="*.pmse",
parent=self.get_qt_parent())
if not save_project_full_path:
return None
self.save_pymod_session(save_project_full_path)
def sequence_save_dialog(self, element):
"""
Save a single sequence to a file.
"""
# Ask to remove indels.
if "-" in element.my_sequence:
remove_indels_choice = self.ask_to_remove_indels()
else:
remove_indels_choice = False
# Choose the file path.
filepath = asksaveasfile_qt("Save FASTA file",
name_filter="*.fasta",
parent=self.get_qt_parent())
if not filepath:
return None
# Actually saves the file. The file extension will not be added automatically.
dirpath = os.path.dirname(filepath)
filename = os.path.basename(filepath)
self.build_sequence_file([element],
filename,
file_format="fasta",
remove_indels=remove_indels_choice,
new_directory=dirpath,
add_extension=False)
def save_to_event(self):
"""
Saves the table data to a .csv file.
"""
# Let the user select the filepath.
filepath = asksaveasfile_qt("Save CSV file", name_filter="*.csv")
if not filepath:
return None
try:
# Writes a .csv file on that path.
with open(filepath, 'w') as csv_fh:
writer = csv.writer(csv_fh,
delimiter=',',
quoting=csv.QUOTE_MINIMAL)
if self.table.row_labels is not None:
writer.writerow([" "] + self.table.column_labels)
else:
writer.writerow(self.table.column_labels)
for row_idx, row in enumerate(self.table.data):
if self.table.row_labels is not None:
writer.writerow([self.table.row_labels[row_idx]] +
[str(v) for v in row])
else:
writer.writerow([str(v) for v in row])
except Exception as e:
print("- WARNING: could not write a csv file: %s" % str(e))
def save_to_csv_event(self):
output_filepath = asksaveasfile_qt("Save to CSV file",
parent=self.pymod.get_qt_parent(),
name_filter="*.csv")
if not output_filepath:
return None
try:
self._save_to_csv_file(output_filepath)
except Exception as e:
print("- WARNING: could not write a csv file: %s" % str(e))
def alignment_save_dialog(self, alignment_element):
"""
Lets the user choose the path to which an alignment file is going to be saved, and saves
an alignment file there.
"""
save_file_full_path = asksaveasfile_qt(
"Save an alignment file",
name_filter="*.fasta;;*.aln;;*.sto",
parent=self.get_qt_parent())
if not save_file_full_path:
return None
alignment_file_name, extension = os.path.splitext(
os.path.basename(save_file_full_path))
extension = extension.replace(".", "")
# The get all the aligned elements.
aligned_elements = alignment_element.get_children()
# Saves a file with all the sequences in the project "Alignments" directory.
if extension == "fasta":
self.save_alignment_fasta_file(alignment_file_name,
aligned_elements)
elif extension == "aln":
self.build_sequence_file(aligned_elements,
alignment_file_name,
file_format="clustal",
remove_indels=False)
elif extension == "sto":
self.build_sequence_file(aligned_elements,
alignment_file_name,
file_format="stockholm",
remove_indels=False)
# If the user didn't provide a valid extension.
else:
title = "Format Error"
if extension != "":
message = "Unknown alignment file extension: '%s'." % (
extension)
else:
message = "No alignment file extension provided."
message += " Please provide a valid extension. Example: .fasta (FASTA), .aln (Clustal) or .sto (Stockholm)"
self.main_window.show_error_message(title, message)
return
# Moves the saved file to the path chosen by the user.
try:
old_path = os.path.join(self.alignments_dirpath,
alignment_file_name + "." + extension)
os.rename(old_path, save_file_full_path)
except Exception as e:
title = "File Error"
message = "Could not save the alignment file to path '%s' for the following reason: %s." % (
save_file_full_path, e)
self.main_window.show_error_message(title, message)
def save_modeling_session(self, modeling_session):
"""
Build a zip file of the modeling directory of a certain session.
"""
archive_path = asksaveasfile_qt("Save PyMod Session file", name_filter="*.zip", parent=self.get_qt_parent())
if not archive_path:
return None
try:
pmos.zip_directory(directory_path=os.path.join(self.models_dirpath, os.path.basename(modeling_session.modeling_directory_path)),
zipfile_path=archive_path)
except:
title = "File Error"
message = "Could not save the modeling session file to path: %s" % (archive_path)
self.main_window.show_error_message(title, message)
def save_to_png_event(self):
output_filepath = asksaveasfile_qt("Save to PNG file",
parent=self.pymod.get_qt_parent(),
name_filter="*.png")
if not output_filepath:
return None
try:
from pymod_lib.pymod_plot.pyqtgraph.exporters import ImageExporter
# Create an exporter instance, as an argument give it the whole plot.
exporter = ImageExporter(self.graphWidget.plotItem)
# Save to file.
exporter.export(output_filepath)
except Exception as e:
print("- WARNING: could not write a pgn file: %s" % str(e))
def save_pdb_chain_to_file_dialog(self, pymod_element):
"""
Save a PDB single chain to a file.
"""
# Choose the file path.
filepath = asksaveasfile_qt("Save PDB file for this chain", name_filter="*.pdb", parent=self.get_qt_parent())
if not filepath:
return None
# Actually saves the file.
try:
if os.path.isfile(filepath):
os.remove(filepath)
shutil.copy(pymod_element.structure.current_chain_file_path, filepath)
except Exception as e:
title = "File Error"
message = "Could not save the PDB chain file to path '%s' for the following reason: %s." % (filepath, e)
self.main_window.show_error_message(title, message)
