#77 Creation of /sources/ works with --quick plus some code cleanup

DDV/AnnotationAlignment.py

@@ -18,7 +18,7 @@
     filter_repeats_by_chromosome_and_family
 from DDV.Span import alignment_chopping_index, AlignedSpans, Span
 from DDV.TransposonLayout import TransposonLayout
-from DDV.DDVUtils import make_output_dir_with_suffix
+from DDV.DDVUtils import make_output_directory
 
 
 def create_aligned_annotation_fragments(alignment, repeat_entries):
@@ -73,7 +73,8 @@ def align_annotation(annotation_filename, ref_fasta, query_fasta, chain_file):
             continue  # There's no usable entries left to use
 
         # modify chain.alignment to only contain annotated stretches
-        chain.output_folder = make_output_dir_with_suffix(chain.output_prefix, ending)  # create a folder specifically for this repeat
+        chain.output_folder = chain.output_prefix + ending
+        make_output_directory(chain.output_folder)  # create a folder specifically for this repeat
         chain.query_seq_gapped = editable_str('')  # these need to be cleared so they don't accumulate the previous family
         chain.ref_seq_gapped = editable_str('')
         trimmed_alignment = create_aligned_annotation_fragments(chain.alignment, repeat_entries)

DDV/ChainParser.py

@@ -19,7 +19,7 @@
 from DNASkittleUtils.DDVUtils import first_word, ReverseComplement, BlankIterator, editable_str
 from DDV.DefaultOrderedDict import DefaultOrderedDict
 from DDV.ChainFiles import chain_file_to_list, match
-from DDV.DDVUtils import make_output_dir_with_suffix, keydefaultdict, read_contigs_to_dict, copy_to_sources
+from DDV.DDVUtils import make_output_directory, keydefaultdict, read_contigs_to_dict, copy_to_sources
 from DDV.Span import AlignedSpans, Span, alignment_chopping_index
 from DDV import gap_char
 from DDV.TileLayout import hex_to_rgb
@@ -510,7 +510,8 @@ def setup_for_reference_chromosome(self, ref_chr, ending=''):
             '__separate_translocations' * self.separate_translocations + \
             '__translocations' * self.show_translocations_only + \
             '__aligned_only' * self.aligned_only
-        self.output_folder = make_output_dir_with_suffix(self.output_prefix, ending)
+        self.output_folder = self.output_prefix + ending
+        make_output_directory(self.output_folder)
         ref_name = first_word(os.path.basename(self.ref_source))
         q_name = first_word(os.path.basename(self.query_source))
         names = {'ref': ref_chr + '_%s.fa' % ref_name,

DDV/DDVUtils.py

@@ -72,16 +72,15 @@ def create_deepzoom_stack(input_image, output_dzi):
     creator.create(input_image, output_dzi)
 
 
-def make_output_dir_with_suffix(base_path, suffix=''):
+def make_output_directory(base_path, no_webpage=False):
     from os import errno
-    output_dir = base_path + suffix
-    print("Creating Chromosome Output Directory...", os.path.basename(output_dir))
     try:
-        os.makedirs(os.path.join(output_dir, 'sources'))
+        os.makedirs(os.path.join(base_path, '' if no_webpage else 'sources'))
+        print("Creating Chromosome Output Directory...", os.path.basename(base_path))
     except OSError as e:  # exist_ok=True
         if e.errno != errno.EEXIST:
             raise
-    return output_dir
+
 
 def copy_to_sources(output_folder, data_file):
     if data_file is None:

DDV/MultipleAlignmentLayout.py

@@ -10,7 +10,7 @@
 from DDV.TileLayout import hex_to_rgb, TileLayout
 from natsort import natsorted
 
-from DDVUtils import make_output_dir_with_suffix
+from DDVUtils import make_output_directory
 from Layouts import level_layout_factory
 
 
@@ -92,7 +92,7 @@ def __init__(self, sort_contigs=False, **kwargs):
 
     def process_all_alignments(self, input_fasta_folder, output_folder, output_file_name):
         start_time = datetime.now()
-        make_output_dir_with_suffix(output_folder)
+        make_output_directory(output_folder)
         self.preview_all_files(input_fasta_folder)
         self.calculate_mixed_layout()
         print("Tallied all contigs :", datetime.now() - start_time)
@@ -113,7 +113,7 @@ def process_all_alignments(self, input_fasta_folder, output_folder, output_file_
             input_path = os.path.join(input_fasta_folder, single_MSA)
             self.output_fasta(output_folder, input_path, False, None, False, append_fasta_sources=False)
         print("\nDrew Nucleotides:", datetime.now() - start_time)
-        self.output_image(output_folder, output_file_name)
+        self.output_image(output_folder, output_file_name, False)
         print("Output Image in:", datetime.now() - start_time)
 
 

DDV/ParallelGenomeLayout.py

@@ -81,7 +81,7 @@ def process_file(self, output_folder, output_file_name, fasta_files=list(),
             traceback.print_exc()
         # self.draw_the_viz_title(fasta_files)  # Needs padding in origins to work
         # self.generate_html(output_folder, output_file_name) # done in fluentdna.py
-        self.output_image(output_folder, output_file_name)
+        self.output_image(output_folder, output_file_name, no_webpage)
         print("Output Image in:", datetime.now() - start_time)
 
     def changes_per_genome(self):

DDV/Sequenaut.py

@@ -8,7 +8,7 @@
 
 from DDV.TileLayout import TileLayout
 from DDV.fluentdna import create_tile_layout_viz_from_fasta
-from DDV.DDVUtils import make_output_dir_with_suffix, base_directories, interpolate
+from DDV.DDVUtils import make_output_directory, base_directories, interpolate
 
 
 def hasDepth(listLike):
@@ -172,7 +172,7 @@ def process_file(self, input_file_path, output_folder, output_file_name):
 def run_sequenaut(args):
     SERVER_HOME, base_path = base_directories(args.output_name)
     # TODO: allow batch of tiling layout by chromosome
-    output_dir = make_output_dir_with_suffix(base_path, '')
+    output_dir = make_output_directory(base_path)
     renderer = Sequenaut(layout=args.layout, oligomer_size=args.oligomer_size, peak=args.peak, baseline=args.baseline, log_scale=not args.linear_scale)
     create_tile_layout_viz_from_fasta(args, args.fasta, args.output_name, renderer)
     sys.exit(0)

DDV/TileLayout.py

@@ -14,7 +14,7 @@
 
 from DDV import gap_char
 from DDV.DDVUtils import multi_line_height, pretty_contig_name, viridis_palette, \
-    make_output_dir_with_suffix, filter_by_contigs, copy_to_sources
+    make_output_directory, filter_by_contigs, copy_to_sources
 from DDV.Layouts import LayoutFrame, LayoutLevel, level_layout_factory, parse_custom_layout
 
 small_title_bp = 10000
@@ -183,7 +183,7 @@ def enable_fat_headers(self):
 
     def process_file(self, input_file_path, output_folder, output_file_name,
                      no_webpage=False, extract_contigs=None):
-        make_output_dir_with_suffix(output_folder, '')
+        make_output_directory(output_folder, no_webpage)
         start_time = datetime.now()
         self.final_output_location = output_folder
         self.image_length = self.read_contigs_and_calc_padding(input_file_path, extract_contigs)
@@ -210,7 +210,7 @@ def process_file(self, input_file_path, output_folder, output_file_name,
             print('Encountered exception while drawing titles:', '\n')
             traceback.print_exc()
 
-        self.output_image(output_folder, output_file_name)
+        self.output_image(output_folder, output_file_name, no_webpage)
         print("Output Image in:", datetime.now() - start_time)
         self.output_fasta(output_folder, input_file_path, no_webpage,
                           extract_contigs, self.sort_contigs)
@@ -246,25 +246,23 @@ def draw_nucleotides(self, verbose=True):
         print('')
 
 
-    def output_fasta(self, output_folder, fasta, no_webpage, extract_contigs, sort_contigs,
-                     append_fasta_sources=True):
+    def output_fasta(self, output_folder, fasta, no_webpage, extract_contigs, sort_contigs, append_fasta_sources=True):
         bare_file = os.path.basename(fasta)
-        fasta_destination = os.path.join(output_folder, 'sources', bare_file)
-        if not no_webpage:  # these support the webpage
+        if append_fasta_sources:
+            self.fasta_sources.append(bare_file)
+
+        #also make single file
+        if not no_webpage:
             write_contigs_to_chunks_dir(output_folder, bare_file, self.contigs)
             self.remember_contig_spacing()
-        #also make single file
-        if extract_contigs or sort_contigs:
-            length_sum = sum([len(c.seq) for c in self.contigs])
-            fasta_destination = '%s__%ibp.fa' % (os.path.splitext(fasta_destination)[0], length_sum)
-            write_contigs_to_file(fasta_destination, self.contigs)  # shortened fasta
-        else:
-            if not no_webpage:
+            fasta_destination = os.path.join(output_folder, 'sources', bare_file)
+            if extract_contigs or sort_contigs:  # customized_fasta
+                length_sum = sum([len(c.seq) for c in self.contigs])
+                fasta_destination = '%s__%ibp.fa' % (os.path.splitext(fasta_destination)[0], length_sum)
+                write_contigs_to_file(fasta_destination, self.contigs)  # shortened fasta
+            else:
                 copy_to_sources(output_folder, fasta)
-        if append_fasta_sources:
-            self.fasta_sources.append(bare_file)
-        print("Sequence saved in:", fasta_destination)
-        return fasta_destination
+            print("Sequence saved in:", fasta_destination)
 
     def calc_all_padding(self):
         total_progress = 0  # pointer in image
@@ -428,12 +426,14 @@ def get_font(self, font_name, font_size):
             font = ImageFont.truetype(font_name, font_size)
         return font
 
-    def output_image(self, output_folder, output_file_name):
+    def output_image(self, output_folder, output_file_name, no_webpage):
         try:
             del self.pixels
             del self.draw
         except BaseException:
             pass  # this is just memory optimization
+        if not no_webpage:  # sources directory only exists for non-quick
+            output_folder = os.path.join(output_folder, 'sources',)
         self.final_output_location = os.path.join(output_folder, output_file_name + ".png")
         print("-- Writing:", self.final_output_location, "--")
         self.image.save(self.final_output_location, 'PNG')

DDV/TransposonLayout.py

@@ -43,7 +43,7 @@ def create_image_from_preprocessed_alignment(self, input_file_path, consensus_wi
         self.initialize_image_by_sequence_dimensions(consensus_width, num_lines)  # sets self.layout
         self.read_contigs_and_calc_padding(input_file_path)
         super(TransposonLayout, self).draw_nucleotides()  # uses self.contigs and self.layout to draw
-        self.output_image(output_folder, output_file_name)
+        self.output_image(output_folder, output_file_name, False)
 
 
     def process_all_repeats(self, ref_fasta, output_folder, output_file_name, repeat_annotation_filename, chromosomes=None):
@@ -61,7 +61,7 @@ def process_all_repeats(self, ref_fasta, output_folder, output_file_name, repeat
         except Exception as e:
             print('Encountered exception while drawing nucleotides:', '\n')
             traceback.print_exc()
-        self.output_image(output_folder, output_file_name)
+        self.output_image(output_folder, output_file_name, False)
         print("Output Image in:", datetime.now() - start_time)
         copy_to_sources(output_folder, ref_fasta)
         copy_to_sources(output_folder, repeat_annotation_filename)

DDV/fluentdna.py

@@ -45,7 +45,7 @@
 import argparse
 
 from DNASkittleUtils.CommandLineUtils import just_the_name
-from DDV.DDVUtils import create_deepzoom_stack, make_output_dir_with_suffix, base_directories, \
+from DDV.DDVUtils import create_deepzoom_stack, make_output_directory, base_directories, \
     hold_console_for_windows, beep, copy_to_sources
 from DDV.ParallelGenomeLayout import ParallelLayout
 from DDV.AnnotatedTrackLayout import  AnnotatedTrackLayout
@@ -549,7 +549,8 @@ def main():
         args.output_dir = os.path.dirname(
             os.path.abspath(args.fasta))  # just place the image next to the fasta
     elif not args.chain_file:
-        args.output_dir = make_output_dir_with_suffix(base_path, '')
+        args.output_dir = base_path
+        make_output_directory(base_path)
 
     ddv(args)