Merge pull request #92 from josiahseaman/python-master

Pull Rename into Pip

.gitignore

@@ -7,12 +7,12 @@ env/
 env365/
 install_test/
 release/
-DDV/results/
+FluentDNA/results/
 release.bat
 scraps/
 env_fresh/
-DDV/data/
-DDV/www-data/
+FluentDNA/data/
+FluentDNA/www-data/
 
 
 # Created by .ignore support plugin (hsz.mobi)

DDV/AnnotatedAlignment.py → FluentDNA/AnnotatedAlignment.py

@@ -12,11 +12,11 @@
 import os
 from DNASkittleUtils.DDVUtils import editable_str
 
-from DDV.ChainParser import ChainParser, scan_past_header, Batch
+from FluentDNA.ChainParser import ChainParser, scan_past_header, Batch
 from DNASkittleUtils.Contigs import pluck_contig
 from DNASkittleUtils.DDVUtils import first_word, ReverseComplement
 
-from DDV.Annotations import create_fasta_from_annotation, GFF
+from FluentDNA.Annotations import create_fasta_from_annotation, GFF
 
 
 class AnnotatedAlignment(ChainParser):
@@ -167,5 +167,5 @@ def markup_annotation_differences(self):
     aligner.parse_chain(['chr20'])
 
     #### ==== Command Line Configuration === ####
-    # fluentdna.py --chainfile=hg38ToPanTro4.over.chain --fasta=hg38.fa --extrafastas panTro4.fa --ref_annotation=DDV\\data\Hg38_genes.gtf
-    # --query_annotation=DDV\data\PanTro_refseq2.1.4_genes.gtf --outname=hg38_panTro4_annotated_
+    # fluentdna.py --chainfile=hg38ToPanTro4.over.chain --fasta=hg38.fa --extrafastas panTro4.fa --ref_annotation=FluentDNA\\data\Hg38_genes.gtf
+    # --query_annotation=FluentDNA\data\PanTro_refseq2.1.4_genes.gtf --outname=hg38_panTro4_annotated_

DDV/AnnotatedTrackLayout.py → FluentDNA/AnnotatedTrackLayout.py

@@ -3,9 +3,9 @@
 from itertools import chain
 from os.path import join, basename
 
-from DDV.Annotations import create_fasta_from_annotation, find_universal_prefix, parseGFF
-from DDV.ParallelGenomeLayout import ParallelLayout
-from DDV.DDVUtils import filter_by_contigs, copy_to_sources
+from FluentDNA.Annotations import create_fasta_from_annotation, find_universal_prefix, parseGFF
+from FluentDNA.ParallelGenomeLayout import ParallelLayout
+from FluentDNA.FluentDNAUtils import filter_by_contigs, copy_to_sources
 
 
 class AnnotatedTrackLayout(ParallelLayout):

DDV/AnnotationAlignment.py → FluentDNA/AnnotationAlignment.py

@@ -12,13 +12,13 @@
 import os
 from DNASkittleUtils.DDVUtils import editable_str
 
-from DDV.ChainParser import ChainParser
+from FluentDNA.ChainParser import ChainParser
 from DNASkittleUtils.CommandLineUtils import just_the_name
-from DDV.RepeatAnnotations import max_consensus_width, read_repeatmasker_csv, \
+from FluentDNA.RepeatAnnotations import max_consensus_width, read_repeatmasker_csv, \
     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_directory
+from FluentDNA.Span import alignment_chopping_index, AlignedSpans, Span
+from FluentDNA.TransposonLayout import TransposonLayout
+from FluentDNA.FluentDNAUtils import make_output_directory
 
 
 def create_aligned_annotation_fragments(alignment, repeat_entries):

DDV/Annotations.py → FluentDNA/Annotations.py

@@ -8,7 +8,7 @@
 from DNASkittleUtils.Contigs import Contig, read_contigs, write_contigs_to_file
 
 from DNASkittleUtils.DDVUtils import editable_str
-from DDV import gap_char
+from FluentDNA import gap_char
 
 try:
     from urllib.parse import unquote
@@ -363,12 +363,12 @@ def find_universal_prefix(annotation_list):
 
 
 if __name__ == '__main__':
-    # annotation = r'DDV\data\Pan_Troglodytes_refseq2.1.4.gtf'
+    # annotation = r'FluentDNA\data\Pan_Troglodytes_refseq2.1.4.gtf'
     # target_chromosome = 'chr20'
     # create_fasta_from_annotation(annotation, target_chromosome, 'Chimp_test_' + target_chromosome + '.fa')
 
-    # annotation = r'DDV\data\Pan_Troglodytes_refseq2.1.4.gtf'
-    # annotation = r'DDV\data\Homo_Sapiens_GRCH38_trimmed.gtf'
+    # annotation = r'FluentDNA\data\Pan_Troglodytes_refseq2.1.4.gtf'
+    # annotation = r'FluentDNA\data\Homo_Sapiens_GRCH38_trimmed.gtf'
     # purge_annotation(annotation)
     path = r"E:\Genomes\Human\Human Unique Annotation merged.fa"
     squished = squish_fasta(read_contigs(path), 20, 100)

DDV/ChainParser.py → FluentDNA/ChainParser.py

@@ -19,12 +19,12 @@
 from DNASkittleUtils.CommandLineUtils import just_the_name
 from DNASkittleUtils.Contigs import pluck_contig, write_complete_fasta
 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_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
+from FluentDNA.DefaultOrderedDict import DefaultOrderedDict
+from FluentDNA.ChainFiles import chain_file_to_list, match
+from FluentDNA.FluentDNAUtils import make_output_directory, keydefaultdict, read_contigs_to_dict, copy_to_sources
+from FluentDNA.Span import AlignedSpans, Span, alignment_chopping_index
+from FluentDNA import gap_char
+from FluentDNA.TileLayout import hex_to_rgb
 
 Batch = namedtuple('Batch', ['chr', 'fastas', 'output_folder'])
 

DDV/DDVUtils.py → FluentDNA/FluentDNAUtils.py

@@ -73,8 +73,8 @@ def read_contigs_to_dict(input_file_path, extract_contigs=None):
 
 
 def create_deepzoom_stack(input_image, output_dzi):
-    import DDV.deepzoom
-    creator = DDV.deepzoom.ImageCreator(tile_size=256,
+    import FluentDNA.deepzoom
+    creator = FluentDNA.deepzoom.ImageCreator(tile_size=256,
                                     tile_overlap=1,
                                     tile_format="png",
                                     resize_filter="antialias")# cubic bilinear bicubic nearest antialias

DDV/HighlightedAnnotation.py → FluentDNA/HighlightedAnnotation.py

@@ -3,10 +3,10 @@
 import sys
 from PIL import Image, ImageFont
 
-from DDV.Annotations import GFFAnnotation, find_universal_prefix, GFF3Record, parseGFF
-from DDV.Span import Span
-from DDV.TileLayout import TileLayout
-from DDV.DDVUtils import linspace, copy_to_sources
+from FluentDNA.Annotations import GFFAnnotation, find_universal_prefix, GFF3Record, parseGFF
+from FluentDNA.Span import Span
+from FluentDNA.TileLayout import TileLayout
+from FluentDNA.FluentDNAUtils import linspace, copy_to_sources
 
 
 def blend_pixel(markup_canvas, pt, c, overwrite=False):

DDV/Ideogram.py → FluentDNA/Ideogram.py

@@ -16,13 +16,13 @@
 
 from DNASkittleUtils.Contigs import read_contigs
 
-from DDV.DDVUtils import beep
-from DDV.HighlightedAnnotation import HighlightedAnnotation
+from FluentDNA.FluentDNAUtils import beep
+from FluentDNA.HighlightedAnnotation import HighlightedAnnotation
 import os
 import numpy as np
 from functools import reduce
 
-from DDV.Layouts import LayoutFrame, LayoutLevel
+from FluentDNA.Layouts import LayoutFrame, LayoutLevel
 
 
 class IdeogramCoordinateFrame(LayoutFrame):

DDV/Layouts.py → FluentDNA/Layouts.py

@@ -1,6 +1,6 @@
 import sys
 from PIL import Image, ImageDraw
-from DDV.DDVUtils import multi_line_height
+from FluentDNA.FluentDNAUtils import multi_line_height
 
 
 class LayoutLevel(object):

DDV/MultipleAlignmentLayout.py → FluentDNA/MultipleAlignmentLayout.py

@@ -10,11 +10,11 @@
 from PIL import Image, ImageDraw
 
 import math
-from DDV.TileLayout import hex_to_rgb, TileLayout, is_protein_sequence
+from FluentDNA.TileLayout import hex_to_rgb, TileLayout, is_protein_sequence
 from natsort import natsorted
 
-from DDV.DDVUtils import make_output_directory
-from DDV.Layouts import level_layout_factory
+from FluentDNA.FluentDNAUtils import make_output_directory
+from FluentDNA.Layouts import level_layout_factory
 
 
 def fastas_in_folder(input_fasta_folder):

DDV/ParallelGenomeLayout.py → FluentDNA/ParallelGenomeLayout.py

@@ -8,8 +8,8 @@
 from PIL import ImageFont, Image
 
 from DNASkittleUtils.CommandLineUtils import just_the_name
-from DDV.TileLayout import TileLayout, hex_to_rgb
-from DDV.Layouts import level_layout_factory
+from FluentDNA.TileLayout import TileLayout, hex_to_rgb
+from FluentDNA.Layouts import level_layout_factory
 
 
 class ParallelLayout(TileLayout):
@@ -102,11 +102,11 @@ def draw_border_boxes(self, fasta_files):
         To help keep track of it correctly, ParallelGenomeLayout demarcates bundles of columns that go
         together.  Mouse over gives further information on each file."""
         from DNASkittleUtils.DDVUtils import pp
-        from DDV.DDVUtils import execution_dir
+        from FluentDNA.FluentDNAUtils import execution_dir
         base_dir = execution_dir()
         # Caution: These corners are currently hard coded to the color and dimension of one image
         try:
-            corner = Image.open(os.path.join(base_dir,'DDV','html_template','img','border_box_corner.png'))
+            corner = Image.open(os.path.join(base_dir,'FluentDNA','html_template','img','border_box_corner.png'))
         except FileNotFoundError:
             corner = Image.open(os.path.join(base_dir, 'html_template', 'img', 'border_box_corner.png'))
         corner_rb = corner.copy().rotate(270, expand=True)

DDV/RepeatAnnotations.py → FluentDNA/RepeatAnnotations.py

@@ -14,8 +14,8 @@
 from DNASkittleUtils.Contigs import pluck_contig
 from DNASkittleUtils.DDVUtils import rev_comp
 
-from DDV.Span import Span
-from DDV import gap_char
+from FluentDNA.Span import Span
+from FluentDNA import gap_char
 
 
 def int_log(num):

DDV/Span.py → FluentDNA/Span.py

@@ -5,7 +5,7 @@
 original and gapped sequence as gaps are added."""
 from __future__ import print_function, division, absolute_import, \
     with_statement, generators, nested_scopes
-from DDV import gap_char
+from FluentDNA import gap_char
 
 class Span(object):
     """ Span can have sections in the middle removed, creating two or less new Spans.

DDV/TileLayout.py → FluentDNA/TileLayout.py

@@ -12,10 +12,10 @@
 from DNASkittleUtils.DDVUtils import copytree
 from PIL import Image, ImageDraw, ImageFont
 
-from DDV import gap_char
-from DDV.DDVUtils import multi_line_height, pretty_contig_name, viridis_palette, \
+from FluentDNA import gap_char
+from FluentDNA.FluentDNAUtils import multi_line_height, pretty_contig_name, viridis_palette, \
     make_output_directory, filter_by_contigs, copy_to_sources
-from DDV.Layouts import LayoutFrame, LayoutLevel, level_layout_factory, parse_custom_layout
+from FluentDNA.Layouts import LayoutFrame, LayoutLevel, level_layout_factory, parse_custom_layout
 
 small_title_bp = 10000
 protein_found_message = False
@@ -143,7 +143,7 @@ def activate_high_contrast_colors(self):
         self.palette['C'] = hex_to_rgb('FF9F00')  # Yellow
         self.palette['T'] = hex_to_rgb('0B56BE')  # Blue originally '0F4FA8'
         self.palette['A'] = hex_to_rgb('00C566')  # Green originally ' 00B25C'
-        # Original DDV Colors
+        # Original FluentDNA Colors
         # self.palette['A'] = (255, 0, 0)
         # self.palette['G'] = (0, 255, 0)
         # self.palette['T'] = (250, 240, 114)
@@ -425,14 +425,14 @@ def get_font(self, font_size):
         if font_size in self.fonts:
             font = self.fonts[font_size]
         else:
-            from DDV.DDVUtils import execution_dir
+            from FluentDNA.FluentDNAUtils import execution_dir
             base_dir = execution_dir()
             try:
                 with open(os.path.join(base_dir, 'html_template', 'img', "ariblk.ttf"), 'rb') as font_file:
                     font = ImageFont.truetype(font_file, font_size)
             except IOError:
                 try:
-                    with open(os.path.join(base_dir, 'DDV', 'html_template', 'img', "ariblk.ttf"), 'rb') as font_file:
+                    with open(os.path.join(base_dir, 'FluentDNA', 'html_template', 'img', "ariblk.ttf"), 'rb') as font_file:
                         font = ImageFont.truetype(font_file, font_size)
                 except IOError:
                     print("Unable to load ariblk.ttf size:%i" % font_size)
@@ -527,8 +527,8 @@ def generate_html(self, output_folder, output_file_name, overwrite_files=True):
             print(html_path, ' already exists.  Skipping HTML.')
             return
         try:
-            import DDV
-            module_path = os.path.dirname(DDV.__file__)
+            import FluentDNA
+            module_path = os.path.dirname(FluentDNA.__file__)
             html_template = os.path.join(module_path, 'html_template')
             copytree(html_template, output_folder)  # copies the whole template directory
             print("Copying HTML to", output_folder)

DDV/TransposonLayout.py → FluentDNA/TransposonLayout.py

@@ -20,10 +20,10 @@
 
 from DNASkittleUtils.Contigs import Contig, read_contigs
 from DNASkittleUtils.DDVUtils import rev_comp
-from DDV.RepeatAnnotations import read_repeatmasker_csv, max_consensus_width, blank_line_array
-from DDV.TileLayout import TileLayout
-from DDV import gap_char
-from DDV.DDVUtils import copy_to_sources
+from FluentDNA.RepeatAnnotations import read_repeatmasker_csv, max_consensus_width, blank_line_array
+from FluentDNA.TileLayout import TileLayout
+from FluentDNA import gap_char
+from FluentDNA.FluentDNAUtils import copy_to_sources
 
 
 class TransposonLayout(TileLayout):

DDV/UniqueOnlyChainParser.py → FluentDNA/UniqueOnlyChainParser.py

@@ -3,10 +3,10 @@
 from bisect import bisect_left
 import os
 from DNASkittleUtils.Contigs import write_complete_fasta
-from DDV import gap_char
-from DDV.ChainParser import ChainParser, Batch
-from DDV.Span import Span
-from DDV.ChainFiles import fetch_all_chains
+from FluentDNA import gap_char
+from FluentDNA.ChainParser import ChainParser, Batch
+from FluentDNA.Span import Span
+from FluentDNA.ChainFiles import fetch_all_chains
 
 
 class UniqueOnlyChainParser(ChainParser):

DDV/deepzoom.py → FluentDNA/deepzoom.py

@@ -1,4 +1,4 @@
-#  This copy of deep zoom has been modified for DDV to fix a bug in .create() for png files.
+#  This copy of deep zoom has been modified for FluentDNA to fix a bug in .create() for png files.
 #
 #
 #  Deep Zoom Tools