ini format

environment.yml

@@ -7,7 +7,7 @@ channels:
    - conda-forge
 dependencies:
     - numpy >=1.16
-    - matplotlib >=3.0
+    - matplotlib =3.1.1
     - intervaltree >=2.1.0
     - pybigwig >=0.3.4
     - future >=0.17.0

pygenometracks/makeTracksFile.py

@@ -41,9 +41,9 @@ def main(args=None):
     args.out.write("""
 [x-axis]
 #optional
-#fontsize=20
+#fontsize = 20
 # default is bottom meaning below the axis line
-# where=top
+# where = top
 
 [spacer]
 # height of space in cm (optional)
@@ -58,7 +58,7 @@ def main(args=None):
                 if file_h.name.endswith(ending):
                     default_values = track_class.OPTIONS_TXT
                     default_values = default_values.replace("title =", "title = {}".format(label))
-                    args.out.write("\n[{label}]\nfile={file}\n{default_values}".
+                    args.out.write("\n[{label}]\nfile = {file}\n{default_values}".
                                    format(label=label, file=file_h.name, default_values=default_values))
 
                     sys.stdout.write("Adding {} file: {}\n".format(track_type, file_h.name))

pygenometracks/plotTracks.py

@@ -12,8 +12,8 @@
 min_value = 0
 #max_value = auto
 height = 1.5
-number of bins = 500
-nans to zeros = True
+number_of_bins = 500
+nans_to_zeros = True
 # options are: line, points, fill. Default is fill
 # to add the preferred line width or point size use:
 # type = line:lw where lw (linewidth) is float
@@ -79,13 +79,13 @@
 # to be printed over many rows. When several images want
 # to be combined this must be set to get equal size
 # genes in all images
-#gene rows = 10
+#gene_rows = 10
 # by default the ymax is the number of
 # rows occupied by the genes in the region plotted. However,
 # by setting this option, the global maximum is used instead.
 # This is useful to combine images that are all consistent and
 # have the same number of rows.
-#global max row = yes
+#global_max_row = yes
 
 
 [chrom states]
@@ -123,8 +123,8 @@
 title =  arcs
 color = red
 # orientation = inverted
-# if line width is not given, the score is used to set the line width
-#line width = 0.5
+# if line_width is not given, the score is used to set the line width
+#line_width = 0.5
 file = arcs.txt
 
 [vlines]

pygenometracks/readGtf.py

@@ -72,9 +72,9 @@ def __next__(self):
         return bed
 
     def get_bed_interval(self):
-        r"""
-        Processes a transcript from the database,
-        retrieve all the values and returns
+        """
+        Process a transcript from the database,
+        retrieve all the values and return
         a namedtuple object
         """
         tr = next(self.all_transcripts)

pygenometracks/tests/test_bedGraphMatrixTrack.py

@@ -9,12 +9,11 @@
 ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
 
 tracks = """
-
 [test bedgraph tabix]
 file = bedgraph_chrx_2e6_5e6.bg.bgz
 color = blue
 height = 2
-title = tabix color=blue; type=fill
+title = tabix color = blue; type = fill
 min_value = -5
 type = fill
 
@@ -25,8 +24,8 @@
 file = bedgraph_chrx_2e6_5e6_2.bg.bgz
 color = brown
 height = 2
-title = tabix color=brown; type=line:0.5;nans to zeros=True; orientation=inverted
-nans to zeros = True
+title = tabix color = brown; type = line:0.5; nans_to_zeros = True; orientation = inverted
+nans_to_zeros = True
 min_value = -5
 max_value = 50
 type = line:0.5
@@ -39,7 +38,7 @@
 file = bedgraph_chrx_2e6_5e6.bg
 color = red
 height = 2
-title = color=red;type=points:0.5
+title = color = red; type = points:0.5
 min_value = 0
 max_value = 50
 type = points:0.5
@@ -50,8 +49,8 @@
 file = bedgraph_chrx_2e6_5e6.bg
 color = red
 height = 2
-title = color=red;type=points:0.5;summary method = max
-summary method = max
+title = color = red; type = points:0.5; summary_method = max
+summary_method = max
 min_value = 0
 max_value = 50
 type = points:0.5
@@ -62,9 +61,9 @@
 file = bedgraph_chrx_2e6_5e6.bg
 color = red
 height = 2
-title = color=red;type=points:0.5;summary method = max;nbins=3000
-summary method = max
-number of bins = 3000
+title = color = red; type = points:0.5; summary_method = max; nbins = 3000
+summary_method = max
+number_of_bins = 3000
 min_value = 0
 max_value = 50
 type = points:0.5
@@ -81,31 +80,32 @@
 
 [test bedgraph matrix lines]
 file = tad_separation_score.bm.gz
-title = type=lines
+title = type = lines
 height = 5
 file_type = bedgraph_matrix
 type = lines
-pos score in bin = block
+pos_score_in_bin = block
 
 [spacer]
 width = 0.01
 
 [test bedgraph matrix lines]
 file = tad_separation_score_with_gap.bm.bgz
-title = type=lines; show data range=no (file type is tabix with a gap)
+title = type = lines; show_data_range = no (file type is tabix with a gap)
 height = 5
 file_type = bedgraph_matrix
 type = lines
-pos score in bin = center
-show data range = no
+pos_score_in_bin = center
+show_data_range = no
 
 [test bedgraph matrix lines tabix]
 file = tad_separation_score.bm.gz
-title = type=lines;plot horizontal lines=yes
+title = type = lines; plot_horizontal_lines = yes
 height = 6
 file_type = bedgraph_matrix
 type = lines
-plot horizontal lines=yes
+plot_horizontal_lines = yes
+
 [spacer]
 
 [x-axis]

pygenometracks/tests/test_bedGraphTrack.py

@@ -36,7 +36,7 @@
 height = 5
 title = bedgraph with use middle = yes
 max_value = 10
-use middle = yes
+use_middle = yes
 
 [genes]
 file = HoxD_cluster_regulatory_regions_mm10.bed
@@ -54,8 +54,9 @@
 def test_plot_bedgraph_tracks():
 
     outfile = NamedTemporaryFile(suffix='.png', prefix='pyGenomeTracks_test_', delete=False)
-    args = "--tracks {0}/bedgraph_useMid.ini --region chr2:73,800,000-75,744,000 --trackLabelFraction 0.2 --width 38 " \
-           "--dpi 130 --outFileName  {1}".format(ROOT, outfile.name).split()
+    args = "--tracks {0}/bedgraph_useMid.ini --region chr2:73,800,000-75,744,000 "\
+           "--trackLabelFraction 0.2 --width 38 --dpi 130 " \
+           "--outFileName  {1}".format(ROOT, outfile.name).split()
     pygenometracks.plotTracks.main(args)
     print("saving test to {}".format(outfile.name))
     res = compare_images(ROOT + '/master_bedgraph_useMid.png', outfile.name, tolerance)
@@ -67,8 +68,9 @@ def test_plot_bedgraph_tracks():
 def test_plot_bedgraph_tracks_rasterize():
 
     outfile = NamedTemporaryFile(suffix='.pdf', prefix='pyGenomeTracks_test_', delete=False)
-    args = "--tracks {0}/bedgraph_useMid.ini --region chr2:73,800,000-75,744,000 --trackLabelFraction 0.2 --width 38 " \
-           "--dpi 130 --outFileName  {1}".format(ROOT, outfile.name).split()
+    args = "--tracks {0}/bedgraph_useMid.ini --region chr2:73,800,000-75,744,000 "\
+           "--trackLabelFraction 0.2 --width 38 --dpi 130 " \
+           "--outFileName  {1}".format(ROOT, outfile.name).split()
     pygenometracks.plotTracks.main(args)
     print("saving test to {}".format(outfile.name))
     res = compare_images(ROOT + '/master_bedgraph_useMid.pdf', outfile.name, tolerance)

pygenometracks/tests/test_bed_and_gtf_tracks.py

@@ -11,16 +11,16 @@
 browser_tracks = """
 [x-axis]
 where = top
-title = where=top
+title = where =top
 
 [spacer]
 height = 0.05
 
 [genes 2]
 file = dm3_genes.bed.gz
 height = 7
-title = genes (bed12) style=flybase;fontsize=10
-style=UCSC
+title = genes (bed12) style = flybase; fontsize = 10
+style = UCSC
 fontsize = 10
 
 [spacer]
@@ -29,26 +29,29 @@
 [test bed6]
 file = dm3_genes.bed6.gz
 height = 7
-title = bed6 border color=black; gene rows=10; fontsize=8; color=Reds (when a color map is used for the color (e.g. coolwarm, Reds) the bed score column mapped to a color)
+title = bed6 border color = black; gene_rows=10; fontsize=8; color=Reds
+        (when a color map is used for the color (e.g. coolwarm, Reds) the bed
+        score column mapped to a color)
 fontsize = 7
 file_type = bed
 color = Reds
-border color = black
-gene rows = 10
+border_color = black
+gene_rows = 10
 
 [spacer]
 height = 1
 
 [test bed4]
 file = dm3_genes.bed4.gz
 height = 10
-title = bed4 fontsize=10; line width=1.5; global max row=yes (global max row sets the number of genes per row as the maximum found anywhere in the genome, hence the white space at the bottom)
+title = bed4 fontsize = 10; line_width = 1.5; global_max_row = yes
+        (global max row sets the number of genes per row as the maximum found
+        anywhere in the genome, hence the white space at the bottom)
 fontsize = 10
 file_type = bed
-global max row = yes
+global_max_row = yes
 interval_height = 200
-line width = 1.5
-
+line_width = 1.5
 
 [spacer]
 height = 1
@@ -60,7 +63,6 @@
 fontsize = 12
 file_type = bed
 
-
 [spacer]
 height = 1
 
@@ -71,25 +73,24 @@
 fontsize = 12
 file_type = bed
 
-
 [spacer]
 height = 1
 
 [test gtf collapsed]
 file = dm3_subset_BDGP5.78.gtf.gz
 height = 10
 title = gtf from ensembl one entry per gene
-merge transcripts = on
-prefered name = gene_name
+merge_transcripts = on
+prefered_name = gene_name
 fontsize = 12
 file_type = bed
 
 [spacer]
 height = 1
 
 [x-axis]
-fontsize=30
-title = fontsize=30
+fontsize = 30
+title = fontsize = 30
 
 """
 with open(ROOT + "bed_and_gtf_tracks.ini", 'w') as fh:
@@ -105,8 +106,8 @@
 [genes 1]
 file = dm3_genes.bed.gz
 height = 7
-title = genes (bed12) style=flybase;fontsize=10
-style=UCSC
+title = genes (bed12) style = flybase; fontsize = 10
+style = UCSC
 fontsize = 10
 
 [spacer]
@@ -115,12 +116,11 @@
 [genes 2]
 file = dm3_genes.bed.gz
 height = 7
-title = genes (bed12) style=flybase;fontsize=10;max_labels = 600
-style=UCSC
+title = genes (bed12) style = flybase; fontsize = 10; max_labels = 600
+style = UCSC
 fontsize = 10
 max_labels = 600
 
-
 """
 with open(ROOT + "bed_maxLab_tracks.ini", 'w') as fh:
     fh.write(browser_tracks)
@@ -131,9 +131,11 @@
 
 def test_plot_tracks_bed_and_gtf():
 
-    outfile = NamedTemporaryFile(suffix='.png', prefix='pyGenomeTracks_test_', delete=False)
-    args = "--tracks {0}/bed_and_gtf_tracks.ini --region X:3000000-3300000 --trackLabelFraction 0.2 --width 38 " \
-           "--dpi 130 --outFileName  {1}".format(ROOT, outfile.name).split()
+    outfile = NamedTemporaryFile(suffix='.png', prefix='pyGenomeTracks_test_',
+                                 delete=False)
+    args = "--tracks {0}/bed_and_gtf_tracks.ini --region X:3000000-3300000 "\
+           "--trackLabelFraction 0.2 --width 38 --dpi 130 "\
+           "--outFileName  {1}".format(ROOT, outfile.name).split()
     pygenometracks.plotTracks.main(args)
     res = compare_images(ROOT + '/master_bed_and_gtf.png', outfile.name, tolerance)
     assert res is None, res
@@ -143,9 +145,11 @@ def test_plot_tracks_bed_and_gtf():
 
 def test_plot_tracks_bed_with_maxLab():
 
-    outfile = NamedTemporaryFile(suffix='.png', prefix='pyGenomeTracks_test_', delete=False)
-    args = "--tracks {0}/bed_maxLab_tracks.ini --region X:2000000-3500000 --trackLabelFraction 0.2 --width 38 " \
-           "--dpi 130 --outFileName  {1}".format(ROOT, outfile.name).split()
+    outfile = NamedTemporaryFile(suffix='.png', prefix='pyGenomeTracks_test_',
+                                 delete=False)
+    args = "--tracks {0}/bed_maxLab_tracks.ini --region X:2000000-3500000 "\
+           "--trackLabelFraction 0.2 --width 38 --dpi 130 " \
+           "--outFileName  {1}".format(ROOT, outfile.name).split()
     pygenometracks.plotTracks.main(args)
     res = compare_images(ROOT + '/master_maxLab.png', outfile.name, tolerance)
     assert res is None, res