Mercurial > repos > greg > repmatch_gff3

changeset 5:53cbf79396d7 draft

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Uploaded
author greg
date Sat, 28 Nov 2015 14:54:22 -0500
parents 1cea96c461a2
children 6df81aade62c
files repmatch_gff3_util.py
diffstat 1 files changed, 6 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/repmatch_gff3_util.py	Tue Nov 24 08:16:39 2015 -0500
+++ b/repmatch_gff3_util.py	Sat Nov 28 14:54:22 2015 -0500
@@ -21,7 +21,6 @@
 pyplot.rc('axes', linewidth=3.00)
 pyplot.rc('font', family='Bitstream Vera Sans', size=32.0)
 
-PLOT_FORMATS = ['png', 'pdf', 'svg']
 COLORS = 'krb'
 
 
@@ -254,19 +253,19 @@
     return (cname, source, type, start, end, score, strand, phase, gff_attrs(attrs))
 
 
-def get_temporary_plot_path(plot_format):
+def get_temporary_plot_path():
     """
     Return the path to a temporary file with a valid image format
     file extension that can be used with bioformats.
     """
     tmp_dir = tempfile.mkdtemp(prefix='tmp-repmatch-')
-    fd, name = tempfile.mkstemp(suffix='.%s' % plot_format, dir=tmp_dir)
+    fd, name = tempfile.mkstemp(suffix='.pdf', dir=tmp_dir)
     os.close(fd)
     return name
 
 
 def process_files(dataset_paths, galaxy_hids, method, distance, step, replicates, up_limit, low_limit, output_files,
-                  plot_format, output_summary, output_orphan, output_detail, output_key, output_histogram):
+                  output_summary, output_orphan, output_detail, output_key, output_histogram):
     output_histogram_file = output_files in ["all"] and method in ["all"]
     if len(dataset_paths) < 2:
         return
@@ -284,14 +283,13 @@
                                      up_limit,
                                      low_limit,
                                      output_files,
-                                     plot_format,
                                      output_summary,
                                      output_orphan,
                                      output_detail,
                                      output_key,
                                      output_histogram)
     if output_histogram_file:
-        tmp_histogram_path = get_temporary_plot_path(plot_format)
+        tmp_histogram_path = get_temporary_plot_path()
         frequency_histogram([stat['distribution'] for stat in [statistics]],
                             tmp_histogram_path,
                             METHODS.keys())
@@ -299,7 +297,7 @@
 
 
 def perform_process(dataset_paths, galaxy_hids, method, distance, step, num_required, up_limit, low_limit, output_files,
-                    plot_format, output_summary, output_orphan, output_detail, output_key, output_histogram):
+                    output_summary, output_orphan, output_detail, output_key, output_histogram):
     output_detail_file = output_files in ["all"] and output_detail is not None
     output_key_file = output_files in ["all"] and output_key is not None
     output_orphan_file = output_files in ["all", "simple_orphan"] and output_orphan is not None
@@ -458,7 +456,7 @@
                                     orphan.distance,
                                     orphan.replicate.id))
     if output_histogram_file:
-        tmp_histogram_path = get_temporary_plot_path(plot_format)
+        tmp_histogram_path = get_temporary_plot_path()
         frequency_histogram([freq], tmp_histogram_path)
         shutil.move(tmp_histogram_path, output_histogram)
     return {'distribution': freq}