methplotlib 0.23.1__py3-none-any.whl → 0.23.3__py3-none-any.whl

methplotlib/import_methylation.py

@@ -91,6 +91,7 @@ def parse_nanopolish(filename, file_type, name, window, smoothen=5):
                 raise
             header = gzip.open(filename, "rt").readline().rstrip().split("\t")
             table = pd.read_csv(tabix_stream.stdout, sep="\t", header=None, names=header)
+            check_tabix(tabix_stream, filename, window)
         else:
             logging.info(f"Reading {filename} slowly by splitting the file in chunks.")
             sys.stderr.write(f"\nReading {filename} would be faster with bgzip and tabix.\n")
@@ -235,6 +236,19 @@ def no_records_warning(filename, window):
     sys.stderr.write(f"\nWARNING: {message}\nThis dataset is skipped.\n")
 
 
+def check_tabix(tabix_stream, filename, window):
+    """
+    Exit if tabix failed, as a failing tabix also writes nothing to stdout,
+    which would otherwise be reported as a window without records.
+    Only call this after its stdout has been read.
+    """
+    if tabix_stream.wait() != 0:
+        sys.exit(
+            f"\n\nERROR: tabix failed to read {window.chromosome}:{window.begin}-{window.end} "
+            f"from {filename}:\n{tabix_stream.stderr.read().decode()}"
+        )
+
+
 def read_in_chunks(filename, window, sep, usecols, index_suggestion):
     """
     Read a headerless file in chunks, keeping only the lines of the chromosome of interest.
@@ -303,6 +317,7 @@ def parse_bedgraph(filename, name, window):
                 names=colnames,
                 dtype={0: str},
             )
+            check_tabix(tabix_stream, filename, window)
         else:
             table = read_in_chunks(
                 filename,
@@ -380,13 +395,21 @@ def parse_bedmethyl(filename, name, window, smoothen=5, flavor="modkit", mods_of
                 sys.stderr.write("\n\nERROR when opening a tabix stream.\n")
                 sys.stderr.write("Is tabix installed and on the PATH?.")
                 raise
-            table = pd.read_csv(
-                tabix_stream.stdout,
-                sep=sep,
-                header=None,
-                usecols=usecols,
-                dtype={0: str},
-            ).rename(columns=colnames)
+            try:
+                table = pd.read_csv(
+                    tabix_stream.stdout,
+                    sep=sep,
+                    header=None,
+                    usecols=usecols,
+                    dtype={0: str},
+                ).rename(columns=colnames)
+            except pd.errors.EmptyDataError:
+                table = None
+            check_tabix(tabix_stream, filename, window)
+            # tabix writes nothing if the window has no records or the chromosome is not in the index
+            if table is None:
+                no_records_warning(filename, window)
+                return []
         else:
             table = read_in_chunks(
                 filename,

methplotlib/qc.py

@@ -45,7 +45,6 @@ def num_sites_bar(meth_data):
     layout = dict(title="Number of called positions")
     return plotly.offline.plot(dict(data=[trace], layout=layout),
                                output_type="div",
-                               show_link=False,
                                include_plotlyjs='cdn')
 
 
@@ -72,7 +71,6 @@ def pairwise_correlation_plot(full):
 
     return plotly.offline.plot(dict(data=[trace], layout=layout),
                                output_type="div",
-                               show_link=False,
                                include_plotlyjs='cdn')
 
 
@@ -99,7 +97,6 @@ def pca(full):
                   )
     return plotly.offline.plot(dict(data=data, layout=layout),
                                output_type="div",
-                               show_link=False,
                                include_plotlyjs='cdn')
 
 
@@ -110,7 +107,6 @@ def global_box(data):
                  x="dataset", y="freq", title="Global frequency of modification")
     return plotly.offline.plot(fig,
                                output_type="div",
-                               show_link=False,
                                include_plotlyjs='cdn')
 
 
@@ -129,5 +125,4 @@ def modified_fraction_histogram(full):
     return plotly.offline.plot(dict(data=traces,
                                     layout=layout),
                                output_type="div",
-                               show_link=False,
                                include_plotlyjs='cdn')

methplotlib/utils.py

@@ -405,5 +405,5 @@ def create_browser_output(fig, outfile, window):
 def write_html_output(fig, outfile):
     with open(outfile, "w+") as output:
         output.write(
-            plotly.offline.plot(fig, output_type="div", show_link=False, include_plotlyjs="cdn")
+            plotly.offline.plot(fig, output_type="div", include_plotlyjs="cdn")
         )

methplotlib/version.py

@@ -1 +1 @@
-__version__ = "0.23.1"
+__version__ = "0.23.3"

{methplotlib-0.23.1.dist-info → methplotlib-0.23.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: methplotlib
-Version: 0.23.1
+Version: 0.23.3
 Summary: Plot nucleotide modification data from nanopore sequencing
 Home-page: https://github.com/wdecoster/methplotlib
 Author: Wouter De Coster

methplotlib-0.23.3.dist-info/RECORD

@@ -0,0 +1,19 @@
+methplotlib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+methplotlib/annotation.py,sha256=c-b5bUlVTi2Mc0QDBzsKe4V7N0ETw8BEtvY-e0ZtCjQ,7541
+methplotlib/helpers.py,sha256=D69CLM_M8D0wNoV4p-ODr81uatfeCBUUzYdifUmjL88,432
+methplotlib/import_methylation.py,sha256=K9OvjwcjDyEmNBrtU31rllrDjp3CwnjEoJ4J8GgIKKk,23715
+methplotlib/methplotlib.py,sha256=Gk07ODKVfDlA33SlzgIsqRLP0j1DYng24ku87DyYrXY,6264
+methplotlib/plots.py,sha256=MPViIwPrrYn_gx_1VYs3ZECthll3OPrbcyoVAC00cLU,14757
+methplotlib/qc.py,sha256=jvZnkl9KNiZGstcZRt17W3Bngr5z9BmkNPTxrEjJoW4,5350
+methplotlib/utils.py,sha256=KKdb7R6l7i8oVuybnN5srDc2iB8KDjOPoDpXr6E8nrw,14519
+methplotlib/version.py,sha256=HTz96uK4_QHPX5i3NrEcr4eXcxlyepsy_nU-3niBQe8,23
+methplotlib/differential/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+methplotlib/differential/differential.py,sha256=YSWUAeMaI_yERj6oAdvyWM3vKn2laTtWp6Y8ZuwvLA4,1773
+methplotlib-0.23.3.data/scripts/allele_specific_modification,sha256=PpBdGIiVm8M6OjM0m68OPWnsyDeXJZDnbSNCrH3CaHY,1403
+methplotlib-0.23.3.data/scripts/differential_modification,sha256=SZ0odGaykx_cqIHh5tOKSVUCbXOdHR4PSv4Yv6V04Zw,1461
+methplotlib-0.23.3.dist-info/licenses/LICENSE,sha256=qan9p7Fjhl7WzXuiZoaXCViH5si1PSKBNm9K2f0_51c,1073
+methplotlib-0.23.3.dist-info/METADATA,sha256=58qJ6B-4UVk72VCdKEvvF8pod_mtaz9qavVJcRTeUtY,5718
+methplotlib-0.23.3.dist-info/WHEEL,sha256=YVMoNqKzERt-wjUZwJ33xBGAwnFl-4cqbYkTtWa4itE,91
+methplotlib-0.23.3.dist-info/entry_points.txt,sha256=Tav-_W5yZc2G8ApYYuFLfVKU2QugXuEN8z_AjPZwORs,61
+methplotlib-0.23.3.dist-info/top_level.txt,sha256=w1XBGUmKUyGeE0_ufRQ6Vi5lMIzDq6TwF587aofDxuQ,12
+methplotlib-0.23.3.dist-info/RECORD,,

methplotlib-0.23.1.dist-info/RECORD

@@ -1,19 +0,0 @@
-methplotlib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-methplotlib/annotation.py,sha256=c-b5bUlVTi2Mc0QDBzsKe4V7N0ETw8BEtvY-e0ZtCjQ,7541
-methplotlib/helpers.py,sha256=D69CLM_M8D0wNoV4p-ODr81uatfeCBUUzYdifUmjL88,432
-methplotlib/import_methylation.py,sha256=XyI52b6GYPDlxm_JbUMFqeDkEMUu8Sg51BcT9a2aEm8,22728
-methplotlib/methplotlib.py,sha256=Gk07ODKVfDlA33SlzgIsqRLP0j1DYng24ku87DyYrXY,6264
-methplotlib/plots.py,sha256=MPViIwPrrYn_gx_1VYs3ZECthll3OPrbcyoVAC00cLU,14757
-methplotlib/qc.py,sha256=1EvpxeU7xfwKcQeNflrO4pgsZbc9gbCTcMbShumB_Mo,5590
-methplotlib/utils.py,sha256=ffRDe2ITycIj7_5JV2NBjU6XA4qYYIK3HuWUkqhfJLI,14536
-methplotlib/version.py,sha256=EmtVqV41YmZp6Mj5pkm4iGXDMznVEE4GQEUYGGidq30,23
-methplotlib/differential/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-methplotlib/differential/differential.py,sha256=YSWUAeMaI_yERj6oAdvyWM3vKn2laTtWp6Y8ZuwvLA4,1773
-methplotlib-0.23.1.data/scripts/allele_specific_modification,sha256=PpBdGIiVm8M6OjM0m68OPWnsyDeXJZDnbSNCrH3CaHY,1403
-methplotlib-0.23.1.data/scripts/differential_modification,sha256=SZ0odGaykx_cqIHh5tOKSVUCbXOdHR4PSv4Yv6V04Zw,1461
-methplotlib-0.23.1.dist-info/licenses/LICENSE,sha256=qan9p7Fjhl7WzXuiZoaXCViH5si1PSKBNm9K2f0_51c,1073
-methplotlib-0.23.1.dist-info/METADATA,sha256=-khfgkXsY0_Jr48VBRtkrn1YYX4r4_qYPZhzS-lGQuo,5718
-methplotlib-0.23.1.dist-info/WHEEL,sha256=YVMoNqKzERt-wjUZwJ33xBGAwnFl-4cqbYkTtWa4itE,91
-methplotlib-0.23.1.dist-info/entry_points.txt,sha256=Tav-_W5yZc2G8ApYYuFLfVKU2QugXuEN8z_AjPZwORs,61
-methplotlib-0.23.1.dist-info/top_level.txt,sha256=w1XBGUmKUyGeE0_ufRQ6Vi5lMIzDq6TwF587aofDxuQ,12
-methplotlib-0.23.1.dist-info/RECORD,,