diff --git a/Figures/Methylation/Methylation_Fig4a.pdf b/Figures/Methylation/Methylation_Fig4a.pdf index e83ebf8..6c3a20a 100644 Binary files a/Figures/Methylation/Methylation_Fig4a.pdf and b/Figures/Methylation/Methylation_Fig4a.pdf differ diff --git a/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation.html b/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation.html index e63e5d3..d5d9d86 100644 --- a/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation.html +++ b/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation.html @@ -7491,6 +7491,8 @@ import seaborn as sns from matplotlib.lines import Line2D import warnings +import ssl +from urllib.request import urlopen %matplotlib inline warnings.filterwarnings("ignore") @@ -7784,9 +7786,16 @@ filename_methyl_fraction_non_BRC_OVA = r"https://www.bcgsc.ca/downloads/nanopore_pog/ts_methylation//BRCA1_RAD51C_fraction_of_methylated_sites_non_BRC_OVA.tsv" filename_BRCA1_RAD51C_logTPM = r"https://www.bcgsc.ca/downloads/nanopore_pog/ts_methylation//BRCA1_RAD51C_logTPM.tsv" - df_methyl_BRC_OVA = pd.read_csv(filename_methyl_fraction_BRC_OVA, sep = "\t", index_col = "tumour_original_source") - df_methyl_non_BRC_OVA = pd.read_csv(filename_methyl_fraction_non_BRC_OVA, sep = "\t", index_col = "tumour_original_source") - df_BRCA1_RAD51C_logTPM = pd.read_csv(filename_BRCA1_RAD51C_logTPM, sep = "\t", index_col = "tumour_original_source") + context=ssl.create_default_context() + context.set_ciphers("DEFAULT") + + result_BRC_OVA = urlopen(filename_methyl_fraction_BRC_OVA, context=context) + result_non_BRC_OVA = urlopen(filename_methyl_fraction_non_BRC_OVA, context=context) + result_BRCA1_RAD51C_logTPM = urlopen(filename_BRCA1_RAD51C_logTPM, context=context) + + df_methyl_BRC_OVA = pd.read_csv(result_BRC_OVA, sep = "\t", index_col = "tumour_original_source") + df_methyl_non_BRC_OVA = pd.read_csv(result_non_BRC_OVA, sep = "\t", index_col = "tumour_original_source") + df_BRCA1_RAD51C_logTPM = pd.read_csv(result_BRCA1_RAD51C_logTPM, sep = "\t", index_col = "tumour_original_source") generate_HRDetect_plot_BRC_OVA(df_methyl_BRC_OVA, df_methyl_non_BRC_OVA, PALETTE, OFFSET_METHYLATED) @@ -7810,82 +7819,670 @@
-
CRITICAL:__main__:Failure: <urlopen error [SSL: SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c:1006)>
-Traceback (most recent call last):
-  File "/opt/conda/lib/python3.11/urllib/request.py", line 1348, in do_open
-    h.request(req.get_method(), req.selector, req.data, headers,
-  File "/opt/conda/lib/python3.11/http/client.py", line 1286, in request
-    self._send_request(method, url, body, headers, encode_chunked)
-  File "/opt/conda/lib/python3.11/http/client.py", line 1332, in _send_request
-    self.endheaders(body, encode_chunked=encode_chunked)
-  File "/opt/conda/lib/python3.11/http/client.py", line 1281, in endheaders
-    self._send_output(message_body, encode_chunked=encode_chunked)
-  File "/opt/conda/lib/python3.11/http/client.py", line 1041, in _send_output
-    self.send(msg)
-  File "/opt/conda/lib/python3.11/http/client.py", line 979, in send
-    self.connect()
-  File "/opt/conda/lib/python3.11/http/client.py", line 1458, in connect
-    self.sock = self._context.wrap_socket(self.sock,
-                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/ssl.py", line 517, in wrap_socket
-    return self.sslsocket_class._create(
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/ssl.py", line 1108, in _create
-    self.do_handshake()
-  File "/opt/conda/lib/python3.11/ssl.py", line 1379, in do_handshake
-    self._sslobj.do_handshake()
-ssl.SSLError: [SSL: SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c:1006)
-
-During handling of the above exception, another exception occurred:
-
-Traceback (most recent call last):
-  File "/tmp/ipykernel_14/4130098315.py", line 17, in <module>
-    main()
-  File "/tmp/ipykernel_14/4130098315.py", line 6, in main
-    df_methyl_BRC_OVA = pd.read_csv(filename_methyl_fraction_BRC_OVA, sep = "\t", index_col = "tumour_original_source")
-                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
-    return _read(filepath_or_buffer, kwds)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 620, in _read
-    parser = TextFileReader(filepath_or_buffer, **kwds)
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1620, in __init__
-    self._engine = self._make_engine(f, self.engine)
-                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine
-    self.handles = get_handle(
-                   ^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/site-packages/pandas/io/common.py", line 728, in get_handle
-    ioargs = _get_filepath_or_buffer(
-             ^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/site-packages/pandas/io/common.py", line 384, in _get_filepath_or_buffer
-    with urlopen(req_info) as req:
-         ^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/site-packages/pandas/io/common.py", line 289, in urlopen
-    return urllib.request.urlopen(*args, **kwargs)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/urllib/request.py", line 216, in urlopen
-    return opener.open(url, data, timeout)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/urllib/request.py", line 519, in open
-    response = self._open(req, data)
-               ^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/urllib/request.py", line 536, in _open
-    result = self._call_chain(self.handle_open, protocol, protocol +
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/urllib/request.py", line 496, in _call_chain
-    result = func(*args)
-             ^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/urllib/request.py", line 1391, in https_open
-    return self.do_open(http.client.HTTPSConnection, req,
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/conda/lib/python3.11/urllib/request.py", line 1351, in do_open
-    raise URLError(err)
-urllib.error.URLError: <urlopen error [SSL: SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c:1006)>
+
INFO:__main__:generating HRDetect plots for BRC and OVA samples
+INFO:__main__:BRCA1
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
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+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
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+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+INFO:__main__:RAD51C
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
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+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+INFO:__main__:generating HRDetect plots for non BRC and OVA samples
+INFO:__main__:BRCA1
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
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+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
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+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
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+INFO:__main__:RAD51C
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
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+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
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+INFO:__main__:generating TPM plots for BRC and OVA samples
+INFO:__main__:BRCA1
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+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found.
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+INFO:__main__:RAD51C
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diff --git a/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation.md b/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation.md index 32b6277..04b40bf 100644 --- a/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation.md +++ b/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation.md @@ -7,6 +7,8 @@ from matplotlib.pylab import plt import seaborn as sns from matplotlib.lines import Line2D import warnings +import ssl +from urllib.request import urlopen %matplotlib inline warnings.filterwarnings("ignore") @@ -282,9 +284,16 @@ def main(): filename_methyl_fraction_non_BRC_OVA = r"https://www.bcgsc.ca/downloads/nanopore_pog/ts_methylation//BRCA1_RAD51C_fraction_of_methylated_sites_non_BRC_OVA.tsv" filename_BRCA1_RAD51C_logTPM = r"https://www.bcgsc.ca/downloads/nanopore_pog/ts_methylation//BRCA1_RAD51C_logTPM.tsv" - df_methyl_BRC_OVA = pd.read_csv(filename_methyl_fraction_BRC_OVA, sep = "\t", index_col = "tumour_original_source") - df_methyl_non_BRC_OVA = pd.read_csv(filename_methyl_fraction_non_BRC_OVA, sep = "\t", index_col = "tumour_original_source") - df_BRCA1_RAD51C_logTPM = pd.read_csv(filename_BRCA1_RAD51C_logTPM, sep = "\t", index_col = "tumour_original_source") + context=ssl.create_default_context() + context.set_ciphers("DEFAULT") + + result_BRC_OVA = urlopen(filename_methyl_fraction_BRC_OVA, context=context) + result_non_BRC_OVA = urlopen(filename_methyl_fraction_non_BRC_OVA, context=context) + result_BRCA1_RAD51C_logTPM = urlopen(filename_BRCA1_RAD51C_logTPM, context=context) + + df_methyl_BRC_OVA = pd.read_csv(result_BRC_OVA, sep = "\t", index_col = "tumour_original_source") + df_methyl_non_BRC_OVA = pd.read_csv(result_non_BRC_OVA, sep = "\t", index_col = "tumour_original_source") + df_BRCA1_RAD51C_logTPM = pd.read_csv(result_BRCA1_RAD51C_logTPM, sep = "\t", index_col = "tumour_original_source") generate_HRDetect_plot_BRC_OVA(df_methyl_BRC_OVA, df_methyl_non_BRC_OVA, PALETTE, OFFSET_METHYLATED) @@ -298,79 +307,659 @@ if __name__ == "__main__": logger.critical("Failure: %s", err, exc_info=True) ``` - CRITICAL:__main__:Failure: - Traceback (most recent call last): - File "/opt/conda/lib/python3.11/urllib/request.py", line 1348, in do_open - h.request(req.get_method(), req.selector, req.data, headers, - File "/opt/conda/lib/python3.11/http/client.py", line 1286, in request - self._send_request(method, url, body, headers, encode_chunked) - File "/opt/conda/lib/python3.11/http/client.py", line 1332, in _send_request - self.endheaders(body, encode_chunked=encode_chunked) - File "/opt/conda/lib/python3.11/http/client.py", line 1281, in endheaders - self._send_output(message_body, encode_chunked=encode_chunked) - File "/opt/conda/lib/python3.11/http/client.py", line 1041, in _send_output - self.send(msg) - File "/opt/conda/lib/python3.11/http/client.py", line 979, in send - self.connect() - File "/opt/conda/lib/python3.11/http/client.py", line 1458, in connect - self.sock = self._context.wrap_socket(self.sock, - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/ssl.py", line 517, in wrap_socket - return self.sslsocket_class._create( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/ssl.py", line 1108, in _create - self.do_handshake() - File "/opt/conda/lib/python3.11/ssl.py", line 1379, in do_handshake - self._sslobj.do_handshake() - ssl.SSLError: [SSL: SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c:1006) + INFO:__main__:generating HRDetect plots for BRC and OVA samples + INFO:__main__:BRCA1 + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + 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WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + + + - During handling of the above exception, another exception occurred: +![png](HR_gene_methylation_HRDetect_correlation_files/HR_gene_methylation_HRDetect_correlation_2_1.png) + + + + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + 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"/tmp/ipykernel_147/4130098315.py", line 17, in - main() - File "/tmp/ipykernel_147/4130098315.py", line 6, in main - df_methyl_BRC_OVA = pd.read_csv(filename_methyl_fraction_BRC_OVA, sep = "\t", index_col = "tumour_original_source") - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv - return _read(filepath_or_buffer, kwds) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 620, in _read - parser = TextFileReader(filepath_or_buffer, **kwds) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1620, in __init__ - self._engine = self._make_engine(f, self.engine) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine - self.handles = get_handle( - ^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/common.py", line 728, in get_handle - ioargs = _get_filepath_or_buffer( - ^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/common.py", line 384, in _get_filepath_or_buffer - with urlopen(req_info) as req: - ^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/common.py", line 289, in urlopen - return urllib.request.urlopen(*args, **kwargs) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/urllib/request.py", line 216, in urlopen - return opener.open(url, data, timeout) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/urllib/request.py", line 519, in open - response = self._open(req, data) - ^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/urllib/request.py", line 536, in _open - result = self._call_chain(self.handle_open, protocol, protocol + - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/urllib/request.py", line 496, in _call_chain - result = func(*args) - ^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/urllib/request.py", line 1391, in https_open - return self.do_open(http.client.HTTPSConnection, req, - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/urllib/request.py", line 1351, in do_open - raise URLError(err) - urllib.error.URLError: diff --git a/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation_files/HR_gene_methylation_HRDetect_correlation_2_1.png b/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation_files/HR_gene_methylation_HRDetect_correlation_2_1.png new file mode 100644 index 0000000..b6b0a0a Binary files /dev/null and b/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation_files/HR_gene_methylation_HRDetect_correlation_2_1.png differ diff --git a/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation_files/HR_gene_methylation_HRDetect_correlation_2_3.png b/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation_files/HR_gene_methylation_HRDetect_correlation_2_3.png new file mode 100644 index 0000000..978c099 Binary files /dev/null and b/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation_files/HR_gene_methylation_HRDetect_correlation_2_3.png differ diff --git a/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation_files/HR_gene_methylation_HRDetect_correlation_2_5.png b/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation_files/HR_gene_methylation_HRDetect_correlation_2_5.png new file mode 100644 index 0000000..33dfccb Binary files /dev/null and b/Figures/ts_methylation/HR_gene_methylation_HRDetect_correlation_files/HR_gene_methylation_HRDetect_correlation_2_5.png differ diff --git a/Figures/ts_methylation/haplotype_specific_methylation_DNA_repair.html b/Figures/ts_methylation/haplotype_specific_methylation_DNA_repair.html index 43a239a..499eff0 100644 --- a/Figures/ts_methylation/haplotype_specific_methylation_DNA_repair.html +++ b/Figures/ts_methylation/haplotype_specific_methylation_DNA_repair.html @@ -7488,6 +7488,8 @@ import numpy as np from matplotlib.pylab import plt from statsmodels.nonparametric.smoothers_lowess import lowess +import ssl +from urllib.request import urlopen %matplotlib inline params = {"font.family":"Arial", @@ -7555,10 +7557,15 @@ files_BRCA1 = BRCA1_files[tumour_type] logger.info("generating BRCA1 haplotype plots for {}".format(tumour_type)) + context=ssl.create_default_context() + context.set_ciphers("DEFAULT") + if len(files_BRCA1[0]) >0: - df_blood = pd.read_csv(files_BRCA1[0], sep = "\t", index_col = ["gene","start", "end"]) + result_blood = urlopen(files_BRCA1[0], context=context) + df_blood = pd.read_csv(result_blood, sep = "\t", index_col = ["gene","start", "end"]) if len(files_BRCA1[1])>0: - df_tumour = pd.read_csv(files_BRCA1[1], sep = "\t", index_col = ["gene","start", "end"]) + result_tumour = urlopen(files_BRCA1[1], context=context) + df_tumour = pd.read_csv(result_tumour, sep = "\t", index_col = ["gene","start", "end"]) fig_BRCA1, ax_BRCA1 = plt.subplots(ncols=1, nrows=3, sharex = True, figsize = (8.5, 4.2), dpi = 600) @@ -7704,10 +7711,15 @@ files_RAD51C = RAD51C_files[tumour_type] + context=ssl.create_default_context() + context.set_ciphers("DEFAULT") + if len(files_RAD51C[0]) >0: - df_blood = pd.read_csv(files_RAD51C[0], sep = "\t", index_col = ["gene","start", "end"]) + result_blood = urlopen(files_RAD51C[0], context=context) + df_blood = pd.read_csv(result_blood, sep = "\t", index_col = ["gene","start", "end"]) if len(files_RAD51C[1])>0: - df_tumour = pd.read_csv(files_RAD51C[1], sep = "\t", index_col = ["gene","start", "end"]) + result_tumour = urlopen(files_RAD51C[1], context=context) + df_tumour = pd.read_csv(result_tumour, sep = "\t", index_col = ["gene","start", "end"]) logger.info("generating RAD51C haplotype plots for {}".format(tumour_type)) @@ -7833,8 +7845,13 @@ logger.info("generating MLH1 haplotype plots") - df_blood = pd.read_csv(filename_MLH1_blood, sep = "\t", index_col = ["gene","start", "end"]) - df_tumour = pd.read_csv(filename_MLH1_tumour, sep = "\t", index_col = ["gene","start", "end"]) + context=ssl.create_default_context() + context.set_ciphers("DEFAULT") + + result_blood = urlopen(filename_MLH1_blood, context=context) + df_blood = pd.read_csv(result_blood, sep = "\t", index_col = ["gene","start", "end"]) + result_tumour = urlopen(filename_MLH1_tumour, context=context) + df_tumour = pd.read_csv(result_tumour, sep = "\t", index_col = ["gene","start", "end"]) fig_MLH1, ax_MLH1 = plt.subplots(ncols=1, nrows=2, sharex = True, figsize = (5.2, 4), dpi = 600) @@ -7991,84 +8008,839 @@ +
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diff --git a/Figures/ts_methylation/haplotype_specific_methylation_DNA_repair.md b/Figures/ts_methylation/haplotype_specific_methylation_DNA_repair.md index 81f8ba2..637d74a 100644 --- a/Figures/ts_methylation/haplotype_specific_methylation_DNA_repair.md +++ b/Figures/ts_methylation/haplotype_specific_methylation_DNA_repair.md @@ -4,6 +4,8 @@ import logging import numpy as np from matplotlib.pylab import plt from statsmodels.nonparametric.smoothers_lowess import lowess +import ssl +from urllib.request import urlopen %matplotlib inline params = {"font.family":"Arial", @@ -62,10 +64,15 @@ def generate_BRCA1_haplotype_plots(BRCA1_files, BRCA1_methylated_cases_BRC_OVA, files_BRCA1 = BRCA1_files[tumour_type] logger.info("generating BRCA1 haplotype plots for {}".format(tumour_type)) + context=ssl.create_default_context() + context.set_ciphers("DEFAULT") + if len(files_BRCA1[0]) >0: - df_blood = pd.read_csv(files_BRCA1[0], sep = "\t", index_col = ["gene","start", "end"]) + result_blood = urlopen(files_BRCA1[0], context=context) + df_blood = pd.read_csv(result_blood, sep = "\t", index_col = ["gene","start", "end"]) if len(files_BRCA1[1])>0: - df_tumour = pd.read_csv(files_BRCA1[1], sep = "\t", index_col = ["gene","start", "end"]) + result_tumour = urlopen(files_BRCA1[1], context=context) + df_tumour = pd.read_csv(result_tumour, sep = "\t", index_col = ["gene","start", "end"]) fig_BRCA1, ax_BRCA1 = plt.subplots(ncols=1, nrows=3, sharex = True, figsize = (8.5, 4.2), dpi = 600) @@ -203,10 +210,15 @@ def generate_RAD51C_haplotype_plots(RAD51C_files, RAD51C_methylated_cases_BRC_OV files_RAD51C = RAD51C_files[tumour_type] + context=ssl.create_default_context() + context.set_ciphers("DEFAULT") + if len(files_RAD51C[0]) >0: - df_blood = pd.read_csv(files_RAD51C[0], sep = "\t", index_col = ["gene","start", "end"]) + result_blood = urlopen(files_RAD51C[0], context=context) + df_blood = pd.read_csv(result_blood, sep = "\t", index_col = ["gene","start", "end"]) if len(files_RAD51C[1])>0: - df_tumour = pd.read_csv(files_RAD51C[1], sep = "\t", index_col = ["gene","start", "end"]) + result_tumour = urlopen(files_RAD51C[1], context=context) + df_tumour = pd.read_csv(result_tumour, sep = "\t", index_col = ["gene","start", "end"]) logger.info("generating RAD51C haplotype plots for {}".format(tumour_type)) @@ -323,8 +335,13 @@ def generate_MLH1_haplotype_plots(filename_MLH1_blood, filename_MLH1_tumour, MLH logger.info("generating MLH1 haplotype plots") - df_blood = pd.read_csv(filename_MLH1_blood, sep = "\t", index_col = ["gene","start", "end"]) - df_tumour = pd.read_csv(filename_MLH1_tumour, sep = "\t", index_col = ["gene","start", "end"]) + context=ssl.create_default_context() + context.set_ciphers("DEFAULT") + + result_blood = urlopen(filename_MLH1_blood, context=context) + df_blood = pd.read_csv(result_blood, sep = "\t", index_col = ["gene","start", "end"]) + result_tumour = urlopen(filename_MLH1_tumour, context=context) + df_tumour = pd.read_csv(result_tumour, sep = "\t", index_col = ["gene","start", "end"]) fig_MLH1, ax_MLH1 = plt.subplots(ncols=1, nrows=2, sharex = True, figsize = (5.2, 4), dpi = 600) @@ -462,79 +479,818 @@ if __name__ == "__main__": ``` INFO:__main__:generating BRCA1 haplotype plots for BRC_OVA - CRITICAL:__main__:Failure: - Traceback (most recent call last): - File "/opt/conda/lib/python3.11/urllib/request.py", line 1348, in do_open - h.request(req.get_method(), req.selector, req.data, headers, - File "/opt/conda/lib/python3.11/http/client.py", line 1286, in request - self._send_request(method, url, body, headers, encode_chunked) - File "/opt/conda/lib/python3.11/http/client.py", line 1332, in _send_request - self.endheaders(body, encode_chunked=encode_chunked) - File "/opt/conda/lib/python3.11/http/client.py", line 1281, in endheaders - self._send_output(message_body, encode_chunked=encode_chunked) - File "/opt/conda/lib/python3.11/http/client.py", line 1041, in _send_output - self.send(msg) - File "/opt/conda/lib/python3.11/http/client.py", line 979, in send - self.connect() - File "/opt/conda/lib/python3.11/http/client.py", line 1458, in connect - self.sock = self._context.wrap_socket(self.sock, - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/ssl.py", line 517, in wrap_socket - return self.sslsocket_class._create( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/ssl.py", line 1108, in _create - self.do_handshake() - File "/opt/conda/lib/python3.11/ssl.py", line 1379, in do_handshake - self._sslobj.do_handshake() - ssl.SSLError: [SSL: SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c:1006) - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/tmp/ipykernel_186/2671134438.py", line 37, in - main() - File "/tmp/ipykernel_186/2671134438.py", line 14, in main - generate_BRCA1_haplotype_plots(BRCA1_files, BRCA1_METHYLATED_CASES_BRC_OVA, BRCA1_METHYLATED_CASES_NON_BRC_OVA, BRCA1_LOH_CASES) - File "/tmp/ipykernel_186/1885639513.py", line 25, in generate_BRCA1_haplotype_plots - df_blood = pd.read_csv(files_BRCA1[0], sep = "\t", index_col = ["gene","start", "end"]) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv - return _read(filepath_or_buffer, kwds) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 620, in _read - parser = TextFileReader(filepath_or_buffer, **kwds) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1620, in __init__ - self._engine = self._make_engine(f, self.engine) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine - self.handles = get_handle( - ^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/common.py", line 728, in get_handle - ioargs = _get_filepath_or_buffer( - ^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/common.py", line 384, in _get_filepath_or_buffer - with urlopen(req_info) as req: - ^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/site-packages/pandas/io/common.py", line 289, in urlopen - return urllib.request.urlopen(*args, **kwargs) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/urllib/request.py", line 216, in urlopen - return opener.open(url, data, timeout) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/urllib/request.py", line 519, in open - response = self._open(req, data) - ^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/urllib/request.py", line 536, in _open - result = self._call_chain(self.handle_open, protocol, protocol + - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/urllib/request.py", line 496, in _call_chain - result = func(*args) - ^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/urllib/request.py", line 1391, in https_open - return self.do_open(http.client.HTTPSConnection, req, - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/conda/lib/python3.11/urllib/request.py", line 1351, in do_open - raise URLError(err) - urllib.error.URLError: + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + 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+![png](haplotype_specific_methylation_DNA_repair_files/haplotype_specific_methylation_DNA_repair_4_1.png) + + + + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. + WARNING:matplotlib.font_manager:findfont: Font family 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