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. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font 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. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font 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. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font 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 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+WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +INFO:__main__:generating TPM 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. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font 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.
INFO:__main__:generating BRCA1 haplotype plots for BRC_OVA -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_48/2671134438.py", line 37, in <module> - main() - File "/tmp/ipykernel_48/2671134438.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_48/1885639513.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: <urlopen error [SSL: SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c:1006)> +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font 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 BRCA1 haplotype plots for non_BRC_OVA +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font 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 RAD51C haplotype plots for BRC_OVA +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font 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 RAD51C haplotype plots for non_BRC_OVA +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font 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 MLH1 haplotype plots +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font family 'Arial' not found. +WARNING:matplotlib.font_manager:findfont: Font 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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