geney 1.1.8__py2.py3-none-any.whl → 1.1.10__py2.py3-none-any.whl
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geney/netchop.py
CHANGED
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@@ -24,21 +24,22 @@ class NetChop(object):
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The i'th list corresponds to the i'th sequence. Each list gives
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the cleavage probability for each position in the sequence.
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"""
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temp_file = config_setup['NETCHOP'] / 'netchop_input.fsa'
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with open(temp_file, 'w') as input_fd:
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print(f"Writing to {input_fd}...")
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with tempfile.NamedTemporaryFile(dir=config_setup['NETCHOP'], suffix=".fsa", mode="w") as input_fd:
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# temp_file = config_setup['NETCHOP'] / 'netchop_input.fsa'
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# with open(temp_file, 'w') as input_fd:
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for (i, sequence) in enumerate(sequences):
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print(f"\tseq{i}: {sequence}")
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_ = input_fd.write("> %d\n" % i)
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_ = input_fd.write(sequence)
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_ = input_fd.write("\n")
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# input_fd.flush()
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# print(str(temp_file))
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try:
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output = subprocess.check_output(["
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output = subprocess.check_output(["netchop", str(input_fd.name)])
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except subprocess.CalledProcessError as e:
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logging.error("Error calling netChop: %s:\n%s" % (e, e.output))
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raise
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parsed = self.parse_netchop(output)
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assert len(parsed) == len(sequences), \
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"Expected %d results but got %d" % (
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@@ -7,7 +7,7 @@ geney/config_setup.py,sha256=SePeooA4RWAtR_KAT1-W1hkD3MT5tH6YMyp80t_RNPQ,385
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geney/data_setup.py,sha256=DZeksRPr2ZT7bszMo33W0r3OwmqHokVXtZ4gx5Lu_Mo,10725
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geney/gtex.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
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geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
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-
geney/netchop.py,sha256=
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geney/netchop.py,sha256=AMiy9YsdTmX4B3k3Y5Yh7EmoGAojM1O3AzhPKOiB--g,3050
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geney/oncosplice.py,sha256=Fyc_UtAhV3Pv0vk8V55rO_jnb2Dwj5sW98KVwP3PHwU,68964
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geney/oncosplice_pipeline.py,sha256=hpGqFHOdn8i8tvvs1-t3-G9Ko18zInwoDXBJbbrfbC4,68036
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geney/performance_utils.py,sha256=FQt7rA4r-Wuq3kceCxsSuMfj3wU1tMG8QnbL59aBohs,4700
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@@ -43,7 +43,7 @@ geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFW
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geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
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geney/translation_termination/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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geney/translation_termination/tts_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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geney-1.1.
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geney-1.1.
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geney-1.1.
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geney-1.1.
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geney-1.1.10.dist-info/METADATA,sha256=Et_H-jo1c9eYsqEnjk1_gVLRtJYzS9-RXs8RE7Z-u6c,1131
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geney-1.1.10.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
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geney-1.1.10.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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geney-1.1.10.dist-info/RECORD,,
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File without changes
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File without changes
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