- Jun 09, 2020
- Apr 10, 2020
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alapendr authored
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alapendr authored
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alapendr authored
config_interactions.py: add couple_exon and couple_gene to store the final result of features_interactions.py
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alapendr authored
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alapendr authored
__main__.py: update to integrate the filling of cin_exon_interaction and cin_gene_interaction tables
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- Apr 09, 2020
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alapendr authored
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- Apr 06, 2020
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alapendr authored
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- Mar 27, 2020
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nfontrod authored
src/db_utils/interactions/features_interactions.py: mojor modifications to speedup teh creation of interaction tables
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- Mar 26, 2020
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nfontrod authored
src/db_utils/interactions/features_interactions.py: Creation of a function create_interaction_table that calls every other function from that file
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nfontrod authored
src/db_utils/interactions/bedtools.py: creation of the required directory if they don't exist at the beginning of function 'main_bedtools'
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alapendr authored
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alapendr authored
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- Mar 11, 2020
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alapendr authored
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- Mar 10, 2020
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nfontrod authored
src/db_utils/projects_metadata/get_fill_metadata.py: modification in launch_pmagicGEO_script function: we call subprocess.check_call instead of subprocess.check_output
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nfontrod authored
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nfontrod authored
src/db_utils/projects_metadata/get_fill_metadata.py: fix fill_projects_table to make it launch launch_pmagicGEO_script + pep8 modifications
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alapendr authored
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alapendr authored
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alapendr authored
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- Mar 09, 2020
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alapendr authored
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alapendr authored
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alapendr authored
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alapendr authored
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nfontrod authored
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nfontrod authored
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alapendr authored
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alapendr authored
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nfontrod authored
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nfontrod authored
src/db_utils/frequency_scripts/create_n_fill_exon_frequency_file.py : modification of compute_gene_orf_data to compute codon/aa/properties frequencies at gene level
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nfontrod authored
src/db_utils/frequency_scripts/frequency_function.py: modification of frequencies for better performances
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nfontrod authored
src/db_utils/frequency_scripts/config_freq.py: modification of iupac_dic variable : it links for each 'degenerated' nucleotides (SWKMRY) the nucleotides they can be
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alapendr authored
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- Mar 06, 2020
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nfontrod authored
src/db_utils/frequency_scripts/create_n_fill_exon_frequency_file.py: fix multiprocess_freq_orf and compute_gene_orf_data function (rename the column new_freq to frequency) + fix of create_or_load_freq_table (concatenation of wrong tables to create the final gene frequency table) + columns adjustement in fill_frequency_tables
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- Mar 05, 2020
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nfontrod authored
src/db_utils/frequency_scripts/create_n_fill_exon_frequency_file.py: fix fill_frequency_tables by creating theresults/frequencies directory it it doesn't exist
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nfontrod authored
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nfontrod authored
src/db_utils/config.py: add cpu variable. src/db_utils/__main__.py: add the function to fill frequency table
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nfontrod authored
src/db_utils/frequency_scripts/create_n_fill_exon_frequency_file.py: add multiprocessing to create frequency file + compute fre frequency of codon, aa, and properties for gene (corresponding to the frequency obtained by the concatenation of every exon coding sequences within the gene)
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nfontrod authored
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