- Mar 09, 2020
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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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nfontrod authored
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nfontrod authored
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nfontrod authored
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nfontrod authored
src/db_utils/frequency_scripts: script allowing to populate the frequency tables of chia-pet database
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nfontrod authored
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- Mar 04, 2020
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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/db_creation.py: modification of cin_gene_frequency and cin_exon_frequency tables: add a ft_type column
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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
src/db_utils/fill_splicing_lore_tables.py, src/db_utils/__main__.py: creation of fill_splicing_lore_tables.py that fills cin_ase_event and cin_project_splicing_lore tables
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nfontrod authored
src/db_utils/populate_database.py - src/db_utils/config.py: modification of check_table_name, it now checks if the table name given exists in the database, not if it presents in Config.tables (so, this last variable was removed)
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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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- Mar 03, 2020
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alapendr authored
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nfontrod authored
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nfontrod authored
src/db_utils/creation_of_exon_table.py: major modification, this script will create and fill the cin_exon and cin_gene table of the new database model
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nfontrod authored
src/db_utils/populate_database.py: creation of populate_df function (and other functions to lower code duplication) that fill the database directly with a pandas dataframe
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nfontrod authored
src/db_utils/config.py: modification of prefixes gin to cin in Config.table + creation of Config.bed_exon and Config.bed_gene variable
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nfontrod authored
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nfontrod authored
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nfontrod authored
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nfontrod authored
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nfontrod authored
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