parsing_scripts.utils package¶
Submodules¶
parsing_scripts.utils.column_identifier module¶
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parsing_scripts.utils.column_identifier.sample_column_identifier(query, header)¶ Tries to automatically identify the header column that contains the raw data given some query information (like the dye color)
Multi-channel array might have different dye color on different samples (dye-swap) and thus it would be tedious to manually define it for each single sample. This function tries to do it for you and is tipically invoked for the SOFT sample files.
- PARAMETERS:
query (string): The query string is usually something that contains information about the color i.e. cy3, red, green etc.
header (list): The header is a list of string from which to chose one that will match the query
parsing_scripts.utils.rnaseq module¶
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parsing_scripts.utils.rnaseq.create_fasta(file, compendium)¶ Create a FASTA file using the BIOLOGICAL FEATURE of the current Organism
- PARAMETERS:
file (string): The output FASTA file name
compendium (string): The organism (nick) name