Module utilities

returns a list with one line each element

Non of the elements will be lines that started with a '#', and lines were not empty

method that returns a list with potential types of protein code (ie database column) of a given protein name "protein_id" for which we do not know the type of code

This method should be called prior to PianaDBaccess.get_list_proteinPiana() if the identifier type is not known

Attention!!! This function is only being used by string2piana

THIS IS CURRENTLY ONLY BEING USED IN THE STRING PARSER string2piana: that is why I am currently only looking for codes that might appear in STRING

parses a string that has field_names and values and returns a list of pairs [[field_name,value], [field_name, value], ...]

global_separators is a list with all the string separators that can act as a string separator (e.g. [" ", "|", ";" ])

separator_field_value can only be one character

string must follow format:

[global_separator]*field[separator_field_value]value[global_separator]*field[separator_field_value]value[global_separator]*.....

meaning that each field has a value

for example, stringX

"    ;Name=Ramon    ;   and   Name=Pedro   , Synonim=Juan  ;  "

could be converted into a list [[Name, Ramon], [Name, Pedro], [Synonim, Juan] by calling parse_string_field_value(input_string=stringX,
                                                                                                                    separator_field_value="=",
                                                                                                                    global_separators=[" ",";"])

Attention!!! Even if space (ie " ") is not in global_separators, a strip() is done before returning the pairs, to remove trailing spaces from the
field names and field values. So, if trailing spaces are needed, something else has to be done...

returns a dictionary { gi: tax_id,
                       gi: tax_id,
                       ......
                       }

filled with info from "file_name" (gis and tax_ids are both integers

"file_name" is a file name of a file that has two tab-separated columns
1st one is gi code
2nd one is tax id for that gi