| Definition part: |
| Connection variables (undertaken by Biopython package) |
| Bacteria phyla (bacteria_main_groups) |
| List of geographical areas (list from file: countries_list_all.txt) see supplementary |
| materials. |
| The query structure (term = “country AND Geographical area’s name AND |
| Bacteria [Organism] AND Date of publication”) |
| gi_list (list of records verifying the query structure) |
| listWC (number of records with the existence of the qualifier/country) |
| lisV (number of records with a real/country qualifier attributed to the right |
| geographical area) |
| // all variables are set at zero (0) or an empty list. |
| Define treatments and operations: |
| For every geographical area form the list found in “countries_list_all.txt”: |
| (i) Query the NCBI database, using the query structure. |
| (ii) Retrieve the count of gi_list |
| (iii) Retrieve all the records (Genbank format) one by one |
| (iv) Access each record: |
| If the qualifier/country exists then: |
| + 1 |
| If the qualifier value matches the geographical area of |
| interest: |
| + 1 |
| Check for the taxonomy: |
| Count the sequence regarding the appropriate phylum. |
| If there is not taxonomy for the sequence (no |
| bacteria) then register the GI in |
| file “geographical_area_Absence_Bact.txt”, see |
| supplementary materials. |
| Save results for all records of the geographical area on a row in the result file |
| (country_all.txt) see supplementary materials. |
| Remove the geographical area from the list of geographical areas. |
| If any errors occurred, save the error type in “error.txt”, see supplementary materials. |
