BLASTER Arguments

1. **repetitive_blaster**

1.1. genome_fasta

1.2. path_input

1.3. folder_path

1.4. naming_short

1.5. numbering

1.6. max_diff

1.7. maximun_runs

2. **boxymcboxface**

2.1. message

3. **genome_specific_chromosome_main**

3.1. path_input

3.2. chromosome_ID

3.3. main_folder_path

3.4. genome_fasta

3.5. naming_short

3.6. nax_diff

4. **specific_sequence_extractor**

4.1. path_input

4.2. chromosome_ID

4.3. main_folder_path

5. **specific_sequence_1000nt**

5.1. path_input

5.2. chromosome_ID

5.3. main_folder_path

6. **fasta_creator**

6.1. path_input

6.2. fasta_output_path

7. **blastn_dic**

7.1. path_input

8. **blastn_blaster**

8.1. query_path

8.2. dict_path

8.3. outfile_path

8.4. perc_identity

8.4.1. **85** -> for the 1000nt expanded 1st Run

8.4.2. **60** -> for the 2nd Run

9. **specific_sequence_corrected**

9.1. path_input

9.2. nucleotides1000_directory

9.3. main_folder_path

9.4. chromosome_ID

10. **filter_by_column**

10.1. path_input

10.2. column

10.2.1. "length" -> **1st Run** 1000nt BLAST against each other

10.2.2. "length" -> **2nd Run**

10.3. size_filter

10.3.1. 100 -> **1st run** of 1000nt BLAST against each other

10.3.2. 100 -> **2nd Run**

10.4. writing_path_input

11. **csv_creator**

11.1. writing_path_input

11.2. writing_input

12. **global_filters_main**

12.1. path_input

12.2. writing_path_input

12.3. genome_fasta

12.4. naming_short

12.5. max_diff

13. **dash_filter**

13.1. path_input

13.2. writing_path_input

14. **genome_duplicate_filter**

14.1. genome_fasta

14.2. naming_short

14.3. path_input

14.4. max_diff

14.5. writing_path_input

15. **genome_pre_duplicate_filter**

15.1. genome_fasta

15.2. naming_short

15.3. path_input

15.4. DNA_sense

15.5. max_diff

16. **chromosome_filter**

16.1. path_input

16.2. name

17. **genome_solap_main**

17.1. genome_fasta

17.2. naming_short

17.3. path_input

17.4. max_diff

17.5. writing_path_input

18. **genome_solap_minmax**

18.1. chromosome_rows

18.2. max_diff

19. **genome_solap_location_grouping**

19.1. chromosome_rows

19.2. DNA_sense

19.3. max_diff

20. **genome_solap_location_filter**

20.1. chromosome_rows

21. **genome_solap_by_pairs**

21.1. rows_to_filter

22. **csv_mixer**

22.1. path_input1

22.2. path_input2

22.3. writing_path_input

23. **folder_creator**

23.1. options