The script combines fasta files of different loci located in different directories into one fasta file for each sample.
To achieve the distribution of locus files to folders that correspond to the name of the locus, please see the "move_to_folder" script https://github.com/Vladislav-Shevtsov/Sort-files-by-pattern
The script receive files in .fasta format
example : file.fasta
-
folder_1_sample_1:
locus_1.fasta locus_2.fasta locus_3.fasta ........ ........ locus_n.fasta -
Folder_2_sample_2:
locus_1.fasta locus_2.fasta locus_3.fasta ........ ........ locus_n.fasta -
Folder_3_sample_3:
locus_1.fasta locus_2.fasta locus_3.fasta ........ ........ locus__n.fasta
As a result, the script will generate following files:
Sample_1_all_loci_in_one_file.fasta
Sample_2_all_loci_in_one_file.fasta
Sample_3_all_loci_in_one_file.fasta
output represents files(reads) with .fasta extension located in output folder that you specify in code.
The script receives two arguments: path to folder containing fasta files and output directory
python3 Fa_to_one.py /path/to/folders_containing_fasta_files /path/to/out_dir #This will generate bash file named "fa_to_one.sh"
./fa_to_one.sh #This will execute the bash file
#written by Shevtsov V. xatabadich(at)gmail.com