Goal

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

input

The script receive files in .fasta format

example : file.fasta

Example of files distribution before run the script:

• 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
  

output

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.

command line examples

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