Script dna2pro.py is created for translating DNA sequences in FASTA to proteins FASTA. Can filter out short translated sequences.
Script frag_align.py is created for extracting specific fragment from all sequences in an alignment.
Before run install biopython library:
pip install biopython
Before running specify initial data in dna2pro.py script:
- DNA_FILE_NAME - input filename with DNA sequences in FASTA format
- PRO_FILE_NAME - output filename for writing proteins sequences in FASTA format
- FILTERING - filtering of translated protein sequences, integer number (0 - no filtering, 1 and more - translations that has continuous sequence of length less than specified value will be dropped, continuous sequence - protein sequence before first stop '*')
To run program from terminal print:
python dna2pro.py
Before running specify initial data in frag_align.py script:
- ALIGNMENT_FILE_NAME - input filename with alignment in FASTA format
- FRAGMENTS_FILE_NAME - output filename for writing fragments in FASTA format
- START - start position of fragment in an alignment (numerating from 0)
- END - end position of fragment in an alignment (numerating from 0)
- REMOVE_GAPS - removing gaps in fragments
To run program from terminal print:
python frag_align.py