BiotextUtils

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.

Requirements

Before run install biopython library:

    pip install biopython

dna2pro.py script

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 

frag_align.py script

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