stanbar / bio-linear-aligner

DNA sequence linear aligner using BioPython

Bio Linear Aligner

Linear Alignment using BioPython

How to use

setup venv and install dependencies

python -m venv venv
. venv/bin/activate
pip install -r requirements.txt

show all options

python aligner.py -h

Usage:
  aligner.py (local|global) INPUT ...
  [-o OUT_FILE] 
  [--matchscore MATCH_SCORE] 
  [--mismatchscore MISMATCH_SCORE] 
  [--opengapscore OPEN_GAP_SCORE] 
  [--extendgapscore EXTEND_GAP_SCORE] 
  [--informat FORMAT] 
  [--matrix MATRIX]
  aligner.py (-h | --help)

Examples:
  aligner.py local sample_sequences/two_sequences.fasta
  aligner.py global sample_sequences/dna-1.txt sample_sequences/dna-2.txt
  aligner.py local sample_sequences/two_sequences.fasta -o alignments.txt
  aligner.py local sample_sequences/two_sequences.fasta --matrix blosum62

Options:
  -h --help  Show this screen.
  -o OUT_FILE  output file [default: ./output.txt]
  --matchscore MATCH_SCORE  match score [default: 2]
  --mismatchscore MISMATCH_SCORE  mismatch score [default: -1]
  --opengapscore OPEN_GAP_SCORE  open gap score [default: -1]
  --extendgapscore EXTEND_GAP_SCORE  extend gap score [default: -1]
  --informat FORMAT  input format [default: fasta]
  --matrix MATRIX  substitution matrice

run local alignment on sample sample_sequences/two_sequences.fasta sequences

python aligner.py local sample_sequences/two_sequences.fasta

output

Maximum score: 11.0
MKLKKTIGAMALATLFATMGASAVEKTISVTASVDPTVDLLQSDGSALPNSVALTYSPAV                   
                                              ||-|-|-|--|||                    
              MLKIKYLLIGLSLSAMSSYSLAAAGPTLTKELAL-N-V-L--SPAALDATWAPQDNLTLSNTGVS
Score: 11.0

you can also provie 2 input files

python aligner.py global sample_sequences/dna-1.txt sample_sequences/dna-2.txt

Maximum score: 5.0
tcgattata----gag
---||-||.----|||
---at-atcccccgag
Score: 5.0

tcgattata----gag
---|-|||.----|||
---a-tatcccccgag
Score: 5.0

tcgattat-a---gag
---||-||-.---|||
---at-atcccccgag
Score: 5.0

tcgattat-a---gag
---|-|||-.---|||
---a-tatcccccgag
Score: 5.0

tcgattat--a--gag
---||-||--.--|||
---at-atcccccgag
Score: 5.0

tcgattat--a--gag
---|-|||--.--|||
---a-tatcccccgag
Score: 5.0

tcgattat---a-gag
---||-||---.-|||
---at-atcccccgag
Score: 5.0

tcgattat---a-gag
---|-|||---.-|||
---a-tatcccccgag
Score: 5.0

tcgattat----agag
---||-||----.|||
---at-atcccccgag
Score: 5.0

tcgattat----agag
---|-|||----.|||
---a-tatcccccgag
Score: 5.0

you can customize the scoring and penality with

--matchscore  match score [default: 2]
--mismatchscore  mismatch score [default: -1]
--opengapscore  open gap score [default: -1]
--extendgapscore  extend gap score [default: -1]

or you can use one of predefined substitution matrices ["benner6", "benner22", "benner74", "blosum100", "blosum30", "blosum35", "blosum40", "blosum45", "blosum50", "blosum55", "blosum60", "blosum62", "blosum65", "blosum70", "blosum75", "blosum80", "blosum85", "blosum90", "blosum95", "feng", "fitch", "genetic", "gonnet", "grant", "ident", "johnson", "levin", "mclach", "miyata", "nwsgappep", "pam120", "pam180", "pam250", "pam30", "pam300", "pam60", "pam90", "rao", "risler", "structure", ]

python aligner.py local sample_sequences/two_sequences.fasta --matrix blosum62

or even specify your own matrice

python aligner.py local sample_sequences/zad_1_u.txt sample_sequences/zad_1_w.txt --matrix custom_matrice.txt

default output file is output.txt but you can specifiy it with -o OUT_FILE, for example

python aligner.py local sample_sequences/two_sequences.fasta -o alignments.txt

preview

cat alignments.txt