Biopython 1.65 example #slurm

script.sh

#!/bin/bash

##this is an example described in section 2.4.1
##http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc10

wget -nc http://biopython.org/DIST/docs/tutorial/examples/ls_orchid.fasta

echo "
from Bio import SeqIO
for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
    print(seq_record.id)
    print(repr(seq_record.seq))
    print(len(seq_record))
" > script.py

python script.py