How to download and process ls_orchid.fasta file?

ls_orchid.fasta file is an example of DNA sequence file in FASTA format provided in the Biopython source code package. You can also download it and use it to test Biopython library.

1. Download ls_orchid.fasta.

fyicenter$ curl https://raw.githubusercontent.com/biopython/biopython/master/Doc/examples/ls_orchid.fasta > ls_orchid.fasta 

fyicenter$ ls -l 
-rw-r--r--. 1 fyicenter staff 76480 Jan 27 23:55 ls_orchid.fasta

2. Bio.SeqIO.parse() function to read the ls_orchid.fasta file.

fyicenter$ python 

>>> 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))
...

gi|2765658|emb|Z78533.1|CIZ78533
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG...CGC')
740
...
gi|2765564|emb|Z78439.1|PBZ78439
Seq('CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT...GCC')
592

⇒ List NCBI Databases with Bio.Entrez.einfo()

⇐ Single Sequence Record in GenBank Format

⇑ Biopython - Tools for Biological Computation

⇑⇑ OBF (Open Bioinformatics Foundation) Tools