seqann 0.0.16

Sequence Annotation

SeqAnn

Sequence Annotation

• Free software: LGPL 3.0

• Documentation: https://seqann.readthedocs.io.

Docker

• docker pull nmdpbioinformatics/pygfe

docker run -it --rm -v $PWD:/opt nmdpbioinformatics/pygfe seq2gfe \
        -f /opt/your_fastafile.fasta -l HLA-A

Features

With mysql connection:

from seqann
from Bio import SeqIO
from BioSQL import BioSeqDatabase

server = BioSeqDatabase.open_database(driver="pymysql", user="root",
                                      passwd="", host="localhost",
                                      db="bioseqdb")
seqann = seqann.BioSeqAnn(server=server)
for seq in SeqIO.parse(input_seq, "fasta"):
        annotation = seqann.annotate(seq, "HLA-A")
        for feat in annotation.annotation:
                print(feat, annotation.annotation[feat], sep="\t")

Without mysql connection:

import seqann
from Bio import SeqIO

# ** If you don't have a copy of the hla.dat
# ** file it will download it
seqann = seqann.BioSeqAnn()
for seq in SeqIO.parse(input_seq, "fasta"):
        annotation = seqann.annotate(seq, "HLA-A")
        for feat in annotation.annotation:
                print(feat, annotation.annotation[feat], sep="\t")

Dependencies

• Clustal Omega 1.2.0 or higher

• Python 3.6

• blastn

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.0.1 (2017-10-19)

• First release on PyPI.