Sequence Annotation
Project description
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
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.
Project details
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