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Sequence Annotation

Project description

SeqAnn

Documentation Status Updates

Sequence Annotation

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

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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seqann-0.0.20-py2.py3-none-any.whl (18.0 MB) Copy SHA256 hash SHA256 Wheel py2.py3 May 17, 2018

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