SeqAnn

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Python package for annotating gene features

Overview

The seqann package allows users to annotate gene features in consensus sequences. Annotations can be created by passing consensus sequences to the annotate method in the BioSeqAnn class. No parameters are required when initalizing a BioSeqAnn class. However, annotations can be created significantly faster when using a BioSQL database. When a BioSQL database is not provided the lastest hla.dat file is downloaded and parsed. A BioSQL database containing all of IPD-IMGT/HLA is available on DockerHub and can be run on any machine that has docker installed.

Install

pip install seq-ann

Parameters

Below are the list of parameters and the default values used when initalizing a BioSeqAnn object.

Parameter Type Default Description
server BioSeqDatabase None A BioSQL database containing all of the sequence data from IPD-IMGT/HLA.
dbversion str Latest The IPD-IMGT/HLA or KIR database release.
datfile str None The IPD-IMGT/HLA or KIR dat file to use in place of the server parameter.
kir bool False Flag for indicating the input sequences are from the KIR gene system.
align bool False Flag for producing the alignments along with the annotations.
verbose bool False Flag for running in verbose mode.
verbosity int None Numerical value to indicate how verbose the output will be in verbose mode.
debug Dict None A dictionary containing a process names as the key and verbosity as the value

Usage

To annotated a sequence initialize a new BioSeqAnn object and then pass the sequence to the annotate method. The sequence must be a Biopython Seq. The locus of the sequence is not required but it will improve the accuracy of the annotation.

The packages ncbi-blast+ and clustalo are required to be installed on your system.

Set variables to BioSQL host/port if using BioSQL.

export BIOSQLHOST="localhost"
export BIOSQLPORT=3306

from seqann import BioSeqAnn
seqann = BioSeqAnn()
ann = seqann.annotate(sequence, "HLA-A")

The annotation of sequence can be done with or without providing a BioSeqDatabase. To use a BioSQL database initialize a BioSeqDatabase with the parameters that match the database you have running. If you are running the imgt_biosqldb from DockerHub then the following parameters we be the same.

from seqann import BioSeqAnn
from BioSQL import BioSeqDatabase
server = BioSeqDatabase.open_database(driver="pymysql", user="root",
                                      passwd="my-secret-pw", host="localhost",
                                      db="bioseqdb", port=3306)
seqann = BioSeqAnn(server=server)
ann = seqann.annotate(sequence, "HLA-A")

You may need to set environment variables: BIOSQLHOST (e.g. “localhost”) and BIOSQLPORT (e.g. 3306) to your docker instance.

Annotations

{
     'complete_annotation': True,
     'annotation': {'exon_1': SeqRecord(seq=Seq('AGAGACTCTCCCG', SingleLetterAlphabet()), id='HLA:HLA00630', name='HLA:HLA00630', description='HLA:HLA00630 DQB1*03:04:01 597 bp', dbxrefs=[]),
                    'exon_2': SeqRecord(seq=Seq('AGGATTTCGTGTACCAGTTTAAGGCCATGTGCTACTTCACCAACGGGACGGAGC...GAG', SingleLetterAlphabet()), id='HLA:HLA00630', name='HLA:HLA00630', description='HLA:HLA00630 DQB1*03:04:01 597 bp', dbxrefs=[]),
                    'exon_3': SeqRecord(seq=Seq('TGGAGCCCACAGTGACCATCTCCCCATCCAGGACAGAGGCCCTCAACCACCACA...ATG', SingleLetterAlphabet()), id='HLA:HLA00630', name='<unknown name>', description='HLA:HLA00630', dbxrefs=[])},
     'features': {'exon_1': SeqFeature(FeatureLocation(ExactPosition(0), ExactPosition(13), strand=1), type='exon_1'),
                  'exon_2': SeqFeature(FeatureLocation(ExactPosition(13), ExactPosition(283), strand=1), type='exon_2')
                  'exon_3': SeqFeature(FeatureLocation(ExactPosition(283), ExactPosition(503), strand=1), type='exon_3')},
     'method': 'nt_search and clustalo',
     'gfe': 'HLA-Aw2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-4',
     'seq': SeqRecord(seq=Seq('AGAGACTCTCCCGAGGATTTCGTGTACCAGTTTAAGGCCATGTGCTACTTCACC...ATG', SingleLetterAlphabet()), id='HLA:HLA00630', name='HLA:HLA00630', description='HLA:HLA00630 DQB1*03:04:01 597 bp', dbxrefs=[])
}

Once a sequence has been annotated the gene features and their corresponding sequences are available in the returned Annotation object. If a full annotation is not able to be produced then nothing will be returned. Below is an example showing how the features can be accessed and printed out.

ann = seqann.annotate(sequence, "HLA-A")
for feat in ann.annotation:
    print(feat, ann.gfe, str(ann.annotation[feat].seq), sep="\t")

Dependencies