API Examples

abstar and abutils both expose a public API containing many of the core functions. This makes it reasonably straightforward to build custom pipelines that include several abstar/abutils components or integrate these tools with third-party tools. A few simple examples are shown below.

Case #1

Sequencing data consists of an Illumina MiSeq run on human samples, with the raw data stored in BaseSpace (project ID: 123456789). Samples are indexed, so each sample will be downloaded from BaseSpace as a separate pair of read files. We’d like to do several things:

  • get a FASTQC report on the raw data
  • remove adapters
  • quality trim
  • get another FASTQC report on the cleaned data
  • merge paired reads
  • annotate with abstar
import os

import abstar
from abstar.utils import basespace, pandaseq

PROJECT_DIR = '/path/to/project'
PROJECT_ID = '123456789'

# download data from BaseSpace
bs_dir = os.path.join(PROJECT_DIR, 'raw_data')
basespace.download(bs_dir, project_id=PROJECT_ID)

# FASTQC on the raw data
fastqc1_dir = os.path.join(PROJECT_DIR, 'fastqc-pre')
abstar.fastqc(bs_dir, output=fastqc1_dir)

# adapter trimming
adapter_dir = os.path.join(PROJECT_DIR, 'adapter_trimed')
adapters = '/path/to/adapters.fasta'
abstar.adapter_trim(bs_dir, output=adapter_dir, adapter_both=adapters)

# quality trimming
quality_dir = os.path.join(PROJECT_DIR, 'quality_trimed')
abstar.quality_trim(adapter_dir, output=quality_dir)

# FASTQC on the cleaned data
fastqc2_dir = os.path.join(PROJECT_DIR, 'fastqc-post')
abstar.fastqc(quality_dir, output=fastqc2_dir)

# read merging
merged_dir = os.path.join(PROJECT_DIR, 'merged')
pandaseq.run(quality_dir, merged_dir)

# run abstar
temp_dir = os.path.join(PROJECT_DIR, 'temp')
json_dir = os.path.join(PROJECT_DIR, 'json')

Case #2

Sequencing data is a directory of single-read FASTQ files that have already been quality/adapter trimmed. We’d like to do the following:

  • get a FASTQC report
  • annotate with abstar
  • import the JSONs into a MongoDB database named MyDatabase

Our FASTQ file names are formatted as: SampleNumber-SampleName.fastq, which means the abstar output file name would be SampleNumber-SampleName.json. We’d like the corresponding MongoDB collection to just be named SampleName.

import os

import abstar
from abstar.utils import mongoimport

PROJECT_DIR = '/path/to/project'
FASTQ_DIR = '/path/to/fastqs'

MONGO_PORT = 27017
MONGO_USER = 'MyUsername'
MONGO_PASS = 'Secr3t'

# FASTQC on the input data
fastqc_dir = os.path.join(PROJECT_DIR, 'fastqc')
abstar.fastqc(FASTQ_DIR, output=fastqc_dir)

# run abstar
temp_dir = os.path.join(PROJECT_DIR, 'temp')
json_dir = os.path.join(PROJECT_DIR, 'json')

# import into MongoDB

Case #3

Now we’d like to use abstar as part of an analysis script in which sequence annotation isn’t the primary output. In the previous examples, we started with raw(ish) sequence data and ended with either a directory of JSON files or a MongoDB database populated with abstar output. In this case, we’re going to start with a MongoDB database, query that database for some sequences, and generate the unmutated common ancestor (UCA). We’d like to annotate the UCA sequence inline (as part of the script) so that we can do world-changing things with the annotated UCA later in our script. For simplicity’s sake, we’re querying a local MongoDB database that doesn’t have authentication enabled, although abutils.utils.mongodb can work with remote MongoDB servers that require authentication.

import abstar

from abutils.utils import mongodb
from abutils.utils.sequence import Sequence

DB_NAME = 'MyDatabase'
COLLECTION_NAME = 'MyCollection'

def get_sequences(db_name, collection_name):
    db = mongodb.get_db(db_name)
    c = db[collection]
    seqs = c.find({'chain': 'heavy'})
    return [Sequence(s) for s in seqs]

def calculate_uca(sequences):
    # code to calculate the UCA sequence, as a string
    return uca

# get sequences, calculate the UCA
sequences = get_sequences(DB_NAME, COLLECTION_NAME)
uca_seq = calculate_uca(sequences)

# run abstar on the UCA, returns an abutils Sequence object
uca = abstar.run(['UCA', uca_seq])

# do amazing, world-changing things with the UCA
# ...
# ...
# ...