Example for extracting SubreadSet Bam files from a SMRT Link Job

slln.py

#!/usr/bin/env python
import logging
import sys

from pbcommand.services import ServiceAccessLayer as S
from pbcore.io.dataset import SubreadSet

log = logging.getLogger(__name__)


def get_subreadset_path(client, dataset_id):
    sset = client.get_subreadset_by_id(dataset_id)
    return sset['path']


def extract_from_sset(sset):
    for f in sset.externalResources:
        if f.metaType == 'PacBio.SubreadFile.SubreadBamFile':
            yield f.resourceId


def get_and_extract_from_sset(client, dataset_id):
    path = get_subreadset_path(client, dataset_id)
    sset = SubreadSet(path)
    for r in extract_from_sset(sset):
        yield r


def get_bam_files_from_job_id(client, job_id):

    # will fail if can't connect to server
    status = client.get_status()

    epts = client.get_analysis_job_entry_points(job_id)

    sset_uuids = [e.dataset_uuid for e in epts if e.dataset_metatype == 'PacBio.DataSet.SubreadSet']

    for u in sset_uuids:
        for r in get_and_extract_from_sset(client, u):
            yield r
        


def example():

    job_id = 29212
    host = "smrtlink-alpha"
    port = 8081

    client = S(host, port)
    resources = list(get_bam_files_from_job_id(client, job_id))

    print "\n".join(resources)

    return 0


if __name__ == '__main__':
    sys.exit(example())