mpkocher

mpkocher

"""Filters sequences based on the pls.h5 file, removing apparently
doubly loaded wells and unloaded wells.

Note: The 'chunking' (i.e., chunkFunc) in the task decorator must be
consistent for each instance of SMRTFile. In other words, inputPlsFofn must be
scattered using the same function in *every* P_module. Therefore, the
chunkFunc must be set to context.numMovies.

"""

mpkocher

#!/usr/bin/env python
"""Get a List of Runs from SMRT Link"""
# From:http://bitbucket.nanofluidics.com:7990/projects/SL/repos/pbcommand/browse/pbcommand/cli/examples/template_simple.py

import os
import sys
import logging

from pbcommand.validators import validate_file
from pbcommand.utils import setup_log

mpkocher

import datetime
import json
import copy
import time
import functools
import itertools
import pickle

import requests
import iso8601

mpkocher

// Run with ammonite use amm ExampleCatsMonoid.sc
// import $ivy.`org.typelevel::cats-core:1.0.1`

import cats.implicits._
import cats.instances.all._
import cats.Monoid

// For demonstration purposes, load a file (csv, json) and
// each item can be converted to a record of type R
case class R(name: String, age: Int, favoriteColor: String)

mpkocher

Arch Overview

Core Nouns of the PacBio System

1. Run (often created/edited from SMRT Link RunDesign, stored as XML)
2. CollectionMetadata a Run has a list of Collection (Primary Analysis will convert a CollectionMetadata to a SubreadSet)
3. PacBio DataSets SubreadSet, ReferenceSet, etc... These are thin-ish XML files that have general metadata as well as pointers to 'external resources' (e.g., BAM, Fasta files) and their companion index files.
4. SMRT Link Job A general (async) unit of work to perform operations on PacBio DataSets
5. ** DataStoreFile** a container for output files from a SMRT Link Job and contains metadata, such as file type, size, path. A list of DataStore Files is called a DataStore. This is the core output of SMRT Link Job.
6. ** Report** a Report is general model to capture Report metrics (also referred to as 'Attributes'), Report Tables and Report Plot Groups. A Report is a specific type of DataStoreFile and are used to communicate details of

mpkocher

@ import akka.http.scaladsl.model.Uri 
import akka.http.scaladsl.model.Uri

@ val u = Uri("http://smrtlink-bihourly:8081") 
u: Uri = Uri("http", Authority(NamedHost("smrtlink-bihourly"), 8081, ""), , None, None)

@ val p1 = Uri.Path("root") / "alpha" / "beta" 
p1: Uri.Path = Segment("root", Slash(Segment("alpha", Slash(Segment("beta", )))))

@ val p2 =  p1 / "gamma" 

mpkocher

Manual creation of sending TS

1. Get Failed Job By Id
2. Use pbservice to create a TS failed job request
3. Manually download the TGZ file from the Job UI page or curl
4. Manulally send TGZ file using `tech-support-uploader'

From SL beta.

mpkocher

#!/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__)

mpkocher

#!/usr/bin/env python
import json
import sys
import argparse
import os
import operator


def extract_table_values(dt, column_id):
    for column_d in dt['columns']: