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import re

FS_RE = "{([GMkp]{0,1})(:)([\.,]{0,1})([0-9]*)([dfg]{1})}(.*)$"
def format_metric(format_str, value):
    """
    Format a report metric (attribute or table column value) according to our
    in-house rules.  These resemble Python format strings (plus optional
    suffix), but with the addition of optional scaling flags.
    """
    if value is None:

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{
  "namespace": "com.pacbio.common.models.datastore",
  "type": "record",
  "name": "DataStoreViewRule",
  "fields": [
    {
      "name": "id",
      "type": "string",
      "desc": "Corresponds to sourceId in datastore, e.g. pbalign.tasks.pbalign-
out-0"

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import scopt.OptionParser

case class BaseConfig(host: String, port: Int)


trait BaseParser { self: OptionParser[BaseConfig] =>
  opt[String]("host") action { (x, c) =>
    c.copy(host = x)
  } text "Hostname of smrt server"

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#!/usr/bin/env python

import json

from pbcommand.models.report import Attribute, Report


class MetaAttribute(object):
    def __init__(self, id_, name, description, type_):
        self.id = id_

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Python 2.7.9 (default, May 31 2015, 05:04:28)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from pbcommand.pb_io.report import load_report_from_json
>>> rpt_old = load_report_from_json("/pbi/dept/secondary/siv/smrtlink/smrtlink-alpha/smrtsuite/userdata/jobs_root/000/000212/tasks/pbreports.tasks.amplicon_analysis_consensus-0/consensus_report.json")
>>> rpt_new = load_report_from_json("/pbi/dept/secondary/siv/smrtlink/smrtlink-alpha/smrtsuite/userdata/jobs_root/000/000215/tasks/pbreports.tasks.amplicon_analysis_consensus-0/consensus_report.json")
>>> table_old = rpt_old.tables[0]
>>> table_new = rpt_new.tables[0]
>>> table_old.columns
[<Column id:barcodename header:Barcode nvalues:370 >, <Column id:coarsecluster header:Sequence Cluster nvalues:370 >, <Column id:phase header:Sequence Phase nvalues:370 >, <Column id:sequencelength header:Length (bp) nvalues:370 >, <Column id:predictedaccuracy header:Estimated Accuracy nvalues:370 >, <Column id:totalcoverage heade

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{"num_polyA_seen": 13, "num_filtered_short_reads": 0, "num_flnc_bases": 35563, "num_3_seen": 13, "num_reads": 22, "num_nflc": null, "num_fl": 9, "num_nflnc": null, "num_flnc": 9, "num_flc": 0, "num_5_seen": 11, "num_nfl": 13}