New upstream version 0.6.1+git20180425.27a1878

SHELL = /bin/bash -e

utest:

	PYTHONPATH=.:${PYTHONPATH} py.test -s -v test/test_internal.py

all: build install

build:

test: tests

check: tests

tests: cram-tests unit-tests extra-tests

tests: cram-tests py-tests extra-tests

cram-tests:

	cram --xunit-file=cramtests.xml test/cram/*.t

long-tests:

	cram test/cram/long_running/*.t

unit-tests:

	nosetests -s -v --with-xunit test/*.py

py-tests:

	#nosetests -s -v --with-xunit test/*.py

	py.test -s -v --junit-xml=nosetests.xml test/*.py

extra-tests:

	cram --xunit-file=cramtests-extra.xml test/cram/extra/*.t

Documentation:

 * [Tool documentation](http://github.com/PacificBiosciences/kineticsTools/blob/master/doc/manual.rst)

 * [Methods description](http://github.com/PacificBiosciences/kineticsTools/blob/master/doc/whitepaper/kinetics.pdf)

DISCLAIMER

----------

THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.

#!/bin/bash -ex

NX3PBASEURL=http://nexus/repository/unsupported/pitchfork/gcc-6.4.0

export PATH=$PWD/build/bin:/mnt/software/a/anaconda2/4.2.0/bin:$PWD/bin:$PATH

export PYTHONUSERBASE=$PWD/build

export CFLAGS="-I/mnt/software/a/anaconda2/4.2.0/include"

PIP="pip --cache-dir=$bamboo_build_working_directory/.pip"

type module >& /dev/null || . /mnt/software/Modules/current/init/bash

module load gcc

rm -rf   build

mkdir -p build/bin build/lib build/include build/share

$PIP install --user \

  iso8601

$PIP install --user \

  $NX3PBASEURL/pythonpkgs/xmlbuilder-1.0-cp27-none-any.whl \

  $NX3PBASEURL/pythonpkgs/tabulate-0.7.5-cp27-none-any.whl \

  $NX3PBASEURL/pythonpkgs/pysam-0.13-cp27-cp27mu-linux_x86_64.whl \

  $NX3PBASEURL/pythonpkgs/avro-1.7.7-cp27-none-any.whl

$PIP install --user -e repos/pbcommand

$PIP install --user -e repos/pbcore

$PIP install --user -r requirements-ci.txt

$PIP install --user -r requirements-dev.txt

$PIP install --user --no-index $PWD

make test

from __future__ import print_function

#################################################################################

# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.

#

    def run(self):

        import time

        print "self.arr[10] = %f, Process = %s" % (self.arr[10], current_process())

        print("self.arr[10] = %f, Process = %s" % (self.arr[10], current_process()))

        print self.arr.shape

        print(self.arr.shape)

        n = self.arr.shape[0] - 1

        print "self.arr[%d] = %f, Process = %s" % (n, self.arr[n], current_process())

        print("self.arr[%d] = %f, Process = %s" % (n, self.arr[n], current_process()))

        time.sleep(10)

#################################################################################

from __future__ import print_function

import cProfile

from pbcore.io import GffReader, Gff3Record

import os

                if field == 'sequence-header':

                    [internalTag, delim, externalTag] = value.strip().partition(' ')

                    self.seqMap[internalTag] = externalTag

                print >>summaryWriter, line.strip()

                print(line.strip(), file=summaryWriter)

                continue

            if inHeader:

                # We are at the end of the header -- write the tool-specific headers

                for field in headers:

                    print >>summaryWriter, ("##%s %s" % field)

                    print(("##%s %s" % field), file=summaryWriter)

                inHeader = False

            # Parse the line

                rec.modsfwd = strand0Hits

                rec.modsrev = strand1Hits

                print >>summaryWriter, str(rec)

                print(str(rec), file=summaryWriter)

if __name__ == "__main__":

    kt = ModificationSummary()