terrycojones

                           readStartInSubject              readEndInSubject
                           |                               |
                           |   subjectStart    subjectEnd  |
                           |   |               |           |
    Subject:  .................ACGTAAAGGCTTAGGT.................
    Read:                  ....ACGTAAAGGCTT-GGT............
                               |               |
                               |               |
                               readStart       readEnd

terrycojones

Title: Using the new new code
Date: 2014-08-13 16:08
Category: Tools
Tags: iPython notebook, ipython
Summary: Using the newest code base

terrycojones

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terrycojones

#!/usr/bin/env python

class A(object):
    def __iter__(self):
        yield 'i'
        yield 'am'
        yield 'A'

    def fiddleIter(self):
        def newIter(_):

terrycojones

    def filter(self, **kwargs):
        """
        Update self so that __iter__ returns a generator that yields a filtered
        set of C{ReadAlignments}.

        See self._filter for details of arguments.

        @return: C{self}.
        """
        iterator = self._filter(selfIterator=self.__iter__, **kwargs)

terrycojones

g++   -o cpptraj Action_Angle.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AtomMap.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_CheckStructure.o Action_Contacts.o Action_Closest.o Action_ClusterDihedral.o Action_CreateCrd.o Action_Diffusion.o Action_Dihedral.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_DihedralScan.o Action_DNAionTracker.o Action_DSSP.o Action_FixAtomOrder.o Action_Grid.o Action_GridFreeEnergy.o Action_Hbond.o Action_Image.o Action_Jcoupling.o Action_Mask.o Action_MakeStructure.o Action_Outtraj.o Action_Pairwise.o Action_Principal.o Action_Matrix.o Action_MinDist.o Action_Molsurf.o Action_MultiDihedral.o Action_NAstruct.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Rmsd.o Action_Rotate.o Action_Rotdif.o Action_RunningAvg.o Action_Scale.o Action_STFC_Diffusion.o Action_Strip.o Action_SymmetricRmsd.o Action_Volmap.o Action_Spam.o Action_Surf.o Action_Temperature.o Action_Trans

terrycojones

package AC::Location;

use strict;
use Carp;

# The keys in this array should have nothing but A-Z (and maybe 0-9).
# The values give the canonical display names of places.
#
# Make sure that if you have a value with a hyphen (or other punc)
# that you also have that value without the hyphen as a key (that

terrycojones

package AC::Name;

use AC::Location;

my $thisYearFull = `date +%Y`;
# TODO: fix this on Jan 1st, 2100.
my $thisYear = $thisYearFull - 2000;

my $DEFAULT_SUBTYPE = 'H3N2';

terrycojones

{
    "queries" : [
        [ "mike/rating > 5",
          {
              "ntoll/rating" : {
                  "value" : 6
              },
              "ntoll/seen" : {
                  "value" : true
              }

terrycojones

class ReadHit(object):
    """
    Holds information about a single read hit.

    @param read: A C{Read} instance.
    @param alignments: A C{list} of alignments. Each alignment is a C{dict} of
        the following form:

        {
          "hsps": [