terrycojones

class FakeCursor(object):
    def close(self):
        pass

class FakeDbConnection(object):
    def __init__(self, result):
        self._result = result

    def cursor(self):
        return FakeCursor()

terrycojones

1: count=  67, len=   3620, min(e)=                 0.0 median(e)=         1.31674e-63: gi|6561412|gb|AF191073.1|AF191073 Stealth virus 1 clone 3B43, genomic sequence
  2: count=  31, len=    814, min(e)=        2.04982e-153 median(e)=         1.56463e-48: gi|6957471|gb|AF065755.1|AF065755 Stealth virus 1 clone 3B43 T3
  3: count=   7, len=    836, min(e)=         1.70374e-79 median(e)=         4.20903e-35: gi|6940537|gb|AF065756.1|AF065756 Stealth virus 1 clone 3B43 T7
  4: count=   6, len=    290, min(e)=         6.41028e-62 median(e)=        3.398355e-61: gi|38569384|gb|AY397620.1| Bluetongue virus isolate 10 5' UTR
  5: count=  12, len=    193, min(e)=         1.91051e-37 median(e)=        2.744805e-37: gi|84579786|dbj|AB214978.1| Human picobirnavirus pseudogene for RNA-dependent RNA polymerase
  6: count=  18, len= 104710, min(e)=         1.33442e-23 median(e)=        1.571805e-23: gi|84683224|gb|DQ333351.1| Choristoneura occidentalis granulovirus, complete genome
  7: count=   8, len=   1923, min(e)=   

terrycojones

Keybase proof

I hereby claim:

• I am terrycojones on github.
• I am terrycojones (https://keybase.io/terrycojones) on keybase.
• I have a public key whose fingerprint is DA37 724E D2C7 CF8A E792 99A9 F18B DFFA 72B5 F70B

To claim this, I am signing this object:

terrycojones

16SMicrobial: 2.21 MB (1 parts)
cdd_delta: 873.31 MB (1 parts)
env_nr: 0.99 GB (2 parts)
env_nt: 3.06 GB (4 parts)
est: 284 B (1 parts)
est_human: 1.26 GB (2 parts)
est_mouse: 682.56 MB (1 parts)
est_others: 9.52 GB (11 parts)
gss: 6.57 GB (7 parts)
gss_annot: 36.39 MB (1 parts)

terrycojones

#!/usr/bin/env python

import os
from collections import defaultdict


def parseColors(colors):
    """
    Parse read id color specification.

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": [

terrycojones

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

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

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

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