Tag Archives: Programming

absee has underwent a lot of structural changes.

First, it only retrieves the information you want instead of returning all traces and called bases.
Second, it’s a class now, so you can hold onto multiple sequencing data.
Third, it now has quality scores.

%irb
>> require ‘absee’
=> true
>> my_variable = ABSee.new()
=> #<ABSee:0x000001008599d0>
>> my_variable.read("/Users/Jenny/Desktop/my_sequence.ab1")
=> nil
>> my_variable.get_calledSequence()

Class Methods

read(file_location)
- returns nil
get_traceA()
- returns an array with the trace data for adenine
get_traceG()
- returns an array with the trace data for guanine
get_traceC()
- returns an array with the trace data for cytosine
get_traceT()
- returns an array with the trace data for thymine
get_calledSequence()
- returns an array with the Basecalled sequence
get_qualityScores()
- returns an array with the Basecalled quality scores
get_peakIndexes()

absee Module

November 14, 2012

Coding Bits, Iron Chef SynBio

Graphviz + SBOLv1.0

September 8, 2012

Coding Bits, Iron Chef SynBio

1 Comment

Update:

Graphviz now has SBOLv 1.0 support!

I implemented the Synthetic Biology Open Language (SBOLv) symbols for Graphviz to easily generate SBOLv compliant diagrams.

see my original post on using Graphviz to draw genetic circuits

Gene Expression Symbols:

digraph G {
rankdir=LR;

promoter -> operator [arrowhead=none];
operator -> cds [arrowhead=none];
cds -> utr [arrowhead=none];
utr -> terminator [arrowhead=none];

promoter [shape=promoter labelloc="b"];
operator [shape=square width=0.2 label=""];
cds [shape=cds];
utr [shape=utr labelloc="b"];
terminator [shape=terminator labelloc="b"];

}

digraph G {
rankdir=LR;

insulator -> ribosite [arrowhead=none];
ribosite -> rnastab [arrowhead=none];
rnastab -> proteasesite [arrowhead=none];
proteasesite -> proteinstab [arrowhead=none];

insulator [shape=insulator label=""];
ribosite [shape=ribosite label="ribonuclease site" labelloc="b"];
rnastab [shape=rnastab label="rna stability" labelloc="b"];
proteasesite [shape=proteasesite label="protease site" labelloc="b"];
proteinstab [shape=proteinstab label="protein stability" labelloc="b"];

}

DNA Construction Symbols:

digraph G {
rankdir=LR;

origin -> primersite [arrowhead=none];
primersite -> restrictionsite [arrowhead=none];
restrictionsite -> noverhang [arrowhead=none];
noverhang -> assembly [arrowhead=none];

origin [shape=circle width=0.2 label=""];
primersite [shape=primersite label="primer site" labelloc="b"];
restrictionsite [shape=restrictionsite label="restriction site" labelloc="b"];
noverhang [shape=noverhang label=""];
assembly [shape=assembly label=""];

}

digraph G {
rankdir = LR;

fivepoverhang -> signature [arrowhead=none];
signature -> threepoverhang [arrowhead=none];

fivepoverhang [shape=fivepoverhang label=""];
signature [shape=signature];
threepoverhang [shape=threepoverhang label=""];

}

Download:

Download from the official Graphviz site

All the development snapshots newer than 2.29.20120924 should have SBOLv compliant symbols, as well as the non-SBOLv circuit symbols (lpromoter, rarrow, etc.).

Example Diagrams:


digraph a {
rankdir=LR;

subgraph cluster0 {
color=gray;
style=filled;
node [style=filled fillcolor=white];
a -> b [arrowhead=none];
b -> c [arrowhead=none];
}

a [shape=promoter label=""];
b [shape=cds label="rtTA"];
c [shape=terminator label=""];

Dox -> rtTA;
b -> rtTA;

subgraph cluster1 {
color=gray;
style=filled;
node [style=filled fillcolor=white];
d -> e [arrowhead=none];
e -> f [arrowhead=none];
}

d [shape=promoter label=""];
e [shape=cds label="Alfa"];
f [shape=terminator label=""];

rtTA -> d;
e -> Alfa;

subgraph cluster2 {
color=gray;
style=filled;
node [style=filled fillcolor=white];
g -> h [arrowhead=none];
h -> i [arrowhead=none];
}

g [shape=promoter label=""];
h [shape=cds label="Alfa"];
i [shape=terminator label=""];

Alfa -> g;
h -> Alfa;

}

digraph G {
rankdir=LR;

subgraph cluster0 {
color=gray;
style=filled;
node [style=filled fillcolor=white];
a -> b [arrowhead=none];
b -> c [arrowhead=none];
c -> d [arrowhead=none];
}

a [shape=promoter label=""];
b [shape=cds label="rtTA"];
c [shape=cds label="LacI"];
d [shape=terminator label=""];

Dox -> rtTA;
b -> rtTA;

subgraph cluster1 {
color=gray;
style=filled;
node [style=filled fillcolor=white];
e -> f [arrowhead=none];
f -> g [arrowhead=none];
g -> h [arrowhead=none];
}

e [shape=promoter label=""];
f [shape=cds label="Charlie"];
g [shape=cds label="Alfa"];
h [shape=terminator label=""];

rtTA -> e;

c -> LacI;
IPTG -> LacI [arrowhead=tee];

subgraph cluster2 {
color=gray;
style=filled;
node [style=filled fillcolor=white];
i -> j [arrowhead=none];
j -> k [arrowhead=none];
k -> l [arrowhead=none];
}

i [shape=promoter label=""];
j [shape=cds label="India"];
k [shape=cds label="Bravo"];
l [shape=terminator label=""];

LacI -> i [arrowhead=tee];

f -> Charlie;
g -> Alfa;
j -> India;
k -> Bravo;

subgraph cluster3 {
color=gray;
style=filled;
node [style=filled fillcolor=white];
m -> n [arrowhead=none];
n -> o [arrowhead=none];
o -> p [arrowhead=none];
}

m [shape=promoter label=""];
n [shape=cds label="Charlie"];
o [shape=cds label="Alfa"];
p [shape=terminator label=""];

n -> Charlie;
o -> Alfa;
Alfa -> m;

subgraph cluster4 {
color=gray;
style=filled;
node [style=filled fillcolor=white];
q -> r [arrowhead=none];
r -> s [arrowhead=none];
s -> t [arrowhead=none];
t -> u [arrowhead=none];
}

q [shape=promoter label=""];
r [shape=cds label="India"];
s [shape=cds label="Bravo"];
t [shape=cds label="EYFP"];
u [shape=terminator label=""];

r -> India;
s -> Bravo;
t -> EYFP;

subgraph cluster5 {
color=gray;
style=filled;
node [style=filled fillcolor=white];
v -> w [arrowhead=none];
w -> x [arrowhead=none];
}

v [shape=promoter label=""];
w [shape=cds label="Hotel"];
x [shape=terminator label=""];

Charlie -> v [arrowhead=tee];
w -> Hotel;

subgraph cluster6 {
color=gray;
style=filled;
node [style=filled fillcolor=white];
y -> z [arrowhead=none];
z -> aa [arrowhead=none];
}

y [shape=promoter label=""];
z [shape=cds label="Foxtrot"];
aa [shape=terminator label=""];

Hotel -> y [arrowhead=tee];
India -> y [arrowhead=tee];

z -> Foxtrot;

subgraph cluster7 {
color=gray;
style=filled;
node [style=filled fillcolor=white];
bb -> cc [arrowhead=none];
cc -> dd [arrowhead=none];
dd -> ee [arrowhead=none];
}

bb [shape=promoter label=""];
cc [shape=cds label="EBFP2"];
dd [shape=cds label="Foxtrot"];
ee [shape=terminator label=""];

Foxtrot -> bb;
dd -> Foxtrot;

cc -> EBFP2;

}

Caveats:

Color and labelling doesn’t work as nicely as the non-SBOLv symbols.

Labels that include a double-stranded DNA line, such as the promoter, has to have labelloc set to “b”. This is to avoid the intersection of the label and the double-stranded DNA line, since labels are automatically placed in the center of the nodes.


Hef1a [shape=promoter];


Hef1a [shape=promoter labelloc="b"];

Also, for the aforementioned shapes, colorfill has to be specified instead of color. color will color the outline of the node shape, potentially causing non-consistent colorations of the double-stranded DNA line between connected nodes.


Hef1a [shape=promoter labelloc="b" style=filled colorscheme=greens3 color=3];


Hef1a [shape=promoter labelloc="b" style=filled colorscheme=greens3 fillcolor=3];

Acknowledgements:

Thanks to Reshma Shetty and Jake Beal for the inspiration.

easy as absee

April 25, 2012

Coding Bits, Iron Chef SynBio

Leave a comment

1. Introduction

absee is a friendly ABIF reader in Ruby.

Three years ago, I desperately needed to analyze the trace values from DNA sequencing chromatograms (in the form of ABIF files). To my frustration, none of the available ABIF readers exported raw data. Even today, while lots of software are able to visualize ABIF files, very few allow for scripted inputs and custom manipulation of outputs. I want a ABIF reader that simply extracts the data and can be easily incorporated into other projects. Hence, I created absee.

absee is a Ruby gem. It has no GUI, no fluff. It simply reads the ABIF files and returns the values in six arrays, an array for each of the trace data for ACGT at discreet intervals, a called sequence, and an array of peak indexes corresponding to the called sequence.

% irb
>> require 'absee'
=> true
>> readAB("my_sequence.ab1")

With a simple Ruby script, it can be incorporated to rapidly read and process many ABIF files and pipe the data for further downstream processing. absee is a very nifty tool, one that I wish I had three years ago. The above code works for versions less than 0.1.0.0.

[update: new version as a Ruby Module]

2. Background

ABIF is a binary file format, usually with an .ab1 extension. It contains a trace value for A, C, G, and T at each point for a interval. Most ABIF viewing software will interpolate those values at the points to display sinusoidal lines.

ABIF files also contain estimated bases and peak indexes. The way DNA sequencing extracts a sequence from from trace data is to use a base-calling algorithm. The base-calling algorithm will estimate a peak in the trace data and determine a called-base for the peak. If peaks from more than one trace overlap and their values are sufficiently close, the algorithm may use N to denote uncertainty of the base for that peak, and lower the quality score. The sequence of called-bases is the estimated DNA sequence corresponding to a chromatogram.

3. Details

Converting from the ABIF binary files to readable values was no small feat. Even with its file format architecture ready, I still needed a little guidance. I found an open-source ABIF viewer years ago (now no longer available) and translated absee from its ABIF reader.

The primary method to call is readAB. It opens the ABIF file, checking the filetype and version. Major ABIF versions greater than 1 are not supported, due to possible different encodings. If the check fails, readAB will return six empty arrays.

readAB(filename)

parameters:
returns:

There’s more documentation in absee‘s yardoc / RDoc, as well as the source code on github.

4. Source Code

The source code for version 0.0.2.3 can be found at the absee github repository.

—Caret Dash Caret

^-^

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Tag Archives: Programming

absee 1.0

absee Module

Graphviz + SBOLv1.0

easy as absee