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Laros
lectures
Commits
d9b2388c
Commit
d9b2388c
authored
Sep 25, 2016
by
Laros
Browse files
Added some figures.
parent
b0d0334a
Changes
9
Expand all
Hide whitespace changes
Inline
Side-by-side
lectures/data_sharing/.data_sharing.tex.swp
deleted
100644 → 0
View file @
b0d0334a
File deleted
lectures/data_sharing/data_sharing.tex
View file @
d9b2388c
...
...
@@ -23,26 +23,6 @@
\section
{
Introduction
}
\makeTableOfContents
\begin{pframe}
\begin{figure}
[]
\begin{center}
\includegraphics
[height=0.7\textheight]
{
gq
}
\end{center}
\caption
{}
\label
{}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}
[]
\begin{center}
\includegraphics
[height=0.7\textheight]
{
samples
}
\end{center}
\caption
{}
\label
{}
\end{figure}
\end{pframe}
\subsection
{
Types of variants
}
\begin{pframe}
% Data sharing at the LUMC:
...
...
@@ -50,8 +30,6 @@
% - Variant frequencies.
\end{pframe}
% Issues with sharing frequencies:
% - See VKGL discussion.
\subsection
{
Requirements
}
\begin{pframe}
We aim for a solution that has the following properties:
...
...
@@ -73,6 +51,70 @@
Timestamps are essential for
\emph
{
reproducibility
}
.
\end{pframe}
\begin{pframe}
\begin{figure}
[]
\vspace
{
-0.5cm
}
\begin{center}
\includegraphics
[height=0.8\textheight]
{
gq
}
\end{center}
\vspace
{
-0.3cm
}
\caption
{
Callable region (
$
584
$
--
$
1596
$
).
}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}
[]
\vspace
{
-0.5cm
}
\begin{center}
\includegraphics
[height=0.8\textheight]
{
samples
}
\begin{picture}
(0, 0)
\only
<2>
{
\put
(-45, 9.5)
{
\line
(0, 1)
{
50
}}}
\only
<3>
{
\put
(-23, 9.5)
{
\line
(0, 1)
{
50
}}}
\end{picture}
\end{center}
\vspace
{
-0.3cm
}
\caption
{
Sharing observations is not enough.
}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}
[]
\begin{center}
\Large\texttt
{
TTGAATCCT
\color
{
red
}
TGCTC
\color
{
black
}
TGCGATGGA
}
\end{center}
\caption
{
\bt
{
NM
\_
003002.2:c.262
\_
266del
}
.
}
\end{figure}
\begin{figure}
[]
\begin{center}
\Large\texttt
{
TTGAATCCT
\color
{
red
}
TGCTC
\color
{
black
}
TGCGATGGA
}
\\
\Large\texttt
{
TTGAATCCTT
\color
{
red
}
GCTCT
\color
{
black
}
GCGATGGA
}
\\
\Large\texttt
{
TTGAATCCTTG
\color
{
red
}
CTCTG
\color
{
black
}
CGATGGA
}
\\
\Large\texttt
{
TTGAATCCTTGC
\color
{
red
}
TCTGC
\color
{
black
}
GATGGA
}
\end{center}
%\caption{\bt{NM\_003002.2:c.262\_266del}.}
\end{figure}
\begin{figure}
[]
\begin{center}
\Large\texttt
{
TTGAATCCTTGC
\color
{
red
}
TCTGC
\color
{
black
}
GATGGA
}
\end{center}
\caption
{
\bt
{
NM
\_
003002.2:c.265
\_
269del
}
.
}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}
[]
\begin{center}
Genome
\\
{
\Large\texttt
{
AACTTAGGA
\color
{
red
}
ACGAG
\color
{
black
}
ACGCTACCT
}}
\\
{
\Large\texttt
{
TTGAATCCTTGC
\color
{
red
}
TCTGC
\color
{
black
}
GATGGA
}}
\\
Transcript
\end{center}
\caption
{}
\end{figure}
\end{pframe}
\subsection
{
Options
}
\begin{pframe}
Choices for the database layout:
...
...
lectures/data_sharing/generate.sh
0 → 100644
View file @
d9b2388c
#!/bin/sh
python gq.py
'[(500, 1500)]'
>
gq_1.dat
python gq.py
'[(100, 600), (1000, 1600)]'
>
gq_2.dat
python gq.py
'[(1200, 1800)]'
>
gq_3.dat
lectures/data_sharing/gq.gnp
View file @
d9b2388c
...
...
@@ -8,4 +8,4 @@ set multiplot
set nokey
plot "gq_1.dat" notitle
set style data lines
plot 30 lc 0 lw
8
plot 30 lc 0 lw
10
lectures/data_sharing/gq.py
View file @
d9b2388c
#!/usr/bin/env python
import
random
import
sys
coverage
=
eval
(
sys
.
argv
[
1
])
def
target_coverage
(
position
,
coverage
):
for
c
in
coverage
:
if
c
[
0
]
<=
position
<=
c
[
1
]:
return
45
return
0
y
=
0
for
i
in
range
(
2000
):
y
=
max
(
0
,
y
+
random
.
randint
(
-
1
,
1
))
for
x
in
range
(
2000
):
dy
=
random
.
randint
(
-
1
,
1
)
t
=
target_coverage
(
x
,
coverage
)
if
not
random
.
randint
(
0
,
1
):
if
y
>
t
+
5
:
dy
=
min
(
0
,
dy
)
if
y
<
t
-
5
:
dy
=
max
(
0
,
dy
)
y
=
max
(
0
,
y
+
dy
)
print
y
lectures/data_sharing/gq_1.dat
View file @
d9b2388c
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