Recent changes to Walkthrough_toy

Walkthrough_toy modified by Robert Kofler

Robert Kofler — Tue, 25 Jul 2017 13:09:15 -0000

--- v4
+++ v5
@@ -1,5 +1,5 @@
 # Introduction
-Despite our best efforts, it may sometimes be unclear how our DSL for describing TE landscape is behaving in detail. In this case you have the option to either contact the author or test the behaviour yourself using toy examples.
+Despite our best efforts, it may sometimes be unclear how our DSL for describing TE landscape is behaving in detail. In this case, you have the option to either contact the author or test the behaviour yourself using toy examples.

 While you are always welcome to contact me (Robert Kofler), evaluating the behaviour of SimulaTE with toy examples has several key advantages:

@@ -10,7 +10,7 @@

 # Walkthrough: behaviour of TSD algorithm
 ## the questions
-In this walkthrough we are interested in the behaviour of the algorithm generating the TSD. In particular we want to find out i) which bases are duplicated and ii) whether child TEs  inherit the TSD of the parent TEs. (Of course these details are also explained in the manual; we use these details solely to demonstrate how to generate toy examples).
+In this walkthrough we are interested in the behaviour of the algorithm generating the TSD. In particular we want to find out i) which bases are duplicated and ii) whether child TEs  inherit the TSD of the parent TEs. (Of course these details are also explained in the manual; we use these walkthrough solely to demonstrate the generation of toy examples).

 ## the toy example

@@ -24,7 +24,7 @@
 7 * child
 ~~~~~

-**Note**: we used a chassis reference genome of "123456789" to facilitate identification of the exact insertion site. Of course,  apart from toy examples a chassis consisting solely of "ATCG" should be
+**Note**: we used a chassis reference genome of "123456789" to facilitate identification of the exact insertion site. Of course,  apart from toy examples a chassis consisting solely of "ATCG" should be used
 **Note** the parent has the sequence *TTT* and a TSD of 2bp is specificed
 **Note** the child has the sequence of the parent and a nested insertion (*CC*) at position 2
 **Note** we generate two sequences; one with the TE *parent* inserted at position 3 and one with the TE *child* inserted at position 7
@@ -47,7 +47,7 @@
 ~~~~~

 These two sequences demonstrate
-* the 3' bases are used for the TSD (the sequence *23* is duplicated)
+* the 5' bases are used for the TSD (the sequence *23* is duplicated)
 * the child inherits the TSD of the parent (the sequence *67* is duplicated, although we did not specifiy a TSD for the *child* TE)

Walkthrough_toy modified by Robert Kofler

Robert Kofler — Wed, 12 Jul 2017 11:45:44 -0000

--- v3
+++ v4
@@ -1,11 +1,11 @@
 # Introduction
-Despite we tried our best it may sometimes not be clear how the DSL of  SimulaTE is behaving. In this case you have the option to either contact the author or evaluate the behaviour using toy examples.
+Despite our best efforts, it may sometimes be unclear how our DSL for describing TE landscape is behaving in detail. In this case you have the option to either contact the author or test the behaviour yourself using toy examples.

 While you are always welcome to contact me (Robert Kofler), evaluating the behaviour of SimulaTE with toy examples has several key advantages:

  * even authors of tools tend to forget details of the implementation; so a response must not necessarily be correct
- * you can answer any questions immediatelly; so no waiting time for author response
- * you gain confidence in the tool (not relying on second hand lore)
+ * you can answer any questions immediatelly; so its not necessary to wait for the author response
+ * you gain confidence in the tool (because you know the behaviour from first hand experience)

 # Walkthrough: behaviour of TSD algorithm

Walkthrough_toy modified by Robert Kofler

Robert Kofler — Wed, 12 Jul 2017 11:40:48 -0000

--- v2
+++ v3
@@ -8,9 +8,9 @@
  * you gain confidence in the tool (not relying on second hand lore)

-# Walkthrough, behaviour of TSD
+# Walkthrough: behaviour of TSD algorithm
 ## the questions
-In this walkthrough we are interested in the behaviour of the TSD. In particular we want to find out which bases are duplicated and if child TEs (using our DSL) inherit the TSD of the parent. Note these things are mentioned in the manual, so this serves merely as an illustration on how to generate toy examples;
+In this walkthrough we are interested in the behaviour of the algorithm generating the TSD. In particular we want to find out i) which bases are duplicated and ii) whether child TEs  inherit the TSD of the parent TEs. (Of course these details are also explained in the manual; we use these details solely to demonstrate how to generate toy examples).

 ## the toy example

@@ -27,11 +27,12 @@
 **Note**: we used a chassis reference genome of "123456789" to facilitate identification of the exact insertion site. Of course,  apart from toy examples a chassis consisting solely of "ATCG" should be
 **Note** the parent has the sequence *TTT* and a TSD of 2bp is specificed
 **Note** the child has the sequence of the parent and a nested insertion (*CC*) at position 2
+**Note** we generate two sequences; one with the TE *parent* inserted at position 3 and one with the TE *child* inserted at position 7

-We generate the population genome file using
+We generate the population genome file using:

 ~~~~~
-python ~/dev/simulate/build-population-genome.py --pgd toy.pgd --output toy.pg
+python build-population-genome.py --pgd toy.pgd --output toy.pg
 ~~~~~

@@ -45,8 +46,8 @@
 1234567AACCA6789
 ~~~~~

-This demonstrates:
-* the 3' bases are used for the TSD
-* the child inherits the TSD of the parent (i.e. 2bp TSD)
+These two sequences demonstrate
+* the 3' bases are used for the TSD (the sequence *23* is duplicated)
+* the child inherits the TSD of the parent (the sequence *67* is duplicated, although we did not specifiy a TSD for the *child* TE)

Walkthrough_toy modified by Robert Kofler

Robert Kofler — Wed, 12 Jul 2017 10:36:32 -0000

--- v1
+++ v2
@@ -9,10 +9,44 @@

 # Walkthrough, behaviour of TSD
-## Questions
+## the questions
 In this walkthrough we are interested in the behaviour of the TSD. In particular we want to find out which bases are duplicated and if child TEs (using our DSL) inherit the TSD of the parent. Note these things are mentioned in the manual, so this serves merely as an illustration on how to generate toy examples;

 ## the toy example

-We construct a pgd-file that can answer our question
+To answer our question we create the following pgd file

+~~~~~
+chassis="123456789"
+parent="TTT"+2bp
+child=parent-{2:"CC"}
+3 parent *
+7 * child
+~~~~~
+
+**Note**: we used a chassis reference genome of "123456789" to facilitate identification of the exact insertion site. Of course,  apart from toy examples a chassis consisting solely of "ATCG" should be
+**Note** the parent has the sequence *TTT* and a TSD of 2bp is specificed
+**Note** the child has the sequence of the parent and a nested insertion (*CC*) at position 2
+
+We generate the population genome file using
+
+~~~~~
+python ~/dev/simulate/build-population-genome.py --pgd toy.pgd --output toy.pg
+~~~~~
+
+
+## the result
+Following the output (e.g. *less toy.pg*)
+
+~~~~~
+>hg1
+123TTT23456789
+>hg2
+1234567AACCA6789
+~~~~~
+
+This demonstrates:
+* the 3' bases are used for the TSD
+* the child inherits the TSD of the parent (i.e. 2bp TSD)
+
+

Walkthrough_toy modified by Robert Kofler

Robert Kofler — Wed, 12 Jul 2017 10:16:16 -0000

Introduction

Despite we tried our best it may sometimes not be clear how the DSL of SimulaTE is behaving. In this case you have the option to either contact the author or evaluate the behaviour using toy examples.

While you are always welcome to contact me (Robert Kofler), evaluating the behaviour of SimulaTE with toy examples has several key advantages:

even authors of tools tend to forget details of the implementation; so a response must not necessarily be correct
you can answer any questions immediatelly; so no waiting time for author response
you gain confidence in the tool (not relying on second hand lore)

Walkthrough, behaviour of TSD

Questions

In this walkthrough we are interested in the behaviour of the TSD. In particular we want to find out which bases are duplicated and if child TEs (using our DSL) inherit the TSD of the parent. Note these things are mentioned in the manual, so this serves merely as an illustration on how to generate toy examples;

the toy example

We construct a pgd-file that can answer our question