Recent changes to GeneratingSimpleHaplotypes

GeneratingSimpleHaplotypes modified by Christos Vlachos

Christos Vlachos — Tue, 03 Jul 2018 10:09:26 -0000

--- v13
+++ v14
@@ -1,7 +1,7 @@
 [TOC]
 #1 Introduction

-We provide some Python scripts that allow to generate very simple haplotypes that could be used as input for MimicrEE2.
+We provide some Python scripts that allow generating very simple haplotypes that could be used as input for MimicrEE2.
 For simulating more realistic haplotypes that take the actual recombination rate and complex demographic scenarios into account we refer to the next tutorial  [GeneratingHaplotypesWithFastsimcoal].
 Alternatively it is also possible to use real haplotypes that have been inferred from sequencing multiple individuals of a population [UsingExistingHaplotypesEgDGRP]

GeneratingSimpleHaplotypes modified by Christos Vlachos

Christos Vlachos — Wed, 27 Jun 2018 10:08:06 -0000

--- v12
+++ v13
@@ -2,15 +2,15 @@
 #1 Introduction

 We provide some Python scripts that allow to generate very simple haplotypes that could be used as input for MimicrEE2.
-For simulating more realistic haplotypes that take the actual recombination rate and complex demographic scenarious into account we refer to the next tutorial  [GeneratingHaplotypesWithFastsimcoal].
-Alternatively it is also possible to use real haplotypes that have been inferred from sequencing multiple individuals of a popualtion [UsingExistingHaplotypesEgDGRP]
+For simulating more realistic haplotypes that take the actual recombination rate and complex demographic scenarios into account we refer to the next tutorial  [GeneratingHaplotypesWithFastsimcoal].
+Alternatively it is also possible to use real haplotypes that have been inferred from sequencing multiple individuals of a population [UsingExistingHaplotypesEgDGRP]

 #2 Very simple haplotypes

  First download the script: https://sourceforge.net/projects/mimicree2/files/scripts/simple-haplotype.py/download
- This script allows to simulate the genomes for a population consisting of two haploytpes. All SNPs are completly linked.
+ This script allows to simulate the genomes for a population consisting of two haplotypes. All SNPs are completely linked.

  The script accepts the following parameters

@@ -18,9 +18,9 @@
   * --S sites (number of SNPs)
   * --chr-name the name of the chromosome
   * --chr-len the length of the chromosome
-  * --freq the frequency of haploytpe derived allele; the ancestral allele will have the frequency= 1.0-freq
+  * --freq the frequency of haplotype derived allele; the ancestral allele will have the frequency= 1.0-freq
   * --haploid simulate haploids
-  *  --hardy-weinberg simulat the diploids in Hardy-Weinberg equilibrium
+  *  --hardy-weinberg simulate the diploids in Hardy-Weinberg equilibrium

 ## diploids
@@ -94,7 +94,7 @@

 #3 Haplotypes based on a given SFS
 We provide a script that generated haplotypes based on a site frequency spectrum (sfs). 
-The alleles are distributed randomly among haplotypes thus the SNPs are mostly in linkage equilibrium (except for random LD). In case more realistic haplotypes taking popualtion history the recombination rate and many other parameters into account we refer to the next tutorial  [GeneratingHaplotypesWithFastsimcoal] 
+The alleles are distributed randomly among haplotypes thus the SNPs are mostly in linkage equilibrium (except for random LD). In case more realistic haplotypes taking population history the recombination rate and many other parameters into account we refer to the next tutorial  [GeneratingHaplotypesWithFastsimcoal] 

 The script accepts the following parameters

@@ -115,11 +115,11 @@

  * 0.00 - 0.25: with a relative abundance of 10 most SNPs (10 out of 13; where 13=10+1+1+1) will be in this frequency class 
  * 0.25 - 0.50: with a relative abundance of 1 only 1/13 SNPs will be in this class
- * 0.50 - 0.75: with a relative abundanc of 1 only 1/13 SNPs will be in this category
- * 0.75 - 1.0: with a relative abundace of 1 only 1/13 SNPs will be in this category
+ * 0.50 - 0.75: with a relative abundance of 1 only 1/13 SNPs will be in this category
+ * 0.75 - 1.0: with a relative abundance of 1 only 1/13 SNPs will be in this category

 ## example equal distribution
-When only a single frequency class is provided each population frequency has an equal probability (uniform distriubtio of population frequencies).
+When only a single frequency class is provided each population frequency has an equal probability (uniform distriubtion of population frequencies).
 For example given the command:

 ~~~~~~

GeneratingSimpleHaplotypes modified by Robert Kofler

Robert Kofler — Mon, 25 Jun 2018 14:22:43 -0000

--- v11
+++ v12
@@ -1,12 +1,12 @@
 [TOC]
-# Introduction
+#1 Introduction

 We provide some Python scripts that allow to generate very simple haplotypes that could be used as input for MimicrEE2.
 For simulating more realistic haplotypes that take the actual recombination rate and complex demographic scenarious into account we refer to the next tutorial  [GeneratingHaplotypesWithFastsimcoal].
 Alternatively it is also possible to use real haplotypes that have been inferred from sequencing multiple individuals of a popualtion [UsingExistingHaplotypesEgDGRP]

-## Very simple haplotypes
+#2 Very simple haplotypes

  First download the script: https://sourceforge.net/projects/mimicree2/files/scripts/simple-haplotype.py/download
@@ -23,7 +23,7 @@
   *  --hardy-weinberg simulat the diploids in Hardy-Weinberg equilibrium

-### Diploids
+## diploids

 Diploid genomes may be obtained with the following command 
 ~~~~~~
@@ -46,7 +46,7 @@
 ~~~~~~

-### Haploids
+## haploids

 Haploid genomes can be simulated with the following command
 ~~~~~
@@ -69,7 +69,7 @@
 ~~~~~

-### Diploids in Hardy-Weinberg equilibrium
+## diploids in Hardy-Weinberg equilibrium
 Finally it is possible to simulate diploid haplotypes in Hardy-Weinberg equilibrium with the following command.

 ~~~~~
@@ -92,7 +92,7 @@

-## Haplotypes based on a given SFS
+#3 Haplotypes based on a given SFS
 We provide a script that generated haplotypes based on a site frequency spectrum (sfs). 
 The alleles are distributed randomly among haplotypes thus the SNPs are mostly in linkage equilibrium (except for random LD). In case more realistic haplotypes taking popualtion history the recombination rate and many other parameters into account we refer to the next tutorial  [GeneratingHaplotypesWithFastsimcoal] 

@@ -107,7 +107,7 @@

 Download the script here https://sourceforge.net/projects/mimicree2/files/scripts/sfs-haplotype.py/download

-### sfs
+## sfs
 The --sfs is a comma separated list. Each value (integer or float) represents the relative abundance of a site population frequency class.

 This is best explained using an example:
@@ -118,7 +118,7 @@
  * 0.50 - 0.75: with a relative abundanc of 1 only 1/13 SNPs will be in this category
  * 0.75 - 1.0: with a relative abundace of 1 only 1/13 SNPs will be in this category

-### example equal distribution
+## example equal distribution
 When only a single frequency class is provided each population frequency has an equal probability (uniform distriubtio of population frequencies).
 For example given the command:

@@ -143,7 +143,7 @@
 ~~~~~~

-### example skewed sfs
+## example skewed sfs
 We may obtain a sfs that follows the neutral expectations 1/x 
 using a command like the following

@@ -165,7 +165,7 @@
 2L 955 G   G/A GG GG GG GG GG GG GG GG GG GA
 ~~~~~

-### example skewed sfs for haploids
+## example skewed sfs for haploids
 This script also works for haploids
 Given the command:

GeneratingSimpleHaplotypes modified by Robert Kofler

Robert Kofler — Thu, 21 Jun 2018 09:34:14 -0000

--- v10
+++ v11
@@ -93,7 +93,8 @@

 ## Haplotypes based on a given SFS
-We provide a script that generated haplotypes based on a site frequency spectrum (sfs). The alleles are distributed randomly among haplotypes thus the SNPs are mostly in linkage equilibrium (except for random LD). In case more realistic haplotypes taking popualtion history the recombination rate and many other parameters into account we refer to the next tutorial  [GeneratingHaplotypesWithFastsimcoal] 
+We provide a script that generated haplotypes based on a site frequency spectrum (sfs). 
+The alleles are distributed randomly among haplotypes thus the SNPs are mostly in linkage equilibrium (except for random LD). In case more realistic haplotypes taking popualtion history the recombination rate and many other parameters into account we refer to the next tutorial  [GeneratingHaplotypesWithFastsimcoal] 

 The script accepts the following parameters

@@ -103,6 +104,8 @@
 * --chr-len the length of the chromosome
 * --haploid simulate haploids
 * --sfs the site frequency spectrum; for example possible arguments are "10,8,7,5,1,1,1,4" or "1,1,1,1,10" or "1,10"
+
+Download the script here https://sourceforge.net/projects/mimicree2/files/scripts/sfs-haplotype.py/download

 ### sfs
 The --sfs is a comma separated list. Each value (integer or float) represents the relative abundance of a site population frequency class.

GeneratingSimpleHaplotypes modified by Robert Kofler

Robert Kofler — Thu, 21 Jun 2018 08:27:56 -0000

--- v9
+++ v10
@@ -162,3 +162,27 @@
 2L 955 G   G/A GG GG GG GG GG GG GG GG GG GA
 ~~~~~

+### example skewed sfs for haploids
+This script also works for haploids
+Given the command:
+
+~~~~~~
+python sfs-haplotype.py --chr-name 2L --chr-len 1000 --S 10 --N 10 --sfs 10,3,2,1,1,1 --haploid
+~~~~~~
+
+We for example obtain
+
+~~~~~
+2L 146 G   G/A A A A G G G A G G A
+2L 156 G   G/A G G G G A G G G G G
+2L 177 G   G/A G G G G A G G G G A
+2L 305 G   G/A G A G G G G G G G G
+2L 320 G   G/A G G G G G G G G A G
+2L 755 G   G/A G G G G G A G G G G
+2L 816 G   G/A G G G G G A A G G G
+2L 867 G   G/A A G G G G G G G G G
+2L 894 G   G/A G G G G G G G G A A
+2L 901 G   G/A G G G G G A G G G G
+~~~~~
+
+

GeneratingSimpleHaplotypes modified by Robert Kofler

Robert Kofler — Thu, 21 Jun 2018 08:25:33 -0000

--- v8
+++ v9
@@ -115,3 +115,50 @@
  * 0.50 - 0.75: with a relative abundanc of 1 only 1/13 SNPs will be in this category
  * 0.75 - 1.0: with a relative abundace of 1 only 1/13 SNPs will be in this category

+### example equal distribution
+When only a single frequency class is provided each population frequency has an equal probability (uniform distriubtio of population frequencies).
+For example given the command:
+
+~~~~~~
+python sfs-haplotype.py --chr-name 2L --chr-len 1000 --S 10 --N 10 --sfs 1
+~~~~~~
+**Note** --sfs 1  specifies a single frequency class: 0.0 - 1.0; Within the class each population frequency has an equal probability of being randomly picked.
+
+We obtain the following output:
+
+~~~~~~
+2L 62  G   G/A AG GG GA GA GA GA GG GG GG AA
+2L 118 G   G/A AG AA AA AA GG AG AG GA GA GA
+2L 126 G   G/A AA GA AG AA GA AA AA AA AA AA
+2L 224 G   G/A GA GG GG GG GG GG GA GG GG AG
+2L 256 G   G/A AA GA AA GG GA GA GA AG GA GA
+2L 508 G   G/A AA AA GG AA GA AA AA AA AG AA
+2L 693 G   G/A GG GG GG GG GG GG GG GG GA GG
+2L 758 G   G/A GG AG GG GA GA GG GG GA GG GG
+2L 780 G   G/A GA GA AG GG GG AA AA AG AG GG
+2L 862 G   G/A GG GA GG GG GG GG GG GG GG GG
+~~~~~~
+
+
+### example skewed sfs
+We may obtain a sfs that follows the neutral expectations 1/x 
+using a command like the following
+
+~~~~~~
+python sfs-haplotype.py --chr-name 2L --chr-len 1000 --S 10 --N 10 --sfs 10,5,3.3,2.5,2,1.67,1.43,1.25,1.1,1
+~~~~~~
+
+which for example gives:
+~~~~~
+2L 31  G   G/A AA AG GA GA GA GG GA GG GG GG
+2L 274 G   G/A GG GG GG GG GA GG GA AG GG GA
+2L 310 G   G/A AG GG GG GA AG AG GG GG GG AG
+2L 517 G   G/A GG GG GG GG GG GG AG GG GG GA
+2L 631 G   G/A GG GG GG GG AG GG AG GG AA GG
+2L 752 G   G/A AG GG GA AG AG GG GA GG AA GA
+2L 764 G   G/A GG GG AG GG GG GG AG AG GG GG
+2L 770 G   G/A GG GG GG GG AA GG GG GG GG GA
+2L 914 G   G/A GA AG AA AG AA AG GG AG AA GA
+2L 955 G   G/A GG GG GG GG GG GG GG GG GG GA
+~~~~~
+

GeneratingSimpleHaplotypes modified by Robert Kofler

Robert Kofler — Wed, 20 Jun 2018 16:04:49 -0000

--- v7
+++ v8
@@ -92,8 +92,8 @@

-## Simple haplotypes based on a provided SFS
-We provide a script that generated haplotypes based on a site frequency spectrum (sfs). The alleles are distributed randomly among haplotypes thus the SNPs are mostly in linkage equilibrium (except for random LD).
+## Haplotypes based on a given SFS
+We provide a script that generated haplotypes based on a site frequency spectrum (sfs). The alleles are distributed randomly among haplotypes thus the SNPs are mostly in linkage equilibrium (except for random LD). In case more realistic haplotypes taking popualtion history the recombination rate and many other parameters into account we refer to the next tutorial  [GeneratingHaplotypesWithFastsimcoal] 

 The script accepts the following parameters

GeneratingSimpleHaplotypes modified by Robert Kofler

Robert Kofler — Wed, 20 Jun 2018 10:56:26 -0000

--- v6
+++ v7
@@ -109,6 +109,9 @@

 This is best explained using an example:
 Assuming  **--sfs "10,1,1,1"** the population frequency of the SNPs is provided for  4 different frequency classes:
-* 0.00 - 0.25: with a relative abundance of 10 most SNPs (10 out of 13; where 13=10+1+1+1) will be in this class 
-* 0.25 - 0.50: with a relative abundance of 1 only 1/13 SNPs will be in this class

+ * 0.00 - 0.25: with a relative abundance of 10 most SNPs (10 out of 13; where 13=10+1+1+1) will be in this frequency class 
+ * 0.25 - 0.50: with a relative abundance of 1 only 1/13 SNPs will be in this class
+ * 0.50 - 0.75: with a relative abundanc of 1 only 1/13 SNPs will be in this category
+ * 0.75 - 1.0: with a relative abundace of 1 only 1/13 SNPs will be in this category
+

GeneratingSimpleHaplotypes modified by Robert Kofler

Robert Kofler — Wed, 20 Jun 2018 10:49:58 -0000

--- v5
+++ v6
@@ -92,6 +92,23 @@

-## Simple haplotypes
+## Simple haplotypes based on a provided SFS
+We provide a script that generated haplotypes based on a site frequency spectrum (sfs). The alleles are distributed randomly among haplotypes thus the SNPs are mostly in linkage equilibrium (except for random LD).
+
+The script accepts the following parameters

+* --N population size
+* --S sites (number of SNPs)
+* --chr-name the name of the chromosome
+* --chr-len the length of the chromosome
+* --haploid simulate haploids
+* --sfs the site frequency spectrum; for example possible arguments are "10,8,7,5,1,1,1,4" or "1,1,1,1,10" or "1,10"

+### sfs
+The --sfs is a comma separated list. Each value (integer or float) represents the relative abundance of a site population frequency class.
+
+This is best explained using an example:
+Assuming  **--sfs "10,1,1,1"** the population frequency of the SNPs is provided for  4 different frequency classes:
+* 0.00 - 0.25: with a relative abundance of 10 most SNPs (10 out of 13; where 13=10+1+1+1) will be in this class 
+* 0.25 - 0.50: with a relative abundance of 1 only 1/13 SNPs will be in this class
+

GeneratingSimpleHaplotypes modified by Robert Kofler

Robert Kofler — Wed, 20 Jun 2018 10:36:55 -0000

--- v4
+++ v5
@@ -18,7 +18,7 @@
   * --S sites (number of SNPs)
   * --chr-name the name of the chromosome
   * --chr-len the length of the chromosome
-  * --freq the frequency of haploytpe A; haplotype B will have the frequency 1.0-freq
+  * --freq the frequency of haploytpe derived allele; the ancestral allele will have the frequency= 1.0-freq
   * --haploid simulate haploids
   *  --hardy-weinberg simulat the diploids in Hardy-Weinberg equilibrium

@@ -33,16 +33,16 @@
 we obtain the following haploytpes

 ~~~~~~
-2L 133 G   G/A GG GG GG GG GG GG AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-2L 157 G   G/A GG GG GG GG GG GG AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-2L 254 G   G/A GG GG GG GG GG GG AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-2L 321 G   G/A GG GG GG GG GG GG AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-2L 342 G   G/A GG GG GG GG GG GG AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-2L 374 G   G/A GG GG GG GG GG GG AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-2L 557 G   G/A GG GG GG GG GG GG AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-2L 864 G   G/A GG GG GG GG GG GG AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-2L 896 G   G/A GG GG GG GG GG GG AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-2L 955 G   G/A GG GG GG GG GG GG AA AA AA AA AA AA AA AA AA AA AA AA AA AA
+2L 218 G   G/A GG GG GG GG GG GG GG GG GG GG GG GG GG GG AA AA AA AA AA AA
+2L 286 G   G/A GG GG GG GG GG GG GG GG GG GG GG GG GG GG AA AA AA AA AA AA
+2L 343 G   G/A GG GG GG GG GG GG GG GG GG GG GG GG GG GG AA AA AA AA AA AA
+2L 368 G   G/A GG GG GG GG GG GG GG GG GG GG GG GG GG GG AA AA AA AA AA AA
+2L 375 G   G/A GG GG GG GG GG GG GG GG GG GG GG GG GG GG AA AA AA AA AA AA
+2L 612 G   G/A GG GG GG GG GG GG GG GG GG GG GG GG GG GG AA AA AA AA AA AA
+2L 619 G   G/A GG GG GG GG GG GG GG GG GG GG GG GG GG GG AA AA AA AA AA AA
+2L 847 G   G/A GG GG GG GG GG GG GG GG GG GG GG GG GG GG AA AA AA AA AA AA
+2L 888 G   G/A GG GG GG GG GG GG GG GG GG GG GG GG GG GG AA AA AA AA AA AA
+2L 954 G   G/A GG GG GG GG GG GG GG GG GG GG GG GG GG GG AA AA AA AA AA AA
 ~~~~~~

@@ -56,16 +56,16 @@
 An example output:

 ~~~~~
-2L 34  G   G/A G G G G G G A A A A A A A A A A A A A A
-2L 54  G   G/A G G G G G G A A A A A A A A A A A A A A
-2L 395 G   G/A G G G G G G A A A A A A A A A A A A A A
-2L 425 G   G/A G G G G G G A A A A A A A A A A A A A A
-2L 472 G   G/A G G G G G G A A A A A A A A A A A A A A
-2L 710 G   G/A G G G G G G A A A A A A A A A A A A A A
-2L 761 G   G/A G G G G G G A A A A A A A A A A A A A A
-2L 773 G   G/A G G G G G G A A A A A A A A A A A A A A
-2L 880 G   G/A G G G G G G A A A A A A A A A A A A A A
-2L 947 G   G/A G G G G G G A A A A A A A A A A A A A A
+2L 13  G   G/A G G G G G G G G G G G G G G A A A A A A
+2L 98  G   G/A G G G G G G G G G G G G G G A A A A A A
+2L 135 G   G/A G G G G G G G G G G G G G G A A A A A A
+2L 154 G   G/A G G G G G G G G G G G G G G A A A A A A
+2L 354 G   G/A G G G G G G G G G G G G G G A A A A A A
+2L 490 G   G/A G G G G G G G G G G G G G G A A A A A A
+2L 498 G   G/A G G G G G G G G G G G G G G A A A A A A
+2L 548 G   G/A G G G G G G G G G G G G G G A A A A A A
+2L 587 G   G/A G G G G G G G G G G G G G G A A A A A A
+2L 695 G   G/A G G G G G G G G G G G G G G A A A A A A
 ~~~~~

@@ -78,16 +78,16 @@

 which for example yields:
 ~~~~~
-2L 25  G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
-2L 26  G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
-2L 131 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
-2L 138 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
-2L 205 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
-2L 454 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
-2L 489 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
-2L 624 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
-2L 771 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
-2L 991 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
+2L 79  G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
+2L 190 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
+2L 215 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
+2L 239 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
+2L 342 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
+2L 455 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
+2L 610 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
+2L 677 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
+2L 874 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
+2L 953 G   G/A GG GG GG GG GG GA GA GA GA GA GA GA GA GA GA AA AA AA AA AA
 ~~~~~