Recent changes to RandomSNPsQTL

RandomSNPsQTL modified by Christos Vlachos

Christos Vlachos — Tue, 03 Jul 2018 10:19:22 -0000

--- v6
+++ v7
@@ -1,6 +1,6 @@
 [TOC]
 #1 Introduction
-We provide a SNP that allows to randomly pick the QTLs for the qt-mode and the qff-mode. As input the MimicrEE2 haplotypes are required.
+We provide a SNP that allows to randomly picking the QTLs for the qt-mode and the qff-mode. As input the MimicrEE2 haplotypes are required.
 The script allows for two options

  * all selected SNPs may have the same effect size
@@ -23,7 +23,7 @@
 * --d the dominance effect of the selected SNPs; default = 0.0
 * --effect-file provide a file with the effect size distribution of the selected SNPs (this will override any values provided in *--a* or *--d*)

-The script will first selected all loci that fullfill the frequency criteria (thus having a minimum frequency of --f). Than it selectes the requested number of loci randomly from this set. Finally it randomly chooses one of the two alleles at each SNPs as having the effect size *a* while the other allele has effect size *-a*. 
+The script will first select all loci that fullfill the frequency criteria (thus having a minimum frequency of --f). Then it selects the requested number of loci randomly from this set. Finally it randomly chooses one of the two alleles at each SNPs as having the effect size *a* while the other allele has effect size *-a*. 

 #2 Pick SNPs with identical additive effect size

@@ -96,7 +96,7 @@
 python scripts/pick-SNPs-QTL.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --n 20 --effect-file effectsizedistr.txt --f 0.05
 ~~~~~

-and we obtain an output similiar to this one
+and we obtain an output similar to this one

 ~~~~~
 3L 18929259    T/A 1.2 0.0

RandomSNPsQTL modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 16:11:37 -0000

--- v5
+++ v6
@@ -99,6 +99,26 @@
 and we obtain an output similiar to this one

 ~~~~~
+3L 18929259    T/A 1.2 0.0
+2L 19698812    T/C 1.0 0.0
+2L 7021887 G/A 1.0 0.0
+2L 7617017 T/A 1.0 0.0
+3L 348772  G/T 1.5 0.0
+3L 15841049    G/T 1.2 0.0
+3R 13789648    C/G 1.5 0.0
+3R 6987528 C/T 1.0 0.0
+3R 8719965 G/C 1.0 0.0
+X  4412847 A/C 1.0 0.0
+2L 17575441    A/G 1.0 0.0
+3R 25068798    A/G 1.0 0.0
+2R 13307602    T/A 1.0 0.0
+2L 9058000 G/C 1.1 0.0
+2L 13699585    G/T 1.2 0.0
+X  16920825    G/C 1.1 0.0
+3R 7001766 G/A 1.1 0.0
+3L 8041494 T/A 1.0 0.0
+2R 16534711    G/T 1.0 0.0
+2R 7452620 G/A 1.5 0.0
 ~~~~~

RandomSNPsQTL modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 16:09:23 -0000

--- v4
+++ v5
@@ -62,7 +62,7 @@
 #3 Pick SNPs with an additive effect size drawn from a distribution

 ## distribution of effect size
-You have to provide a file containing the distribution of effect sizes. 
+In order to randomly pick SNPs that follow some effect size distribution you have to provide a file containing the desired distribution of effect sizes. 

 The file needs to have two column and may have an arbitrary number of rows:

@@ -85,7 +85,7 @@

 The script will assign a random effect sizes to each selected SNPs. The effect size is  drawn from this file by picking random rows with replacement.
 Thus the  combination of additive effect size and dominance effect as provided in the file will be maintained.  
-Based on this example most SNPs will have an additive effect 1.0 and all SNPs will have a dominance effect of 0.0.
+Based on this example most SNPs will have an additive effect 1.0, some have an additive effect of 1.2 and few will have an effect of 1.5. But all SNPs will have a dominance effect of 0.0.

 ## pick the QTLs

RandomSNPsQTL modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 16:05:40 -0000

--- v3
+++ v4
@@ -1,6 +1,6 @@
 [TOC]
 #1 Introduction
-We provide a SNP that allows to randomly pick the QTLs for the qt and the qff-mode. As input the MimicrEE2 haplotypes are required.
+We provide a SNP that allows to randomly pick the QTLs for the qt-mode and the qff-mode. As input the MimicrEE2 haplotypes are required.
 The script allows for two options

  * all selected SNPs may have the same effect size
@@ -12,7 +12,7 @@
 ## Requirements
 First download the MimicrEE2 haplotypes https://sourceforge.net/projects/mimicree2/files/starvation_resistance/mimicree_format_dgrp_snps_X_chromosome.gz/download

-Than download the script 
+Than download the script https://sourceforge.net/projects/mimicree2/files/scripts/pick-SNPs-QTL.py/download

 the following parameters are important:

RandomSNPsQTL modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 16:02:46 -0000

--- v2
+++ v3
@@ -23,10 +23,9 @@
 * --d the dominance effect of the selected SNPs; default = 0.0
 * --effect-file provide a file with the effect size distribution of the selected SNPs (this will override any values provided in *--a* or *--d*)

-The script will first selected all loci that fullfill the frequency criteria (thus having a minimum frequency of --f). Than it selectes the requested number of loci randomly from this set. Finally it randomly chooses one of the two alleles at each SNPs as the beneficial one. 
+The script will first selected all loci that fullfill the frequency criteria (thus having a minimum frequency of --f). Than it selectes the requested number of loci randomly from this set. Finally it randomly chooses one of the two alleles at each SNPs as having the effect size *a* while the other allele has effect size *-a*. 

-#2 Pick SNPs with identical effect size
-
+#2 Pick SNPs with identical additive effect size

 ~~~~~~
@@ -36,92 +35,70 @@
 and we for example obtain the following output (*cat additive.txt*)

 ~~~~~
-[s]
-3R 13879402    A/T 0.1 0.5
-2R 9477466 C/T 0.1 0.5
-3R 9328727 G/C 0.1 0.5
-3L 16184512    T/C 0.1 0.5
-2L 1969063 C/T 0.1 0.5
-X  16445969    A/G 0.1 0.5
-3L 13434376    C/T 0.1 0.5
-X  2546369 G/C 0.1 0.5
-2L 15610136    G/T 0.1 0.5
-X  1737206 A/T 0.1 0.5
-2R 10601625    T/G 0.1 0.5
-3L 8504833 C/A 0.1 0.5
-2R 10707643    T/G 0.1 0.5
-2R 6685134 G/A 0.1 0.5
-2R 612843  A/T 0.1 0.5
-2R 7289434 T/C 0.1 0.5
-3R 12359406    G/A 0.1 0.5
-2L 4715803 A/C 0.1 0.5
-2L 16304941    G/T 0.1 0.5
-3R 634316  C/T 0.1 0.5
+3L 12964331    C/T 1.0 0.0
+3R 19601182    G/A 1.0 0.0
+3R 24104354    A/C 1.0 0.0
+3R 9187668 T/A 1.0 0.0
+3L 2923043 T/G 1.0 0.0
+2L 6614778 T/C 1.0 0.0
+2L 18900183    G/C 1.0 0.0
+2L 4326294 A/G 1.0 0.0
+3R 6801867 T/G 1.0 0.0
+3R 14995600    A/T 1.0 0.0
+2R 14050081    T/C 1.0 0.0
+3L 13393686    A/T 1.0 0.0
+X  16430602    A/T 1.0 0.0
+X  4327124 G/T 1.0 0.0
+2L 2172947 T/A 1.0 0.0
+2R 18124893    G/A 1.0 0.0
+3L 17693433    G/T 1.0 0.0
+3R 26933314    G/A 1.0 0.0
+2L 15246918    A/G 1.0 0.0
+3L 2598523 G/A 1.0 0.0
 ~~~~~

 For details on this file format see [SelectedLoci]

-#3 Pick SNPs with an effect size drawn from a distribution
+#3 Pick SNPs with an additive effect size drawn from a distribution

 ## distribution of effect size
 You have to provide a file containing the distribution of effect sizes. 

 The file needs to have two column and may have an arbitrary number of rows:

-* column1: the selection coefficient
-* column2: the heterozygous effect
+* column1: the addtive effect size 
+* column2: the dominance effect

 For examle given the following content stored in file *effectsizedistr.txt*
 ~~~~~
-0.1     0.5
-0.1     0.5
-0.1     0.5
-0.1     0.5
-0.2     0.5
-0.3     0.5
-0.4     0.5
-0.5     0.5
+1.0    0.0
+1.5    0.0
+1.0    0.0
+1.1    0.0
+1.2    0.0
+1.2    0.0
+1.0    0.0
+1.0    0.0
 ~~~~~

 The script will assign a random effect sizes to each selected SNPs. The effect size is  drawn from this file by picking random rows with replacement.
-Thus the  combination of selection coefficient and heterozygous effect as provided in the file will be maintained.  
-Based on this example most SNPs will have a selection coefficient of 0.1 and all SNPs will have a heterozygous effect of 0.5.
+Thus the  combination of additive effect size and dominance effect as provided in the file will be maintained.  
+Based on this example most SNPs will have an additive effect 1.0 and all SNPs will have a dominance effect of 0.0.

-## pick the loci
+## pick the QTLs

-With the following command we randomly pick the loci
+With the following command we randomly pick the QTLs

 ~~~~~
-python pick-SNPs-selcoef.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --n 20 --effect-file effectsizedistr.txt --f 0.05
+python scripts/pick-SNPs-QTL.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --n 20 --effect-file effectsizedistr.txt --f 0.05
 ~~~~~

 and we obtain an output similiar to this one

 ~~~~~
-[s]
-3R 6941048 C/T 0.1 0.5
-2R 12592831    C/G 0.1 0.5
-3L 8315781 T/G 0.5 0.5
-2L 15620577    T/C 0.5 0.5
-3R 9870974 C/T 0.5 0.5
-3R 7009549 T/A 0.5 0.5
-3L 14816601    A/C 0.1 0.5
-2R 19007146    G/A 0.5 0.5
-2R 10030750    C/T 0.3 0.5
-3L 12571197    C/T 0.1 0.5
-3L 10579497    T/C 0.2 0.5
-2L 17368433    T/A 0.3 0.5
-3L 12988113    C/T 0.1 0.5
-X  13161667    A/C 0.1 0.5
-2L 2719442 T/C 0.3 0.5
-3R 14201605    T/A 0.1 0.5
-2R 10250433    C/A 0.4 0.5
-2R 9251683 C/G 0.1 0.5
-3R 21063725    C/A 0.4 0.5
-2L 11212417    G/A 0.2 0.5
 ~~~~~

RandomSNPsQTL modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 15:34:51 -0000

--- v1
+++ v2
@@ -1,25 +1,27 @@
 [TOC]
 #1 Introduction
-We provide a SNP that allows to randomly pick the targets of selection for the w-mode. As input the MimicrEE2 haplotypes are required.
-The script provides two options
+We provide a SNP that allows to randomly pick the QTLs for the qt and the qff-mode. As input the MimicrEE2 haplotypes are required.
+The script allows for two options

  * all selected SNPs may have the same effect size
  * the selected SNPs may follow a distribution of effect sizes as provided in a file
+
+**Note** this is quite similar to randomly picking the targets of selection for the w-mode [RandomSNPsWMode]

 ## Requirements
 First download the MimicrEE2 haplotypes https://sourceforge.net/projects/mimicree2/files/starvation_resistance/mimicree_format_dgrp_snps_X_chromosome.gz/download

-Than download the script https://sourceforge.net/projects/mimicree2/files/scripts/pick-SNPs-selcoef.py/download
+Than download the script 

 the following parameters are important:

 * --mimhap the MimicrEE2 haplotype file; may be zipped or unzipped
 * --n the number of selected loci
 * --f the minimum allele frequency; For example if *--f 0.05* is provided all SNPs will have an allele frequency betwee 0.05 and 0.95
-* --s the selection coefficients of the selected SNPs (either --s or --effect-file needs to be provided) 
-* --h the heterozygous effect of the selected SNPs; default = 0.5 
-* --effect-file provide a file with the effect size distribution of the selected SNPs (this will override any values provided in *--s* or *--h*)
+* --a the additive effect size of the selected SNPs (either --a or --effect-file needs to be provided) 
+* --d the dominance effect of the selected SNPs; default = 0.0
+* --effect-file provide a file with the effect size distribution of the selected SNPs (this will override any values provided in *--a* or *--d*)

 The script will first selected all loci that fullfill the frequency criteria (thus having a minimum frequency of --f). Than it selectes the requested number of loci randomly from this set. Finally it randomly chooses one of the two alleles at each SNPs as the beneficial one. 

@@ -28,10 +30,10 @@

 ~~~~~~
-python pick-SNPs-selcoef.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --n 20 --s 0.1 --f 0.05 > sellocus.txt
+python pick-SNPs-QTL.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --n 20 --a 1.0 --d 0.0 > additive.txt
 ~~~~~~

-and we for example obtain the following output (*cat sellocus.txt*)
+and we for example obtain the following output (*cat additive.txt*)

 ~~~~~
 [s]

RandomSNPsQTL modified by Robert Kofler

Robert Kofler — Thu, 28 Jun 2018 15:16:28 -0000

1 Introduction
- Requirements
2 Pick SNPs with identical effect size
3 Pick SNPs with an effect size drawn from a distribution
- distribution of effect size
- pick the loci

1 Introduction

We provide a SNP that allows to randomly pick the targets of selection for the w-mode. As input the MimicrEE2 haplotypes are required.
The script provides two options

all selected SNPs may have the same effect size
the selected SNPs may follow a distribution of effect sizes as provided in a file

Requirements

First download the MimicrEE2 haplotypes https://sourceforge.net/projects/mimicree2/files/starvation_resistance/mimicree_format_dgrp_snps_X_chromosome.gz/download

Than download the script https://sourceforge.net/projects/mimicree2/files/scripts/pick-SNPs-selcoef.py/download

the following parameters are important:

--mimhap the MimicrEE2 haplotype file; may be zipped or unzipped
--n the number of selected loci
--f the minimum allele frequency; For example if --f 0.05 is provided all SNPs will have an allele frequency betwee 0.05 and 0.95
--s the selection coefficients of the selected SNPs (either --s or --effect-file needs to be provided)
--h the heterozygous effect of the selected SNPs; default = 0.5
--effect-file provide a file with the effect size distribution of the selected SNPs (this will override any values provided in --s or --h)

The script will first selected all loci that fullfill the frequency criteria (thus having a minimum frequency of --f). Than it selectes the requested number of loci randomly from this set. Finally it randomly chooses one of the two alleles at each SNPs as the beneficial one.

2 Pick SNPs with identical effect size

python pick-SNPs-selcoef.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --n 20 --s 0.1 --f 0.05 > sellocus.txt

and we for example obtain the following output (cat sellocus.txt)

[s]
3R  13879402    A/T 0.1 0.5
2R  9477466 C/T 0.1 0.5
3R  9328727 G/C 0.1 0.5
3L  16184512    T/C 0.1 0.5
2L  1969063 C/T 0.1 0.5
X   16445969    A/G 0.1 0.5
3L  13434376    C/T 0.1 0.5
X   2546369 G/C 0.1 0.5
2L  15610136    G/T 0.1 0.5
X   1737206 A/T 0.1 0.5
2R  10601625    T/G 0.1 0.5
3L  8504833 C/A 0.1 0.5
2R  10707643    T/G 0.1 0.5
2R  6685134 G/A 0.1 0.5
2R  612843  A/T 0.1 0.5
2R  7289434 T/C 0.1 0.5
3R  12359406    G/A 0.1 0.5
2L  4715803 A/C 0.1 0.5
2L  16304941    G/T 0.1 0.5
3R  634316  C/T 0.1 0.5

For details on this file format see [SelectedLoci]

3 Pick SNPs with an effect size drawn from a distribution

distribution of effect size

You have to provide a file containing the distribution of effect sizes.

The file needs to have two column and may have an arbitrary number of rows:

column1: the selection coefficient
column2: the heterozygous effect

For examle given the following content stored in file effectsizedistr.txt

0.1     0.5
0.1     0.5
0.1     0.5
0.1     0.5
0.2     0.5
0.3     0.5
0.4     0.5
0.5     0.5

The script will assign a random effect sizes to each selected SNPs. The effect size is drawn from this file by picking random rows with replacement.
Thus the combination of selection coefficient and heterozygous effect as provided in the file will be maintained.
Based on this example most SNPs will have a selection coefficient of 0.1 and all SNPs will have a heterozygous effect of 0.5.

pick the loci

With the following command we randomly pick the loci

python pick-SNPs-selcoef.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --n 20 --effect-file effectsizedistr.txt --f 0.05

and we obtain an output similiar to this one

[s]
3R  6941048 C/T 0.1 0.5
2R  12592831    C/G 0.1 0.5
3L  8315781 T/G 0.5 0.5
2L  15620577    T/C 0.5 0.5
3R  9870974 C/T 0.5 0.5
3R  7009549 T/A 0.5 0.5
3L  14816601    A/C 0.1 0.5
2R  19007146    G/A 0.5 0.5
2R  10030750    C/T 0.3 0.5
3L  12571197    C/T 0.1 0.5
3L  10579497    T/C 0.2 0.5
2L  17368433    T/A 0.3 0.5
3L  12988113    C/T 0.1 0.5
X   13161667    A/C 0.1 0.5
2L  2719442 T/C 0.3 0.5
3R  14201605    T/A 0.1 0.5
2R  10250433    C/A 0.4 0.5
2R  9251683 C/G 0.1 0.5
3R  21063725    C/A 0.4 0.5
2L  11212417    G/A 0.2 0.5