Recent changes to validation_linearlandscape

validation_linearlandscape modified by Robert Kofler

Robert Kofler — Wed, 24 Mar 2021 09:52:50 -0000

validation_linearlandscape modified by Robert Kofler

Robert Kofler — Wed, 24 Mar 2021 09:52:07 -0000

--- v10
+++ v11
@@ -44,6 +44,17 @@

 ~~~~~~
 python ~/dev/manna/validation/manna-vs-pgd-mhp.py --min-len 100 --max-div 5 --manna linearlandscape.manna --pgd linearlandscape.pgd > linearlandscape.mhp
+# next use R to visualize the result
+R --vanilla --args linearlandscape.mhp < ~/dev/manna/validation/manhatten.R
 ~~~~~~

+This gives the following figure
+[[img src=linearlandscape.mhp.png width=900]]

+Black circles are the expected population frequency  and red crosses are the observed TE population frequencies.
+
+###Conclusion:
+Both the population frequency (overlap between black circle and red cross) and the order of TEs is correctly reproduced by our approach. The correct order is  ascertained by script manna-vs-pgd-mhp.py. In case of an incorrect order TE insertions would not be reported beginning at the first TE that is out of order.
+
+
+

validation_linearlandscape modified by Robert Kofler

Robert Kofler — Wed, 24 Mar 2021 09:46:32 -0000

validation_linearlandscape modified by Robert Kofler

Robert Kofler — Wed, 24 Mar 2021 09:42:55 -0000

--- v8
+++ v9
@@ -6,7 +6,7 @@
 The "backbone" indivdiual established an unambiguous order for the TEs and thus allows to validate the population frequency as well as the order of the TE insertions.
 # Material and Methods
 ## Data
-All files are available here
+All files are available here https://sourceforge.net/projects/manna/files/validation/val-linland/

 ## pgd
 We use a pgd that speciefies the population described in the Introduction (ie. N=5, with 246 insertions; one individual is the backbone). Here a short example from the file

validation_linearlandscape modified by Robert Kofler

Robert Kofler — Wed, 24 Mar 2021 09:35:19 -0000

--- v7
+++ v8
@@ -40,4 +40,10 @@
 python ~/dev/manna/cluster-msa.py --clusters "" --sample-IDs "" --quick-rm linearlandscape.fasta.out > linearlandscape.manna
 ~~~~~

+## Expected vs Observed 

+~~~~~~
+python ~/dev/manna/validation/manna-vs-pgd-mhp.py --min-len 100 --max-div 5 --manna linearlandscape.manna --pgd linearlandscape.pgd > linearlandscape.mhp
+~~~~~~
+
+

validation_linearlandscape modified by Robert Kofler

Robert Kofler — Wed, 24 Mar 2021 09:22:34 -0000

--- v6
+++ v7
@@ -34,4 +34,10 @@
 RepeatMasker --frag 2000000 -pa 1 -no_is -s -nolow -dir . -lib ../teseq-clean-ml100noS4.fasta linearlandscape.fasta
 ~~~~~~

+## Manna alignemnt
+Here we use an option mainly developed to speed up validation (--quick-rm). Usually it is necessary to provide for each aligend annotation a sample-ID and the annotation in a separate file. Since RepeatMasker provides the sample IDs in the outputfile it is not necessary to have the cluster annotions in a separate file. We utilize this feature with the --quick-rm option. However this option could of course also be used with any data.
+~~~~~
+python ~/dev/manna/cluster-msa.py --clusters "" --sample-IDs "" --quick-rm linearlandscape.fasta.out > linearlandscape.manna
+~~~~~

+

validation_linearlandscape modified by Robert Kofler

Robert Kofler — Wed, 24 Mar 2021 09:07:45 -0000

--- v5
+++ v6
@@ -30,5 +30,8 @@
 ~~~~~~

 ## RepeatMasking
+~~~~~~
+RepeatMasker --frag 2000000 -pa 1 -no_is -s -nolow -dir . -lib ../teseq-clean-ml100noS4.fasta linearlandscape.fasta
+~~~~~~

validation_linearlandscape modified by Robert Kofler

Robert Kofler — Wed, 24 Mar 2021 09:02:39 -0000

--- v4
+++ v5
@@ -29,3 +29,6 @@
 python ~/dev/simulates/build-population-genome.py --chassis ../chasis.txt --pgd linearlandscape.pgd --te-seqs ../teseq.fasta --output linearlandscape.fasta
 ~~~~~~

+## RepeatMasking
+
+

validation_linearlandscape modified by Robert Kofler

Robert Kofler — Wed, 24 Mar 2021 09:02:08 -0000

--- v3
+++ v4
@@ -22,4 +22,10 @@
 ...
 ~~~~~~

-**Note** the first column specifies the position in the chasis. The next column specifiy the 5 individuals in the population.  An integer indicates the ID of a TE (e.g. 37=DM_ROO) and a star indicates the absence of the TE in the individual.
+**Note** the first column specifies the position in the chasis. The next column specifiy the 5 individuals in the population.  An integer indicates the ID of a TE (e.g. 37=DM_ROO) and a star indicates the absence of the TE in the individual. For more background on the pgd-file see https://sourceforge.net/projects/simulates/
+
+## population genome
+~~~~~~
+python ~/dev/simulates/build-population-genome.py --chassis ../chasis.txt --pgd linearlandscape.pgd --te-seqs ../teseq.fasta --output linearlandscape.fasta
+~~~~~~
+

validation_linearlandscape modified by Robert Kofler

Robert Kofler — Wed, 24 Mar 2021 08:59:25 -0000

--- v2
+++ v3
@@ -20,3 +20,6 @@
 478463 15 15 * * *
 479903 7 7 * * *
 ...
+~~~~~~
+
+**Note** the first column specifies the position in the chasis. The next column specifiy the 5 individuals in the population.  An integer indicates the ID of a TE (e.g. 37=DM_ROO) and a star indicates the absence of the TE in the individual.