https://sourceforge.net/p/invade/wiki/truncdeme/Recent changes to truncdemeenFri, 29 Mar 2019 09:51:26 -0000https://sourceforge.net/p/invade/wiki/truncdeme/<div class="markdown_content"><pre>--- v8 +++ v9 @@ -1,3 +1,7 @@ +# Intro + +Section about "invade-td.jar" + # parameters ~~~~~~ :::bash @@ -10,14 +14,15 @@ --- Optional --- --demes the number of demes ; default=1 +--sampleid the sample id ; default=na --u the transposition rate; default=0.0 --v the excision rate; default=0.0 ---fl-id the balance between FL and ID; 0.5 both equal; 0.4 - prefered mobilization of ID; default=0.5 +--fl-id prefered mobilization of either FL or ID; 0.5 no bias, + 0.4 prefered mobilization of ID; default=0.5 --conversions the conversion rate; rate at which FL transpositions are converted to full length; default=0.0 --min-full-length the amount of full length insertions required per individual; - if smaller TE is not active; default=0 + if smaller TE is not active; default=1 --min-fraction-fl the minimum fraction of full length insertions; default=null --mfwd migration rate - forward; migrants = N*m; default=0.0 --mrev migration rate - backwards; migrants = N*m; default=0.0 @@ -29,15 +34,20 @@ --xd deleterious effect of internally deleted insertion; default=0.0 --steps sample output every xx generation; default=20 ---migsteps perform a migration event ever xx generation; default=1 ---replicate-offset the replicate counts is shifted by the given number; - replicate starts at offset + 1; default=0 +--migsteps perform a migration event every xx generation; default=1 +--replicate-offset the replicate count is shifted by the given number; + allows pseudo-parallelization; replicate starts at + offset + 1; default=0 --seed random seed; default=System.currentTimeMillis() --min-w the minimum average fitness of a population; ; default=0.3 ---trunc-file file with the position and abundance of the internal - deletions; default=none ---simid simulation id, will be preprend to output and may simplify - downstream analysis in R with ggplot2; default=none +--trunc-file output file with the position and abundance of the + internal deletions; default=none +--mig-trunc-file output file with the position and abundance of the + internal deletions of migrants; default=none +--mhp-file Manhatten plot file; show position and popfreq of TE + insertions; default=none +--mhp-count number diploid indivdiuals to sample for the Manhatten + plot; default=N --silent only report the final output --help print the help ~~~~~~ </pre> </div>Robert KoflerFri, 29 Mar 2019 09:51:26 -0000https://sourceforge.net6c15ccb4402ca6c7d4c18f53f47d0c52d465f1c3https://sourceforge.net/p/invade/wiki/truncdeme/<div class="markdown_content"><pre>--- v7 +++ v8 @@ -54,15 +54,21 @@ * col1: replicate * col2: generation - * col3: placeholder, indicating that the info for deme 1 follow - * col4: fraction of individuals with TE insertion - * col5: fraction of individuals with piRNA cluster insertion - * col6: fraction of individuals with at least one full length insertion - * col7: average fitness - * col8: average insertions per diploid - * col9: average cluster insertions per diploid - * col10: average number of internally deleted copies per diploid individual - * col11: placeholder, indicating that the infor for deme 2 follow + * col3: sample id + * col4: placeholder, indicating that the info for deme 1 follow + * col5: fraction of individuals with TE insertion + * col6: fraction of individuals with piRNA cluster insertion + * col7: fraction of individuals with at least one full length insertion + * col8: fraction of individuals with at least one internally deleted insertion + * col9: average fitness + * col10: average insertions per diploid + * col11: average cluster insertions per diploid + * col12: average number of internally deleted copies per diploid individual + * col13: unique internal deletions in the population + * col14: fixed cluster insertions + * col15: unique insertion sites in the population + * col16: average population frequency + * col17: placeholder, indicating that the infor for deme 2 follow * .... </pre> </div>Robert KoflerFri, 29 Mar 2019 09:38:42 -0000https://sourceforge.netac0ad109e9688a4194c7108c3b8cd774a115b4c5https://sourceforge.net/p/invade/wiki/truncdeme/<div class="markdown_content"><pre>--- v6 +++ v7 @@ -71,11 +71,11 @@ # Output file: --trunc-file For example: ~~~~~~ -1 80 5 0 1 2907 0 -1 100 1 0 1 2907 23277 -1 100 1 1 1318 1465 159 -1 100 1 1 1343 1824 1096 -1 100 1 1 539 2676 4 +1 80 5 all 1 2907 0 +1 100 1 all 1 2907 23277 +1 100 1 id 1318 1465 159 +1 100 1 id 1343 1824 1096 +1 100 1 id 539 2676 4 ~~~~~~ </pre> </div>Robert KoflerMon, 23 Jul 2018 16:17:02 -0000https://sourceforge.net13187b00d4b24379dda3363eb59adbb68fbfba38https://sourceforge.net/p/invade/wiki/truncdeme/<div class="markdown_content"><pre>--- v5 +++ v6 @@ -82,9 +82,10 @@ * col1: replicate * col2: generation * col3: deme number - * col4; flag either 0 or 1; - * 0 indicates that the provided counts (col7) refer to the total number of insertions in the deme; This is useful to compute the frequency of a truncation in the population, ie: trunc-count divided by this coverage value - * 1 indicates that the provided counts refer to an actual truncation + * col4; flag either all, fl or id + * **all** indicates that the provided counts (col7) refer to the total number of insertions in the deme; This is useful to compute the frequency of a truncation in the population, ie: trunc-count divided by this coverage value + * **id** indicates that the provided counts refer to an actual truncation + * **fl** indicates that the provided counts refer to full length insertions * col5 start position of truncation (ignore for col4 flag 0) * col6 end position of truncation (ignore for col4 flag 0) * col7 counts of the truncation (or with col4 flag 0, the total number of TE insertions, full-length + intneral deleted, in the deme) </pre> </div>Robert KoflerMon, 23 Jul 2018 16:16:41 -0000https://sourceforge.net2eaee71b1be56b8c839e35e46a8bf296a479eddchttps://sourceforge.net/p/invade/wiki/truncdeme/<div class="markdown_content"><pre>--- v4 +++ v5 @@ -1,4 +1,6 @@ +# parameters ~~~~~~ +:::bash --- Mandatory --- --genome the size of the chromosomes, e.g 'MB:2,3,1,5'; also feasible kb or bp; mandatory </pre> </div>Robert KoflerThu, 12 Jul 2018 11:48:18 -0000https://sourceforge.net9b739b75f2b587c495eb1e2b6482f1c2a3c59f58https://sourceforge.net/p/invade/wiki/truncdeme/<div class="markdown_content"><pre>--- v3 +++ v4 @@ -1,3 +1,45 @@ +~~~~~~ +--- Mandatory --- +--genome the size of the chromosomes, e.g 'MB:2,3,1,5'; also + feasible kb or bp; mandatory +--N the population size; mandatory +--gen how many generations to run the simulations; mandatory +--basepop the starting insertions, eg 'seg:40'; mandatory + +--- Optional --- +--demes the number of demes ; default=1 +--u the transposition rate; default=0.0 +--v the excision rate; default=0.0 +--fl-id the balance between FL and ID; 0.5 both equal; 0.4 + prefered mobilization of ID; default=0.5 +--conversions the conversion rate; rate at which FL transpositions + are converted to full length; default=0.0 +--min-full-length the amount of full length insertions required per individual; + if smaller TE is not active; default=0 +--min-fraction-fl the minimum fraction of full length insertions; default=null +--mfwd migration rate - forward; migrants = N*m; default=0.0 +--mrev migration rate - backwards; migrants = N*m; default=0.0 +--rep how often should the simulations be repeated; default=1 +--rr recombination rate for each chromosome, e.g 'cM:3,4,4,5' + ; default=none +--cluster piRNA cluster regions; default=none +--xf deleterious effect of a full length insertion; default=0.0 +--xd deleterious effect of internally deleted insertion; + default=0.0 +--steps sample output every xx generation; default=20 +--migsteps perform a migration event ever xx generation; default=1 +--replicate-offset the replicate counts is shifted by the given number; + replicate starts at offset + 1; default=0 +--seed random seed; default=System.currentTimeMillis() +--min-w the minimum average fitness of a population; ; default=0.3 +--trunc-file file with the position and abundance of the internal + deletions; default=none +--simid simulation id, will be preprend to output and may simplify + downstream analysis in R with ggplot2; default=none +--silent only report the final output +--help print the help +~~~~~~ + # Standard output ~~~~~ 1 0 |1 0.267 0.025 0.267 1.00 0.3 0.0 0.0 |2 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |3 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |4 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |5 0.000 0.000 0.000 1.00 0.0 0.0 0.0 </pre> </div>Robert KoflerThu, 12 Jul 2018 11:47:45 -0000https://sourceforge.net247908faf13d6b2d8cb81a9a65f75adc8dd7076fhttps://sourceforge.net/p/invade/wiki/truncdeme/<div class="markdown_content"><pre>--- v2 +++ v3 @@ -1,6 +1,26 @@ -# Design decision: -* just two transposition rates; --uf (full length) --ut (truncated, internal deleted) -* only full length can get internal deletions +# Standard output +~~~~~ +1 0 |1 0.267 0.025 0.267 1.00 0.3 0.0 0.0 |2 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |3 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |4 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |5 0.000 0.000 0.000 1.00 0.0 0.0 0.0 +1 20 |1 0.915 0.208 0.657 1.00 2.6 0.2 1.5 |2 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |3 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |4 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |5 0.000 0.000 0.000 1.00 0.0 0.0 0.0 +1 40 |1 0.999 0.577 0.752 1.00 9.1 0.8 7.7 |2 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |3 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |4 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |5 0.000 0.000 0.000 1.00 0.0 0.0 0.0 +1 60 |1 1.000 0.799 0.723 1.00 15.8 1.5 14.5 |2 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |3 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |4 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |5 0.000 0.000 0.000 1.00 0.0 0.0 0.0 +1 80 |1 1.000 0.893 0.744 1.00 21.6 2.1 20.2 |2 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |3 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |4 0.000 0.000 0.000 1.00 0.0 0.0 0.0 |5 0.000 0.000 0.000 1.00 0.0 0.0 0.0 +1 +~~~~~ + + * col1: replicate + * col2: generation + * col3: placeholder, indicating that the info for deme 1 follow + * col4: fraction of individuals with TE insertion + * col5: fraction of individuals with piRNA cluster insertion + * col6: fraction of individuals with at least one full length insertion + * col7: average fitness + * col8: average insertions per diploid + * col9: average cluster insertions per diploid + * col10: average number of internally deleted copies per diploid individual + * col11: placeholder, indicating that the infor for deme 2 follow + * .... + </pre> </div>Robert KoflerThu, 12 Jul 2018 11:46:44 -0000https://sourceforge.netbd85015377e196fb0f5e74cebe9f032a6014da4ehttps://sourceforge.net/p/invade/wiki/truncdeme/<div class="markdown_content"><pre>--- v1 +++ v2 @@ -1,4 +1,26 @@ # Design decision: * just two transposition rates; --uf (full length) --ut (truncated, internal deleted) * only full length can get internal deletions -* + + + +# Output file: --trunc-file +For example: +~~~~~~ +1 80 5 0 1 2907 0 +1 100 1 0 1 2907 23277 +1 100 1 1 1318 1465 159 +1 100 1 1 1343 1824 1096 +1 100 1 1 539 2676 4 + +~~~~~~ + + * col1: replicate + * col2: generation + * col3: deme number + * col4; flag either 0 or 1; + * 0 indicates that the provided counts (col7) refer to the total number of insertions in the deme; This is useful to compute the frequency of a truncation in the population, ie: trunc-count divided by this coverage value + * 1 indicates that the provided counts refer to an actual truncation +* col5 start position of truncation (ignore for col4 flag 0) +* col6 end position of truncation (ignore for col4 flag 0) +* col7 counts of the truncation (or with col4 flag 0, the total number of TE insertions, full-length + intneral deleted, in the deme) </pre> </div>Robert KoflerThu, 12 Jul 2018 11:42:20 -0000https://sourceforge.net51ee9ed96c2dbf8885adf57a5bd1f1229c13f1e2https://sourceforge.net/p/invade/wiki/truncdeme/<div class="markdown_content"><h1 id="design-decision">Design decision:</h1> <ul> <li>just two transposition rates; --uf (full length) --ut (truncated, internal deleted)</li> <li>only full length can get internal deletions</li> <li></li> </ul></div>Robert KoflerWed, 04 Jul 2018 09:54:29 -0000https://sourceforge.net05a40027eb12b3cd3347f23cfa98030c5cf9baa6