tag:blogger.com,1999:blog-9142025972629449791.comments2020-07-14T00:04:14.440+01:00Armchair BiologyArmchair Biologisthttp://www.blogger.com/profile/16528412260692313555noreply@blogger.comBlogger28125tag:blogger.com,1999:blog-9142025972629449791.post-28556359872555735582015-12-15T12:12:48.538+00:002015-12-15T12:12:48.538+00:00Thanks for you kind comments, Chris - I'm so p...Thanks for you kind comments, Chris - I'm so pleased you find it useful.<br /><br />The main thing that has changed for Biopython is how you get data from KEGG - there's a much nicer interface that uses the REST API. The object model remains the same, though there are some colour/color spelling changes for consistency with the rest of Biopython.<br /><br />There's a short iPython Armchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-15261745643284335952015-12-12T12:31:08.923+00:002015-12-12T12:31:08.923+00:00Hi,
Thank you for this post it does exactly what ...Hi,<br /><br />Thank you for this post it does exactly what I am looking to do but I note that it has now been deprecated and incorporated into Biopython. Is the usage of the Biopython KGML module identical to the above? Is there a tutorial or examples for using KGML within Biopython available anywhere?<br /><br />Thanks,<br />ChrisAnonymoushttps://www.blogger.com/profile/16207927279992361972noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-29598349382898547862015-07-11T15:03:33.585+01:002015-07-11T15:03:33.585+01:00Hi,
Thank you very much for your help, I started ...Hi,<br /><br />Thank you very much for your help, I started to use pyani and it fix my problem.<br /><br />Fety,Fetyhttps://www.blogger.com/profile/02972248545330706982noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-86617892028093130432015-07-09T14:31:52.556+01:002015-07-09T14:31:52.556+01:00Hi Phil,
Sorry for the delay in replying. Thanks ...Hi Phil,<br /><br />Sorry for the delay in replying. Thanks for your post - I wasn't previously aware of GGDC, but it's interesting for a few reasons.<br /><br />I don't think that any sequence-based method must agree with DDH. DDH is a bulk measure of hybridisation/affinity as a physical process, not a direct measure of sequence identity, and not a direct measure of evolutionary Armchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-19937039658980433492015-07-09T14:07:22.350+01:002015-07-09T14:07:22.350+01:00Hi Fety,
It's certainly possible to use more/...Hi Fety,<br /><br />It's certainly possible to use more/different colours, but you'd have to change the script directly. In the case of that script, using the verbose (-v) option should give you R code that you can modify directly to re-draw the output using the ANI data files you already generated.<br /><br />It's worth noting that the script you're using is out of date now, and Armchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-69637615975960580142015-07-09T09:18:37.434+01:002015-07-09T09:18:37.434+01:00Hi,
Nice script, It's very usefull. I hope t...Hi,<br /><br />Nice script, It's very usefull. I hope that you can fix my issue here. I'm asking if there is a way to extend value shown in the figure and add more color to it? Indeed, I have in my data values above 0.9 but some are below but I can't see them, and all those values turn to be blue.<br /><br />Thanks for the help,<br /><br />Fety,<br />Fetyhttps://www.blogger.com/profile/02972248545330706982noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-70516062448896018152014-10-04T19:56:55.091+01:002014-10-04T19:56:55.091+01:00Hi there!
Did you ever had the chance to have a l...Hi there!<br /><br />Did you ever had the chance to have a look at the easy-to-use Genome-to-Genome Distance Calculator (GGDC; http://ggdc.dsmz.de) which has many advantages over the ANI approach? For example, the most important feature for any genome sequence-based replacement of conventional DDH is that these alternatives (ANI, GGDC, etc.) must have high correlations with the empirical DDH Anonymoushttps://www.blogger.com/profile/10883451001795797368noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-79430073805563783322014-08-14T12:18:30.594+01:002014-08-14T12:18:30.594+01:00Hi Dudu,
Please could you report this issue at ht...Hi Dudu,<br /><br />Please could you report this issue at https://github.com/widdowquinn/scripts/issues?<br /><br />At the moment, I don't have enough information to tell what might be causing your problem. When you report at https://github.com/widdowquinn/scripts/issues could you please provide a full traceback of the errors you see and, ideally, a minimal dataset that reproduces the error?<Armchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-82822602520302258972014-08-13T08:44:55.045+01:002014-08-13T08:44:55.045+01:00Hi,
Nice script, I wish I could make it work here...Hi,<br /><br />Nice script, I wish I could make it work here :-) I installed everything needed on an Ubuntu VM. Then I ran:<br /><br />python calculate_ani.py -o ~/host/Ecoli/ANI/output -i ~/host/Ecoli/ANI -v -f -l ~/host/Ecoli/ANI -g --format png -m ANIm --nucmer_exe /usr/bin<br /><br />And got:<br /><br />No handlers could be found for logger "calculate_ani.py"<br /><br />I double Duduhttps://www.blogger.com/profile/01539835163502989131noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-12608385535176371172014-03-17T19:41:22.658+00:002014-03-17T19:41:22.658+00:00Looking at your error again, my first suspicion is...Looking at your error again, my first suspicion is that you've got at least one pair of species returning zero matches, and this is causing a NaN/Inf in R's clustering process, that hclust() doesn't like. Might that be what's going on?Armchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-71193002653622513222014-03-17T08:11:18.821+00:002014-03-17T08:11:18.821+00:00*rpy2 module, not rp2 module.*rpy2 module, not rp2 module.Armchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-90471508606750590652014-03-17T08:10:50.201+00:002014-03-17T08:10:50.201+00:00Hi GL,
Thanks for trying the script. It looks lik...Hi GL,<br /><br />Thanks for trying the script. It looks like the issue is with one of the functions in the rp2 module but, from the information you give, I can't tell exactly what is causing the problem.<br /><br />You seem to be on OSX 10.8, using Python 2.7, with rpy2 v2.2.3.9 - that much I can tell. But in order to investigate further I will need some example data - as small as possible -Armchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-79804385449161775292014-03-17T01:34:21.220+00:002014-03-17T01:34:21.220+00:00Hello,
I am trying to run this script but I am fa...Hello, <br />I am trying to run this script but I am facing some problems and getting an error. Could you provide some help with this?<br /><br />Error in hclustfun(distfun(x)) : <br /> NA/NaN/Inf in foreign function call (arg 11)<br />Traceback (most recent call last):<br /> File "./calculate_ani.py", line 1124, in <br /> robjects.r(rstr)<br /> File "/Library/Python/2.7/GLhttps://www.blogger.com/profile/05881655350969727710noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-59083460639577063112014-02-06T17:03:24.417+00:002014-02-06T17:03:24.417+00:00Hi Nomaya,
Thank you for the comment, and the com...Hi Nomaya,<br /><br />Thank you for the comment, and the compliment. I'm glad you liked the post.<br /><br />Honestly, I was probably mistaken when writing the post, as looking at the description of H8 on 23andMe now, it clearly says "Region: Near East, Central Asia". Sorry about that.<br /><br />I should clarify that I wasn't saying that H8 indicates European ancestry, but Armchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-11185251765218238782014-02-06T16:24:11.966+00:002014-02-06T16:24:11.966+00:00Hello. Nice post. Well-written!
I am wondering ...Hello. Nice post. Well-written!<br /><br />I am wondering how it's possible to have the markers for H8 but have zero Asian ancestry? I have this configuration too. <br />You say H8 counts as Europe...but if it's rare in Europe and common in Central Asia - how does it count as Europe? Didn't that H8 ancestor come from Central Asia (first the Near East, then expanded to Asia) - so Nomayahttps://www.blogger.com/profile/14892584894000187747noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-89484078553468974452013-03-09T16:04:55.682+00:002013-03-09T16:04:55.682+00:00Thanks JeffJo, but I understood you the first time...Thanks JeffJo, but I understood you the first time. Repeating your point won't help: it's correct, and I see that it's correct, as I said in my reply above.<br /><br />L.Armchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-19899252169219750092013-03-09T13:04:20.381+00:002013-03-09T13:04:20.381+00:00But the whole point is that stating "one is a...But the whole point is that stating "one is a boy," and being compelled to say whether one is a boy, are quite different things. And it is the very act of compelling that causes the unexpected probability fluctuations as facts are added to what is being compelled.JeffJohttps://www.blogger.com/profile/09110352332876400907noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-79326149773899851242013-03-08T18:40:08.487+00:002013-03-08T18:40:08.487+00:00Thanks for the comment, JeffJo.
You really made m...Thanks for the comment, JeffJo.<br /><br />You really made me think about what's going on with the wording of that simple puzzle. I agree: you're correct so long as the parent of a BG/GB family has the opportunity to name either the boy or the girl, and ask the appropriate question (even if phrased as 'I do not have two boys').<br /><br />In my defence, I was explicit about my Armchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-49796497572642967972013-03-06T14:48:17.096+00:002013-03-06T14:48:17.096+00:00Q1) A parent is chosen at random from a large set ...Q1) A parent is chosen at random from a large set of two-child families. What is the probability that both of his/her children have the same gender?<br /><br />The answer is simple: 1/2.<br /><br />Q2) Another parent is chosen at random from the subset of these families that include at least one boy. What is the probability both children have the same gender (which, by necessity, must be "JeffJohttps://www.blogger.com/profile/09110352332876400907noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-92058755347632202382012-09-24T09:51:12.565+01:002012-09-24T09:51:12.565+01:00Nice - our six month wait for a large scale Genome...Nice - our six month wait for a large scale <a href="http://news.open-bio.org/news/2012/03/cross-links-in-genomediagram" rel="nofollow">GenomeDiagram with crosslinks</a> was worth it :)Peter Cockhttps://www.blogger.com/profile/00233221181317137855noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-34616951585539352702012-04-24T17:45:50.824+01:002012-04-24T17:45:50.824+01:00@fmartin54 points out on Twitter: "Agreed. No...@fmartin54 points out on Twitter: "Agreed. Note: Microbes are not the onlyorganisms releasing effectors. Insects do." (https://twitter.com/#!/fmartin1954/status/194814889037004800)<br /><br />And he's absolutely right. I focus on microbes because it's what I'm familiar with, but I think the functional definition can potentially extend beyond microbes, and beyond biology to Armchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-46412407667593677202012-04-22T23:06:54.632+01:002012-04-22T23:06:54.632+01:00I have no issue with the fact that the meaning of ...I have no issue with the fact that the meaning of a word may vary with usage over time (one of my favourites is 'nice': http://slb-ltsu.hull.ac.uk/awe/index.php?title=Nice_(changing_meaning)), nor with the fact that words are proxies for concepts. We certainly agree, there. I meant rather to stress the point that we may control what we intend to be the meaning of a word, but not what itArmchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-5490555803915749812012-04-22T20:37:10.288+01:002012-04-22T20:37:10.288+01:00Fist, on the $variable analogy. I fully agree that...Fist, on the $variable analogy. I fully agree that the concept that we put behind the word "words" is not equivalent to the one behind "variables". My point was that they are still closer than you think. The meaning of words change over time, and that meaning is set by humans. It is true we cannot completely erase one meaning and put in another. It is true that there are Khttps://www.blogger.com/profile/02682248469131896224noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-37411908804765524892012-04-22T19:53:34.895+01:002012-04-22T19:53:34.895+01:00I wouldn't want to staple my colours to a stat...I wouldn't want to staple my colours to a statement like "all proteins occur in complex with many other molecules", but the interior of cells is certainly very crowded, and there is very little chance that an effector, once within the cell, would have an opportunity to 'diffuse freely through a solvent', or engage in any such idealised behaviour. More likely there are a Armchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.comtag:blogger.com,1999:blog-9142025972629449791.post-25106706693425997242012-04-22T19:19:45.178+01:002012-04-22T19:19:45.178+01:00From Kamoun Lab @ TSL at http://www.scoop.it/t/mpm...From Kamoun Lab @ TSL at http://www.scoop.it/t/mpmi:<br /><br />"""<br />This is definitely in line with my favorite definition of effectors as secreted microbial molecules that "alter host-cell and structure". The key aspect in my view is not to get stuck with whether the effect is positive or negative. That was the problem with the somewhat outdated concepts of elicitorArmchair Biologisthttps://www.blogger.com/profile/16528412260692313555noreply@blogger.com