Cell values as rows in a spreadsheet

I have some spreadsheet data where the first column lists the position of a certain amino acid within a protein. There are  many amino acid sites that are skipped, therefore the rows do not follow the actual, uninterrupted, amino acid sequence. I use Gnumeric, and the resulting list looks like that:

data1

 

I want the program to insert empty rows between the non-consecutive amino acids — similarly to the gaps in a multiple sequence alignment. This can be done in a relatively straightforward way:

  • Go to the end of your data, select an empty cell and start enumerating the column downwards consecutively until reaching a value that equals or surpasses the last amino acid number of the protein:

data23

 

  • Then, select the columns that need to be sorted:

data331

 

  • Sort everything. This can be done from Data > Sort, or directly from the toolbar which will sort the data automatically by the first column:

data41

 

  • Now data will be sorted and the missing numbers of column A will be inserted in between the original data. The previously existing rows will be paired with empty ones that share the same value of column A:

data7

 

  • To remove the repeating rows, go to Data > Filter > Advanced Filter, set Criteria range to be listed by column A and check Unique records only. This will eliminate empty duplicates:

data71

 

  • The result is as follows:

data63

This is it! Now just cut and paste! :)

 

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Custom protein topology schemes

I need to generate custom graphics of several proteins (in fact nearly 30). I have the domain organisation predicted at the SMART database, the N-glycosylation sites at NetNGlyc and the possible phosphorylation targets at NetPhos. I also have identified short functional motifs at ELM.

Now I need a program that can generate custom graphics that would combine all of these neatly. Finding such a program proved to be not as trivial as I expected. I have used MyDomains, part of PROSITE, which got the job done, however it is not as customizable as I wanted. I briefly tried DomainDraw, which looks neat. Another tool is DOG which I installed locally, but drawing manually will be too laborious for the amount of proteins I have. Last but not least, one remarkably nice tool is PROTTER, which displays the amino acid sequence in a “snake” view. However, this approach is a bit different from what I wanted to achieve.

PFAM

In the end, I came across the PFAM domain images generator. The input form syntax is JSON, which appears to be fairly simple (well, not as simple as MyDomains), understandable even for me. It is versatile and the specifications of the domains/motifs graphics are described in the help section. The web site even provides an example input for generating a simple graphic:

 

simple

 

or something more complicated:

 

complex

 

Really beautiful, isn’t it?

Syntax highlight

My editor of choice is medit, so I wanted it to display JSON highlight. I found this explanation for gedit and this HowTo (unrelated to JSON) for medit. Therefore, I got this JSON.lang file and saved it as:

~/.local/share/medit-1/language-specs/json.lang

Only thing left was to restart medit. Now, the new syntax highlight is in Document > Language > Sources.

Great! For the record, I stumbled upon several discussions about drawing custom domains and found this list of some general recommendations.

So far, I like PFAM most :)

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Slackonly: packages built from SBo

I read about a new project at SlackWorld, with a domain called Slackonly. It provides a repository of packages (for the x86_64 architecture at the moment) built by the scripts at SlackBuilds.org. The repository contains MD5 sums and GPG signatures for all of its packages. In addition, to resolve dependencies problems, the REQUIRES information from the *.info files will be provided in a separate file.

The ultimate goal seems to be making packages from all categories, which is a serious task.

At the moment, the repository has packages from Accessibility, Desktop, Multimedia and Ruby. I was pleased to see that even the Academic section has two entries (built by scripts that I maintain — EMBOSS and EMBASSY).

However, at the moment the project has several limitations: the work is done by one single person, the packages have to be tested and last but not least the repository has to earn its reputation of providing trusted packages. Therefore, the author of Slackonly will welcome people willing to help. If someone is interested, his contact information is available at the site.

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Recovering installed packages

I came across an interesting discussion at LQ, about extracting a package from its installation and recovering the installable package. Useful if you want to uninstall something, but are not sure if you may need it in the future.

Thanks to the explanation by Ruarí Ødegaard, it is as actually quite straightforward. I decided to try this for leafpad, that I have installed from SlackBuilds.org — here’s how it went:

$ su -
# removepkg -copy leafpad-0.8.18.1-x86_64-1_SBo
# cd /var/log/setup/tmp/preserved_packages/leafpad-0.8.18.1-x86_64-1_SBo/
# mkdir -p install
# grep '^leafpad: ' /var/log/packages/leafpad-0.8.18.1-x86_64-1_SBo > install/slack-desc
# makepkg -l n -c n /tmp/leafpad-0.8.18.1-x86_64-1_SBo.tgz

That’s it!
The package is in /tmp. You may want to clean the contents of /var/log/setup/tmp/preserved_packages/ after that.

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Firefox oldschool toolbar

I do not like the default Firefox toolbar (since whatever version), which looks like this:

1

I prefer to have the old look-an-feel of Firefox, with the back, forward, stop, reload, home and new tab buttons at the traditional places. The solution is easy, but it was not intuitive, at least not to me:

Right click somewhere at the toolbar, select customize. The toolbar will change, so drag and drop the icons as follows:

Diagram1

This is it. I also like to have the download button between the address and search bars.

 

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LibreOffice Impress slideshow

It seems LibreOffice Impress has some bug with the Intel video card of my work computer. Whenever I want to enter slideshow a new entry appears in the task bar, the application becomes unresponsive and nothing happens. I have to press ESC to go back… I use the package created by AlienBob. I also tried the good old OpenOffice.org, by installing the package from Nicolas Kovacs’ Microlinux. OOo worked just fine and its Impress had no trouble entering full screen mode.

Interestingly, my laptop doesn’t have this issue with LibreOffice. So… I googled around and found this rather old entry from Ubuntu that has a workaround.

Following, exactly as they say I went here: Tools -> options > LibreOffice > View > Graphics output and unchecked Use hardware acceleration:

Screenshot - 03172014 - 11:05:37 PM

Seems to work just fine now. To be honest, I did not check what is the default setting for hardware acceleration in OOo.

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Building on multiple cores

Sometimes, I want to build a package as fast as possible. I have done this, when I had to make a new SlackBuild for something large and I just want to see if all requirements are met. The UniPro Ugene SlackBuild comes to mind. In this case I modified the make line within the SlackBuild like this:

make -j4

My build machine has a quad core CPU and this would utilise all cores for the compilation. This, combined with the compiling in RAM approach will speed up the whole process dramatically.

However, the building of some programs would fail if you use multiple cores, and SBo makes sure that only a single core is used. So, I avoid doing this. Recently there was a discussion concerning this at LQ.

I still haven’t tried setting this globally…

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Filed under SlackBuilds, system

ClamAV user permissions

Whenever I install my ready packages from one machine to another, I keep forgetting that ClamAV needs its user and group (uid=210 and gid=210), as suggested. The script will prompt you to add them as this:

groupadd -g 210 clamav
useradd -u 210 -d /dev/null -s /bin/false -g clamav clamav

I then add my user to the clamav:x:210: group in /etc/group, and proceed installing the ClamTK GUI.

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Tangoish clearlooking KDE

Every now and then, I get the masochistic urge to set up KDE to my liking. Don’t get me wrong, KDE is a great desktop IMO. Simply, for a person who prefers the simplicity of GTK, this can be a challenging task. Also, I like to have a consistent look and feel of my desktop, so I have to select matching themes for QT4, GTK3, GTK2 and (yes!) GTK1.

Long story short, here’s what I ended up with:

- QT4: install QtCurve-KDE4 from SBo and use it with this style and color scheme.
- GTK3 and GTK2: install clearlooks-phenix from SBo and select the theme with the help of kde-gtk-config.
- GTK1: install the gtk1-industrial-engine from SBo and select it through gtk1-theme-switch. It’s not exactly Clearlooks but still better than nothing.
- KDE icons: Tangoish
- GTK icons: the tango theme that comes with Slackware

Select them from the System Settings panel. Since I had tried some different icon themes, I had to run pkgtool > Setup > update-desktop-database & update-mime-database & gtk-update-icon-cache. Sure, there is QTCurve for GTK2, but it had some glitches, may be due to my Intel video. Also, I know that the default Oxygen theme supports both GTK2 and GTK3. It is buggy! Some applications do not look very well, for example the menus in Kompozer. Others, like ClamTK simply would not start if Oxygen is the selected theme.

Screenshot?
snapshot5

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QT4 apps and GTK+ icons

When using a desktop environment like XFCE, the only thing required to make QT4 programs look consistent with the rest of the desktop was this. QT4 applications like Clementine inherited the GTK+ theme settings and apparently XFCE took care of the icons theme. However, this is not the case with E17. I googled a bit and found this entry in the excellent Arch Linux wiki. Somehow, the solutions they suggested didn’t fit to my system, for example I do not have gconf, but dconf.

So, I decided to try putting the following orange line in /etc/profile.d/qt4.sh (just below the ones that take care of inheriting the GTK theme):

GTK2_RC_FILES="$HOME/.gtkrc-2.0:/etc/gtk-2.0/gtkrc"
export GTK2_RC_FILES
export DESKTOP_SESSION=gnome

Logged out and in and it works.

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Filed under desktop, system