Eric Raymond’s 17 Unix Rules

http://en.wikipedia.org/wiki/Unix_philosophy#Eric_Raymond.E2.80.99s_17_Unix_Rules

teaching coding

http://www.edutopia.org/blog/7-apps-teaching-children-coding-anna-adam?utm_source=twitter&utm_medium=post&utm_campaign=blog-7-apps-coding-dec-image

code.org

mortality rate change at the first time point, bug fix

When I estimated the mortality rates from simulated network aging data, the first time points always have a very low value.  This abnormality bugged me because it contradicts the theoretic assumption on the initial stage, but I thought it is due to the boundary effect and did not investigate it for several weeks. Also, I thought there may be some differences between theoretical predictions and empirical data. I went over the code today and found out that it is due to typo in the code.  After correction, the initial stage of mortality rate change fit extremely well to the network aging model.
Lesson learned: I should be more confident about my theoretic models and should pay more attention to abnormality during numerical works.

ifelse logical mistake

The following codes has a logical mistake, and will not assign color by categories. The ifelse should be nested.

# tbomegaH2C1S1$color[i] = ifelse( tbomegaH2C1S1$CoatLocation[i]=="OuterCoat", 'red', tbomegaH2C1S1$color[i] )
# tbomegaH2C1S1$color[i] = ifelse( tbomegaH2C1S1$CoatLocation[i]=="InnerCoat", 'blue', tbomegaH2C1S1$color[i] )
   tbomegaH2C1S1$color[i] = ifelse( tbomegaH2C1S1$coatflag[i]=="coat", 'red', tbomegaH2C1S1$color[i] )
   tbomegaH2C1S1$color[i] = ifelse( tbomegaH2C1S1$essenflag[i]=="essential", 'black', tbomegaH2C1S1$color[i] )

Some common bugs in bioinformatics programming and lessons in dealing with them

Many ad hoc scripts are written for bioinformatics projects.  I intend to list here some common bugs that I often made. This is going to be a working list. Hopefully, this can leads to better way of coding and managing.

• Hard-coded links that were not updated after projects have evolved. This often lead to wrong files, or results are output to unintended directories. 
• A hard-coded debugging variable that was not turned back during production runs. 
• Mixing of variables names, file names, etc. 
• Compatibility problems. This can occur after software upgrades. For example, after upgrade to perl 5.10.0, I have re-install bioperl to get previous codes working. 
•  File format problems. With myriads of data format, this problem is going to keep bugging us. 
• Typos 
• logical mistakes, often occur in ifelse statement.

Some experiences and lessons on dealing with these problems:

• Correct the blind spot. 

    I spent 3 hours in fixing a directory problem in a perl script for batch run. I noticed the job was not running in the right directory even when I chdir $homedir every step. The problem is that I copy-paste the directory twice in variable $homedir, so perl always choose the current directory by default. I was so sure that $homedir was correct because I copy-pasted it, and did not check it. I found this out when I copy-pasted the long directory again and found the length did not match. I spent 2 hours on this before 1am. I then decided to go sleep and look it fresh again in the morning. The fresh morning working energy helped me spotted this error.

• Switch between different syntax

In perl, qw and string quotes use different syntax. In qw, no comma is needed.
 case 1: qw(results.H0.txt results.H1C.Gblocks.model1.txt results.H2C1S1.txt);
 case 2: qw(results.H0.txt, results.H1C.Gblocks.model1.txt, results.H2C1S1.txt);
In case 2, the file name will actually be treated as "results.H0.txt,". This extra comma is a obvious mistake.