The two shell scripts (t1prog and t2prog) are given below they are working fine. The input for the first program is 't1.det' and for second program is 't1.rnaml'. These two input files are in 'dir1' folder. I am executing the shell like 'sh t1prog > t1out' and 'sh t2prog > t2out' from this directory only. Then I am executing a java program 'java RNA'; for this, t1out and t2out are input files used in the program and I am getting the final output on screen.
The input files 't1.det' and 't1.rnaml' are in different folders with same name and with different values. Each folder specifies one gene sequence input files.
In mfold directory there are 5 directors and each directory contains these input files as shown below
I need a shell script to automate this process like t1prog and t2prog first take the inputs from dir1 folder, run the shell and redirect the output to t1out and t2out and after executing the java program with statment 'java RNA' the output will be redirected to a file like 'RNAout1'. Then takes the inputs from dir2 folder, same process again, and redirect the output to 'RNAout2'. Like this for all inputs values from 5 folders. Modify the two shell scripts given below, to accept the inputs in that way (i think last line of each script to be modified).
shell 1: t1prog
shell 2: t2prog
for one input set in 'dir1' i am executing like this
for inputs in different directories and executing these and redirecting the final ouput after executing 'java RNA' statement to a file is needed.
WRITING A SHELL SCRIPT FOR THIS IS HIGHLY APPRCIATED. THANKS IN ADVANCE.
For the script that would wrap the whole process, that's my proposition:
If You want just one script to perform that, use functions and the script would look like:
Last edited by frans; 11-07-2010 at 04:04 AM..
Reason: forgot java RNA
I used the second code using Parse T1 and Parse T2. After execution of that code output files 't1out' and 't2out' are generated in sub directories 'dir1' and 'dir2' but final output is not coming and giving the following errors. I am giving Java code also for information. . When executing t1prog, t2prog followed by JAVA, I am getting output for a single data set like 'sh t1prog > t1out; sh t2prog > t2out; java RNA'. For this, it is giving errors, I am in confusion.
The above set of errors are coming for each 'dir'. If two direcotries are there 'dir1' and 'dir2'; two times the same set of errors coming and finally getting the $ prompt.
[/CODE]
Quote:
Originally Posted by frans
Please, use code tags to make the code more readable.
Howto:
Select the text corresponding to code
Click on the 'code' button in the editor's toolbar
The t2prog can really be optimized. Here is my proposition for the same functionality:
For the script that would wrap the whole process, that's my proposition:
If You want just one script to perform that, use functions and the script would look like:
Last edited by kswapnadevi; 11-08-2010 at 09:48 PM..
Reason: modified
The optimized code t2prog is executed. When I am working with real datasets it consists of additional data values in the tag like <secondary-structure-display> .....</secondary-structure-dispaly> that are also coming in output. For each sequence of data, these secondary structure is also there. This secondary structure not taking into the consideration for output sir. I am giving the additional part of the data part in input file that is to be ommitted. The given shell script 't2prog' to be modified sir.
Quote:
Originally Posted by frans
Please, use code tags to make the code more readable.
Howto:
Select the text corresponding to code
Click on the 'code' button in the editor's toolbar
The t2prog can really be optimized. Here is my proposition for the same functionality:
For the script that would wrap the whole process, that's my proposition:
If You want just one script to perform that, use functions and the script would look like:
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