Shell Programming and Scripting

Hey gyuz,

I wanna calculate the number of mapped reads of a bam file in a region of interest. I used this code to do so :

Code:

samtools view input.bam chrname:region1 > region1.txt

This will store all the reads from given bam file within the region of interest in region1.txt

Now I have several bam files and several regions for each which are different. (regions are not the same in all bam files)

I prepared a list of them like below:


I want the script to read from the table and apply the function on proper bam file and regions and report the output for each region in a single file. region1.txt, region2.txt, region3.txt,.....

If you can help me with this you saved my time so much!!

Thanks in advance.

Try this:

Code:

while read BAM REGION; do samtools view $BAM chrname:$REGION >> $REGION.txt; done <file

remove the region*.txt files before use.

Thanks RudiC. It seems it's working just fine.
Now I have many files which I cannot open them. I believe it's because of their name:

one example:
gi|16799079|ref|NC_003212.1|:2769071-2769101.txt

How can I rename them all by replacing pipes and colons by underscore for example to have something like this:

gi_16799079_ref_NC_003212.1__2769071-2769101.txt

I appreciate your help!

to make it easy and quick loop through while or for loop in that directory and mv the files with the below command...

Code:

 
echo "gi|16799079|ref|NC_003212.1|:2769071-2769101.txt"|sed -e 's/[:|]/_/g'

Try

Code:

for i in gi*; do echo mv \"$i\" ${i//[|:]/_}; done

The ${i//[|:]/_} is a bash Pattern substitution, so don't expect it to work with other shells.

If happy with the result, remove the echo cmd. You may need to play around with the double quotes and their escapes.

Thanks RudiC once more.
It works just fine with this code:

Code:

for i in gi*.txt; do mv $i ${i//[|:]/_}; done