script suggestion (SAM file)

Sergio.pv · 11-21-2013, 10:35 AM

Hi everyone!
In this attached example, i would like to know how many times the element
"bta-miR-191" and "bta-miR-10" in the header of a SAM file is repeated in the rest of
the document (in this case: 6 and 5 respectively).

Could you give me an idea for an script based on this example?

Thanks

shoegame2001 · 11-21-2013, 11:00 AM

grep -v '@SQ' example.txt | awk '{if ($3=="bta-miR-191") print}' | wc -l

grep -v '@SQ' example.txt | awk '{if ($3=="bta-miR-10") print}' | wc -l

dariober · 11-22-2013, 12:12 AM

Hello- To expand a bit shoegame2001's answer... If your input file is big you might want to read thorough it only once and count the two (or more) patterns at the same time:

Code:

grep -v '@SQ' example.txt \
| awk '{if ($3=="bta-miR-191")
            mir191+=1;
        else if ($3 == "bta-miR-10")
            mir10+=1}
        END {print "bta-miR-191:" mir191, "\nbta-miR-10:", mir10}'

Dario

Sergio.pv · 11-22-2013, 02:28 AM

thanks, the grep function was very usufull to remove the headers.
After doing that, i did a count ot he repited elements on column 3.
cat myfile-noheaders.out | awk '{print$3}' | sort | uniq -c | sort -rnk1 >SAM-counts.out

I hope this can be helpfull for somebody else!

Sergio.pv · 11-22-2013, 02:41 AM

if it is usefull, here the complete script to remove the headers ('@') and then count repeated terms in column 3 of the SAM file:

grep -v '@' myfile.out | awk '{print$3}' | sort | uniq -c | sort -rnk1 >SAM-counts.out

Cheeers

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11-22-2013, 12:12 AM	#3
dariober Senior Member Location: Cambridge, UK Join Date: May 2010 Posts: 311	Hello- To expand a bit shoegame2001's answer... If your input file is big you might want to read thorough it only once and count the two (or more) patterns at the same time: Code: grep -v '@SQ' example.txt \ \| awk '{if ($3=="bta-miR-191") mir191+=1; else if ($3 == "bta-miR-10") mir10+=1} END {print "bta-miR-191:" mir191, "\nbta-miR-10:", mir10}' Dario

11-21-2013, 11:00 AM	#2
shoegame2001 Member Location: California Join Date: Dec 2010 Posts: 21	grep -v '@SQ' example.txt \| awk '{if ($3=="bta-miR-191") print}' \| wc -l grep -v '@SQ' example.txt \| awk '{if ($3=="bta-miR-10") print}' \| wc -l

11-22-2013, 02:28 AM	#4
Sergio.pv Member Location: Berlin Join Date: Jul 2013 Posts: 20	thanks, the grep function was very usufull to remove the headers. After doing that, i did a count ot he repited elements on column 3. cat myfile-noheaders.out \| awk '{print$3}' \| sort \| uniq -c \| sort -rnk1 >SAM-counts.out I hope this can be helpfull for somebody else!

11-22-2013, 02:41 AM	#5
Sergio.pv Member Location: Berlin Join Date: Jul 2013 Posts: 20	if it is usefull, here the complete script to remove the headers ('@') and then count repeated terms in column 3 of the SAM file: grep -v '@' myfile.out \| awk '{print$3}' \| sort \| uniq -c \| sort -rnk1 >SAM-counts.out Cheeers