Select specific nt in the pileup file

[cascoamarillo]

Hi all,

I know this is a noob question but I'm really bad with the basic commands: I'm trying to trim the pileup file:

contig00001	9749	C	121	,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
contig00001	9750	A	121	,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
contig00001	9751	T	121	,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

by selecting the nucleotide position (3rd column). So it should be something like: Select only position with A:

cat input.pileup | grep .A ...... > output.pileup

Thanks in advance.

[krobison]

perl -n -e '@a=split(/\t/); print $_ if ($a[2] eq 'A')' input.pileup

# perl -- useful, if not always pretty, interpreted language
# -n -- automatically stream a file through the code, but do not automatically print lines
# -e -- the next item is the code
# @=split(/\t/); -- break up into fields on tab
# remainder -- print current line if 3rd field is equal to the letter A

[cascoamarillo]

Thanks mate!
Nice approach with perl. But one more question: I'd also like to check the 5th column ($a[4]) and look if there's any change in the reads with the reference (RNA editing):
input.pileup

contig00006	1386	C	17	.................	IIIIIIIIIIIIIIIII
contig00006	1396	C	17	TTTTTTTTTTTTTTTTT	IIIIIIIIIIIIIIIII
contig00006	1399	C	17	TT.........TTTTTTTTTT	IIIIIIIIIIIIIIIII

output.pileup

contig00006	1396	C	17	TTTTTTTTTTTTTTTTT	IIIIIIIIIIIIIIIII
contig00006	1399	C	17	TT.........TTTTTTTTTT	IIIIIIIIIIIIIIIII

How would you do that?