way to select lines that show variations

Question

I have a huge file that contains 80 genomes and five chromosomes. I was wondering is there is an easy way to select only the lines from ONE chromosome (for example 1) but only at the position showing SNP VARIATIONS.

1   180754  GGGGGGGCC   
1   180755  CCCCCCCCC

1   180756  CCTCCCCTC   
1   180757  AAAAAAAAA   
1   180759  TTTTTTTTT   
3   7874113 TTTTTTTTT   
3   7874114 GGGGGGGGG   
3   7874115 GGGGGGGGG   
3   7874116 GGGGGGGGG

This is what I want to get in the end:

1   180754  GGGGGGGC        
1   180756  CCTCCCCT    

Answer 1

For your example:

egrep '1 [[:digit:]]+ (GGGGGGGC|CCTCCCCT)' file

--- edit: so try this:

egrep -v '([A-Z])\1{8}' data

Answer 2

Based on the sample data you've provided you can do this using grep. Given the only valid values for nucleotides is A,C,G,T we can create a set of characters with just those included.

$ grep -Ev '([ACGT])\1{8}|^$' sample.txt 
1   180754  GGGGGGGCC
1   180756  CCTCCCCTC

This works by ignoring all the results that are mono-typed. The regular expression [ACGT]\1{8} matches all the strings that are of the form AAAAAAAA, CCCCCCCC, etc. The reversal of the matching is accomplished through the -v switch.

   -v, --invert-match
        Invert the sense of matching, to select non-matching lines.  (-v 
        is specified by POSIX.)

The use of -E makes our argument to grep a regular expression that matches the above, [ACGT]\1{8} or empty lines (^$).

   -E, --extended-regexp
        Interpret PATTERN as an extended regular expression (ERE, see 
        below).  (-E is specified by POSIX.)

The vertical bar (aka. pipe (|)) between the 2 arguments makes this an either this or that type of matching situation.

For example grep -Ev "arg1|arg2" <file>. arg1 would be [ACGT]\1{8} while arg2 would be ^$.

Answer 3

I'm not sure exactly what you're asking (it would be helpful to explain your requirement lexically rather than semantically) but

sed -r sed -r '/^[0-9]+[[:space:]]+[0-9]+[[:space:]]+(.)\1+\>/d'

will delete (i.e. not print) any lines in which the third space-delimited field consists entirely of repeats of the same initial character e.g.

$ sed -r '/^[0-9]+[[:space:]]+[0-9]+[[:space:]]+(.)\1+\>/d' genomes.txt
1   180754  GGGGGGGCC   

1   180756  CCTCCCCTC   

If you know that only the genome field can contain uppercase letters, it might be safe to do a much simpler expression

sed -r '/\<([A-Z])\1+\>/d' genomes.txt