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extract groups of SnPs and store them in separate files

Hi all,

I have a genotype file containing 500K SNPs (i.e 500000 lines), I want to create groups of SNPs taken every 5K and store each group in seperate files. This means take SNPs 1-5000 and store in file 1(I want to keep the whole line), take SNPs 5001-10000 and store in file 2, take SNPs 10001- 15000 and store in file 3 and so on ....., in the end I should have 500 files! I know that I can do it to create a single group by using sed command in Unix like 

sed -n 1,500p geno.file > out.file

but how can I do that sequentially to create all groups?

this is the first few lines of my genotype file.

HanXRQChr01 145635054   N   N   N   T   N   N   N   N   N   N   N   
HanXRQChr01 145798243   N   N   N   C   N   N   N   N   N   N   N   
HanXRQChr01 145823740   N   N   N   N   N   N   N   N   N   N   N   
HanXRQChr01 145933533   N   N   N   N   N   N   N   N   N   N   N   
HanXRQChr01 146276377   N   N   N   N   N   N   N   N   N   N   N
HanXRQChr01 146433063   N   N   N   G   N   G   N   N   N   N   N

Thanks in advance for any suggestion or help

snp subsetting
• 1,688 views • link
written by Ana Ana

1 answer

use split with option -l https://linux.die.net/man/1/split

SPLIT(1)                  BSD General Commands Manual                 SPLIT(1)

NAME
     split -- split a file into pieces

SYNOPSIS
     split [-a suffix_length] [-b byte_count[k|m]] [-l line_count]
           [-p pattern] [file [name]]

DESCRIPTION
     The split utility reads the given file and breaks it up into files of
     1000 lines each.  If file is a single dash (`-') or absent, split reads
     from the standard input.

     The options are as follows:

     -l line_count
             Create smaller files n lines in length.
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thank Pierre for giving me the hint. I had forgotten "split". Actually it was quite easy. I simply used $ split -n 5000 geno.file

• 0 views • link
written by Ana Ana

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