How to split a large SNP file into individual chunks

To convert this (one animal per line, UGA format as explained here and here)

         1 012202001001000020202000

         2 012202001001000021211110

         3 012202001001000020202000

         4 012211001100010020202000

         5 111211101100010110111001

         6 002202000000000021211110

         7 012211001100010021211110

         8 022220002200020020202000

         9 012202001001000020202000

        10 111211101100010110111001

into as many individual SNP files as loci,e.g.

zcat singlemarker/x000001.gz | head

        1   1

        2   1

        3   1

        4   1

        5   2

        6   1

        7   1

        8   1

        9   1

       10   2

zcat singlemarker/x000002.gz | head

         1   2

         2   2

         3   2

         4   2

         5   2

         6   1

         7   2

         8   3

         9   2

        10   2

How to do it efficiently?

1-transpose the file (in my case via Fortran program) to:

0000100001

1111101211

2222122221

2222222222

0001101201

e.g. the first line is the first marker, and so on

2-use the extraordinary GNU split to split into files, one line (=one marker) at a time:

split -l 1 -d BB.700K.gen_transposed -a 6 --numeric-suffixes=1 --filter='gzip >$FILE.gz'

This command splits one line at a time (-l 1) creates a series of files with numeric suffixes starting in 1 (--numeric-suffixes=1) of width 6 (-a 6) like x000002.gz and finnaly "piped" through gzip to obtain compressed files (--filter='gzip >$FILE.gz')

Still the files look

0000100001

1111101211

2222122221

3-use  GNU fold to insert a newline after each character:

zcat  singlemarker/x000001.gz | fold -w 1