Orsdxy

I have the following type of file:

transcr_25793 +

YAL039C -

transcr_25793 +

YAL037C-B -

transcr_20649 +

YBL100C -

transcr_7135 +

YBL029C-A -

transcr_11317 +

YBL067C -

transcr_25793 +

YAL038W +

transcr_7135 +

YBL029W +

I was trying to get something like this:

transcr_7135 +

YBL029C-A -

transcr_7135 +

YBL029W +

transcr_11317 +

YBL067C -

transcr_20649 +

YBL100C -

transcr_25793 +

YAL039C -

transcr_25793 +

YAL037C-B -

transcr_25793 +

YAL038W +

Then, afterward, I was looking for something like this:

transcr_7135 +

YBL029C-A -

YBL029W +

transcr_11317 +

YBL067C -

transcr_20649 +

YBL100C -

transcr_25793 +

YAL039C -

YAL037C-B -

YAL038W +

Could someone help me? I've scrolled through sort manual and some posts, but couldn't find anything that fit near this, just sort using numerical values to get odd lines...

Thanks a ton in advance!

Not exactly the sorting order you've showed, but maby right as well?

$ cat input.txt|paste - -| sort -k1,1V -k2,2| tr "t" "n" | awk '{if($0 in line == 0) {line[$0]; print}}'

    transcr_7135 +

    YBL029C-A -

    YBL029W +

    transcr_11317 +

    YBL067C -

    transcr_20649 +

    YBL100C -

    transcr_25793 +

    YAL037C-B -

    YAL038W +

    YAL039C -

Pure gawk solution:

awk -F_ '/transcr/{i=$2} /^Y/{a[i]=a[i]"n"$0} 

              END{PROCINFO["sorted_in"]="@ind_num_asc";

                  for(i in a) printf "%s","transcr_"i""a[i]"n"}' file

The trick is to sort indexes of array a numerically with a little help of gawk's PROCINFO special array.

transcr_7135

YBL029C-A -

YBL029W +

transcr_11317

YBL067C -

transcr_20649

YBL100C -

transcr_25793

YAL039C -

YAL037C-B -

YAL038W +

for element in $(sed -n 'p;n' a.txt |sort -nk 1.9 |uniq |awk '{print $1}')

do

    echo $element; cat a.txt |grep -A1 $i |grep -v trans |grep -v \\--

done

Where a.txt is your input. Tested:

[root@megatron ~]# cat a.txt

transcr_25793 +

YAL039C -

transcr_25793 +

YAL037C-B -

transcr_20649 +

YBL100C -

transcr_7135 +

YBL029C-A -

transcr_11317 +

YBL067C -

transcr_25793 +

YAL038W +

transcr_7135 +

YBL029W +

[root@megatron ~]# for i in $(sed -n 'p;n' a.txt |sort -nk 1.9 |uniq |awk '{print $1}')

do

echo $i; cat a.txt |grep -A1 $i |grep -v trans |grep -v \\--

done

transcr_7135

YBL029C-A -

YBL029W +

transcr_11317

YBL067C -

transcr_20649

YBL100C -

transcr_25793

YAL039C -

YAL037C-B -

YAL038W +

[root@megatron ~]#

With GNU sort and assuming the lines don't contain TAB characters:

paste - - < file | sort -V | tr 't' 'n' | awk '!seen[$0]++'

If you don't have GNU sort, and assuming the odd lines always follow that pattern, you can replace sort -V with sort -k1.9n.