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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 +

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...

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 -

EDIT:

Insert the line number and uses it as a sorting key, should produce the exact output you like:

$ cat input.txt | paste - - | nl | sort -k2,2V -k1,1g | cut -f2- | tr "t" "n" | awk '{if($0 in line == 0) {line[$0]; print}}'

Pure gawk solution:

awk -F_ 'NR%2{i=$2;next}{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 +

BTW, its a pity awk doesn't offer an option to sort naturally a.k.a. version sort (according to text with numbers).

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

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

Or sort -t$'t' -sk1,1V to preserve the original order for entries with identical odd lines like in your expected output.

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.

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 ~]#