Copy and insert header into respective lines

[GiovanniC]

Hi all,

I have the following input file:

START
Query= TaBa0-000001
>gnl|UG|Ta#S13248438 ug=Ta.24021
>gnl|UG|Ta#S17880947 ug=Ta.8115
>gnl|UG|Ta#S17984398 ug=Ta.29549
Query= TaBa0-000002
>gnl|UG|Ta#S17988614 ug=Ta.30772
>gnl|UG|Ta#S16202639 ug=Ta.25603
>gnl|UG|Ta#S13134499 ug=Ta.16563
>gnl|UG|Ta#S16238874 ug=Ta.10196
Query= TaBa0-000003
>gnl|UG|Ta#S17987015 ug=Ta.28640
>gnl|UG|Ta#S17897903 ug=Ta.27673
END

What I'd line to do is take the Query= header and place it in the same line as the >gnl numbers under it to get the following output format:

START
Query= TaBa0-000001 >gnl|UG|Ta#S13248438 ug=Ta.24021
Query= TaBa0-000001 >gnl|UG|Ta#S17880947 ug=Ta.8115
Query= TaBa0-000001 >gnl|UG|Ta#S17984398 ug=Ta.29549
Query= TaBa0-000002 >gnl|UG|Ta#S17988614 ug=Ta.30772
Query= TaBa0-000002 >gnl|UG|Ta#S16202639 ug=Ta.25603
Query= TaBa0-000002 >gnl|UG|Ta#S13134499 ug=Ta.16563
Query= TaBa0-000002 >gnl|UG|Ta#S16238874 ug=Ta.10196
Query= TaBa0-000003 >gnl|UG|Ta#S17987015 ug=Ta.28640
Query= TaBa0-000003 >gnl|UG|Ta#S17897903 ug=Ta.27673
END

Would anyone have an idea how I might be able to do this?

Thanks for any help.

Cheers,

Giovanni

 

[PHV]

Something like this ?
awk '
/^Query=/{q=$2;next}
$1!~/START|END/{print q,$0}
' /path/to/input

Hope This Helps, PH.
Want to get great answers to your Tek-Tips questions? Have a look at FAQ219-2884 or FAQ222-2244

 

[GiovanniC]

Hi PHV,

Thanks for the suggestion. It worked well mostly, but I just noticed one important thing (for me anyway). In cases where the Query= string is not followed by the string starting with >gnl on the next line, the Query= header is not printed. ie if I have this situation:

Query= Taba0-00001
Query= Taba0-00002
>gnl|UG|Ta#S13248438 ug=Ta.24021
>gnl|UG|Ta#S17880947 ug=Ta.8115
>gnl|UG|Ta#S17984398 ug=Ta.29549
Query= Taba0-00003

The output does not include Taba0-00001 and Taba0-00003. How do I go about modifying the script so that they don't get left out?

Giovanni

 

[PHV]

you may try this:
awk '
/^Query=/{if(t)print q;q=$0;t=1;next}
$1!~/START|END/{t=0;print q,$0;next}1
END{if(t)print q}
' /path/to/input

Hope This Helps, PH.
Want to get great answers to your Tek-Tips questions? Have a look at FAQ219-2884 or FAQ222-2244

 

[GiovanniC]

Thanks PHV ... works perfectly!