how reformat kegg reconstruct pathway in vim?

Question

I need to reformat the kegg reconstruct pathway output, I have something like this in file1:

00550 Peptidoglycan biosynthesis (2)

K01000

K02563

00511 Other glycan degradation (8)

K01190

K01191

K01192

K01201

K01227

K12309

I need something like:

00550 Peptidoglycan biosynthesis (2)   K01000   K02563
00511 Other glycan degradation (6)   K01190   K01191   K01192   K01201   K01227   K12309

How could I reformat this like that in vim or linux

This can be done using a :g command. Something like this: g/^0/,/^0\|\%$/-j, which will mark each line starting with 0 and join until the next line starting with 0 (or end of line). However, it will miss the last line, so you need to add a final :$-j command to fix this. Posting here as comment, since question is on hold and answers can't be written — Christian Brabandt, Oct 23, 2018 at 12:56
@ChristianBrabandt the original question asked "how can I do that on linux or python" that's why I closed it. IMO it still lacks some details to be really useful but you can post your answer. — statox, Oct 23, 2018 at 12:58

Christian Brabandt · Accepted Answer · 2018-10-23 14:51:11Z

1

This can be done using a :g command.

Something like this:

g/^0/,/^0\|\%$/-j

This will mark each line (e.g. on which lines to act) starting with 0 and join until the next line starting with 0 (or end of line).

However, it will miss the last line, so you need to add a final

:$-j

command to fix this

answered Oct 23, 2018 at 14:51

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