Include the sample/input file name on each line of the output

[flashton2003]

Hello,

It would be really helpful uf you could include the sample/input file name on each line of the output, to make it straightforward to combine the output of multiple runs into a single file.

Thanks,

Phil

[evolarjun]

Hi Phil,

You may be right. I usually process the results to prepend with a sed "s/^/$sample\t/'.

e.g:

amrfinder -p $sample.faa -n $sample.fna -g $sample.gff | sed "s/^/$sample\t/" > $sample.amrfinder

Prepending the filename could eliminate that, but a big part of why I haven't pushed for that is the decision of which filename prepend? There can be 3: --nucleotide, --protein, and --gff.

The other option would be to offer a command-line option to prepend a sample name column e.g.: --samplename <sample> to add a column with that text to the beginning, but until now I felt like that's a bit of feeping creatureism. I could be convinced otherwise.

Arjun

[flashton2003]

Hi Arjun,

Thanks for the quick response. IMHO, I don't think a --samplename flag would be over-board, as maybe some of the intended users of amrfinder might not be sed literate? But, up to you.

Thanks,

Phil

[azat-badretdin]

grep "" *blah > big.blah

[evolarjun]

Hi Phil,

Thanks, I think you've convinced me. I'll discuss it with the team, but you're right that even though there are a bunch of ways to do it with shell commands there are also a bunch of people who don't know them. (Thanks @azat-badretdin I hadn't thought of that one.)

Arjun

[flashton2003]

Ok, thanks Arjun!

[evolarjun]

With release version 3.8.28 we finally added a --name option to prepend an identifier to every row of the results.

[flashton2003]

thank you!