Get list of sequences from a shared file

OK, I might be missing something obvious, so sorry if this is stupid question

I have a shared file where 602 otus were found between each of my (7) samples. Is there any way of linking this data to the list file so I can get a list of the sequences for each column in the shared file. The get.sharedotu does not work because I am not interested in only the OTUs that are shared between ALL the samples.


PS, I can grep and parse the sequences from the list file, but it is not sorted the same way as the OTUs in shared file!

the get.sharedotu command, now called get.sharedseqs, has a group parameter. By default the command reports the otus unique to all groups, but you can set groups=group1 to see the otus unique to group1. What you really want is a parse.list command which is on the to do list. :slight_smile:

Thank you for the reply.
I have the 1.6 version, so I still just have the get.sharedotu. Will the 1.8 version be of more help with this particular issue? The reason I need it is to identify the groups of interest (those who are really abundant in some groups and not others) so I can do some more phylogeny etc. on those particular sequences.
yeah, I was thinking of parsing the list file myself somehow, but my programming skills are really not there! (just know some basic sed and awk and that’s it…)
Anyway, thanks for a really good program, I just started using it and I really find it VERY helpful!

Cheers, Sonja

Actually, I got exactly what I wanted! I had misunderstood the list file, I thought the OTUs were delimited by commas, but the different OTU’s are of course limited by tabs. When I imported the data from the .shared file and the data from .list file for the same same distance into excel, I can now see that these files ARE sorted in the same order!! The numbers match perfectly. Jippii!!!