get.seqs from list file

mothur bugs
1

get.seqs doesn’t seem to be working correctly with list files.

For example:
mothur > list.seqs(group=AGSS.group)
mothur > get.seqs(accnos=AGSS.accnos, list=Ag_Ss.list)
mothur > read.otu(list=Ag_Ss.pick.list, label=0.01-0.03-0.05-0.10, group=AGSS.group)
Your group file contains 194035 sequences and list file contains 194204 sequences. Please correct.
For a list of names that are in your list file and not in your group file, please refer to Ag_Ss.pick.missing.group.

Ag_Ss.pick.missing.group contains 169 blank lines (no text at all).

2

Do you have duplicate names in your groupfile? If you want me to take a look you could send your files to mothur.bugs@gmail.com.

3

This seems to be a problem with extra commas left behind/carried forward in the list file.
It works fine after I do a replace all ,\t with \t in a text editor.

This what the list file looks like with extra commas:
…
0.03 1238 Ag283a08_196_1_1, Lc064a32_3…
0.04 925 Ss064a32_575_1_1, Lp012a…
…

And after removing them:
…
0.03 1238 Ag283a08_196_1_1 Lc064a32_3…
0.04 925 Ss064a32_575_1_1 Lp012a…
…

4

Thanks for helping us find this bug. It will be fixed in 1.9