Hi Aaron, Hi Andreas, Please, have a look at my two last commits ( https://salsa.debian.org/med-team/ncbi-tools6/commits/master). Actually, the first one was made a month ago.
On Tue, 17 Apr 2018 at 03:48 Aaron M. Ucko <u...@debian.org> wrote: > Liubov Chuprikova <chuprikov...@gmail.com> writes: > > > At the moment, the following commands are still lacking tests: > > > > - *asn2ff*, *gbseqget*, *findspl* (their output indicates they are > > obsolete and/or unsupported) > > - asn2ff plays the same general role as asn2flat, and should be possible to > test similarly. > I tried to run it in a similar way to *asn2asn*. It throws an error which starts with "The asn2ff flatfile generator is obsolete and unsupported. Please switch to using asn2gb/SeqEntryToGnbk in the future." - gbseqget is like insdseqget, but formally uses GenBank-specific > notation; as such, it requires network access. I added a test for *gbseqget* within if statement which checks for internet connection. > - findspl also requires network access, and will need to be patched in the > same fashion as taxblast; I'll take care of it when I get a chance. > > > - *asndhuff*, *nps2gps* (I can't figure out what kind of inputs they > > require) > > - I'm not sure where you'd find input for asndhuff. > - nps2gps takes a text Bioseq-set or Seq-entry of class nuc-prot, as > obtained by (for instance) idfetch -g1234. A test for *nps2gps* also presents now. > > - *fa2htgs*, *spidey* (they look too complicated for me and require > much > > time to understand how they work) > > That's fair. You can always come back to them later if you feel inspired. > I have also finished with *spidey* and *fa2htgs* today. > > - *taxblast* doesn't generate an output file and only generates an > > *incomplete* html > > I'm not sure what's up with that, but as previously noted, it requires > network access anyway. > > > - *errhdr*, *sortbyquote* (I can't figure out even what they are > > supposed to do) > > - errhdr is a developer tool, working with files of the format found in > errmsg/. > - sortbyquote is also a developer tool, essentially a variant of sort > that ignores everything outside quotation marks (and generally has far > fewer options). > I'm not sure any of these is critical to test, but some > should be relatively straightforward to work in at this point, and as > noted I'm not quite ready to upload a new version anyway. > Aaron, thank you for the explanations! They helped me a lot! Aaron, Andreas: what is your opinion about the whole test? Could we consider it as completed? With regards, Liubov