<div dir="ltr">Hi Aaron, Hi Andreas,<br><div><br></div><div>Please, have a look at my two last commits (<a href="https://salsa.debian.org/med-team/ncbi-tools6/commits/master">https://salsa.debian.org/med-team/ncbi-tools6/commits/master</a>). Actually, the first one was made a month ago.</div><div><br><div><div class="gmail_quote"><div dir="ltr">On Tue, 17 Apr 2018 at 03:48 Aaron M. Ucko <<a href="mailto:ucko@debian.org">ucko@debian.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Liubov Chuprikova <<a href="mailto:chuprikovalv@gmail.com" target="_blank">chuprikovalv@gmail.com</a>> writes:<br>
<br>> At the moment, the following commands are still lacking tests:<br>
><br>
> - *asn2ff*, *gbseqget*, *findspl* (their output indicates they are<br>
> obsolete and/or unsupported)<br>
<br>
- asn2ff plays the same general role as asn2flat, and should be possible to<br>
test similarly.<br></blockquote><div><br></div><div>I tried to run it in a similar way to <i>asn2asn</i>. It throws an error which starts with "The asn2ff flatfile generator is obsolete and unsupported.<span class="inbox-inbox-Apple-converted-space"> </span>Please switch to using asn2gb/SeqEntryToGnbk in the future."</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
- gbseqget is like insdseqget, but formally uses GenBank-specific<br>
notation; as such, it requires network access.</blockquote><div><br></div><div>I added a test for <i>gbseqget</i> within if statement which checks for internet connection.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">- findspl also requires network access, and will need to be patched in the<br></blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
same fashion as taxblast; I'll take care of it when I get a chance.<br>
<br>
> - *asndhuff*, *nps2gps* (I can't figure out what kind of inputs they<br>
> require)<br>
<br>
- I'm not sure where you'd find input for asndhuff.<br>
- nps2gps takes a text Bioseq-set or Seq-entry of class nuc-prot, as<br>
obtained by (for instance) idfetch -g1234.</blockquote><div><i><br></i></div><div>A test for <i>nps2gps</i> also presents now.<br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">> - *fa2htgs*, *spidey* (they look too complicated for me and require much<br></blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
> time to understand how they work)<br>
<br>
That's fair. You can always come back to them later if you feel inspired.<br></blockquote><div><br></div><div>I have also finished with <i>spidey</i> and <i>fa2htgs</i> today.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">> - *taxblast* doesn't generate an output file and only generates an<br>
> *incomplete* html<br>
<br>
I'm not sure what's up with that, but as previously noted, it requires<br>
network access anyway.<br>
<br>
> - *errhdr*, *sortbyquote* (I can't figure out even what they are<br>
> supposed to do)<br>
<br>
- errhdr is a developer tool, working with files of the format found in<br>
errmsg/.<br>
- sortbyquote is also a developer tool, essentially a variant of sort<br>
that ignores everything outside quotation marks (and generally has far<br>
fewer options).</blockquote><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I'm not sure any of these is critical to test, but some<br></blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
should be relatively straightforward to work in at this point, and as<br>
noted I'm not quite ready to upload a new version anyway.<br></blockquote><div><br></div><div>Aaron, thank you for the explanations! They helped me a lot!</div><div><br></div><div>Aaron, Andreas: what is your opinion about the whole test? Could we consider it as completed?</div><div><br></div><div>With regards,</div><div>Liubov</div></div></div></div></div>