Hello Andreas,
Thanks for rapid response again i talk with my friend he will send an
introduction email to list. In test issue i'm confused about something if i
delete dh_make section and run adt-run package do automatic test in built
time and give no erors i notice that now but can't figure it out why
already and working on it. Also i make set -e in unit test file but that
fatal eror strings wont exit and work through the end it is another
abnormality i found so i want to give you a little update about it.
And CC issue i do it right now i think :-)
Best Regards
Canberk
2016-04-07 9:32 GMT+03:00 Andreas Tille <[email protected]>:
> Hi Canberk,
>
> On Thu, Apr 07, 2016 at 04:42:56AM +0300, Canberk Koç wrote:
> > >[I think I gave a warning that non-private messages will be answered on
> > >the mailing list and I hereby doing so shamelessly violating netiquette.
> > >It would be great if you would answer on list as well.]
> >
> > Sorry for miss clicking i forget to reply all.
>
> No problem. BTW, the mailing list policy for Debian list is to not CC
> the original poster but just send to the mailing list. The mail client
> mutt supports "list-reply" (L) to do this efficiently. I have no idea
> about other mail clients and whether these might support this. Just
> telling you that if you might write on other Debian lists people might
> send angry replies for personal CCs. :-)
>
> > I committed the changes to exonerate package i hope i do it right.
>
> Yes. You did. :-) I turned your "NMU" into a "Team upload". The test
> suite can implemented in this way. However, when I actually run the
> test I get:
>
> ...
> /tmp/exonerate-test.nhNsuB/util/fastasplit.test.sh
> Split fastasplit.test.fasta OK
> Split into two files as expected
> Input len 2136
> Output len 2136
> Input and output lengths match
>
> /tmp/exonerate-test.nhNsuB/util/fastadiff.test.sh
> fastadiff: id mismatch: CALM_HUMAN P53_HUMAN
> Different seqs recognised as different
> Identity test OK
>
> /tmp/exonerate-test.nhNsuB/util/fastasubseq.test.sh
> Generated correct subseq
>
> /tmp/exonerate-test.nhNsuB/util/fastavalidcds.test.sh
>
> ** (process:7647): WARNING **: odd_length length (7) not divisible by 3
>
> ** (process:7647): WARNING **: too_short length (4) not divisible by 3
>
> ** (process:7647): WARNING **: no_start missing start codon (has:AAA)
>
> ** (process:7647): WARNING **: no_end missing stop codon (has:TTT)
>
> ** (process:7647): WARNING **: in_frame_stop contains in-frame stop codon
> (pos:9, codon:TAG)
>
> ** (process:7647): WARNING **: non_acgt_base contains non-ACGT base: [pos:
> 5 base: N]
> Validiated CDS sequences OK
> >valid_seq
> ATGAAACCCGGGTTTTAA
> Validated correctly a single seq from input
>
> /tmp/exonerate-test.nhNsuB/util/fastaindex.fastafetch.test.sh
> Made index fastafetch.test.idx
> /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx CALM_HUMAN
> expect 0
> >CALM_HUMAN
> MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL
> TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE
> EFVQMMTAK
> /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx P53_HUMAN
> expect 0
> >P53_HUMAN
> MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA
> PPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT
> CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN
> TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVHVCACPGR
> DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL
> KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
> /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> A_MISSING_FROM_START
> expect 1
> ** FATAL ERROR **: Could not find identifier [A_MISSING_FROM_START]
> (missing -F ?)
> exiting ...
> /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> M_MISSING_FROM_MIDDLE
> expect 1
> ** FATAL ERROR **: Could not find identifier [M_MISSING_FROM_MIDDLE]
> (missing -F ?)
> exiting ...
> /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> z_MISSING_FROM_END
> expect 1
> ** FATAL ERROR **: Could not find identifier [z_MISSING_FROM_END] (missing
> -F ?)
> exiting ...
> fastaindex fastafetch test OK
>
> /tmp/exonerate-test.nhNsuB/util/fastaremove.test.sh
> Have calmodulin in input
> ** FATAL ERROR **: Could not open list for removal [CALM_HUMAN]
> exiting ...
> Calmodulin successfully removed
> PASS
>
>
> These "FATAL ERROR" strings in connection with "PASS" do not sound
> convincing. I wonder whether the build time tests are different
> in this aspect.
>
>
> > In MoM issue i want to do it but my mid-term exams start and they'll
> finish
> > 25 April i can do it after that date. And i want to ask you one friend of
> > mine wants to work it on too can we work together in that project.
>
> We'd be happy about any volunteer contributing to the Debian Med project.
>
> Kind regards
>
> Andreas.
>
> --
> http://fam-tille.de
>
>
--
[image: --]
Canberk Koç
[image: https://]about.me/canberkkoc
<https://about.me/canberkkoc?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links>
