Re: GSOC [Continuous Integration for all biological applications inside Debian]
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
Reply to: