Bugs in the new version

dudimarcus commented 7 years ago

Some minor changes but might worth mentioning.

In the alignments results files some things have changed:

fasta are now one liner instead of 80 char limit (no big issue)
title for the query first instance in each file changed (now without start-end)
some alignment are not matching the query with variable lengths

for example two lines from the same file are not in the same length:

biomap|4.1.0|44065ac602ae7ac62af1debdc451ff77 ......................acrlrkcyevgmmkggirkdrrggrmlkhkrqrddgegrgevgSagdmraa.......nlwpsplmIKRSKKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLN...SGI--------------------------------------------------------SHVEAKK--------------------RILNLHP-..... cath|4.1.0|2ertA00/1-261 ..............................................................mdpM......................IKRSKKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLN...SGVYTFLSSTLK

sillitoe commented 7 years ago

Can you provide the query sequence that returned this alignment?

dudimarcus commented 7 years ago

I think it was this one:

>p03372
MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANAQVYGQTGLPY
GPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLENEPSGYTVREAGPPAFYRPNSDNRRQG
GRERLASTNDKGSMAMESAKETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQAC
RLRKCYEVGMMKGGIRKDRRGGRMLKHKRQRDDGEGRGEVGSAGDMRAANLWPSPLMIKRSKKNSLALSLTADQMVSALL
DAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPG
KLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLD
KITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAPTSRGGASV
EETDQSHLATAGSTSSHSLQKYYITGEAEGFPATV

sillitoe commented 7 years ago

Looks like this was affecting the last sequence in the alignment.

Result of the server sending the file before closing (and flushing) the file handle.

Applied fix at the backend and added test to confirm.

UCLOrengoGroup / cath-tools-seqscan

Bugs in the new version #8