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Closed Issue: Install error for Sequence Assembler [10909]

VivekX — Thu, 16 May 2013 02:17:13 GMT

When attempting to install the M9 Sequence Assembler, I received the attached error indicating I had to remove the previous version to install it. Need to ensure we are reving the version of each installer.

Vivek - please assign as appropriate.

Closed Issue: WiX Installer : Uninstallation of Bio_Excel also removes MBF installed DLLs [11322]

zyskowski — Thu, 16 May 2013 02:16:46 GMT

Uninstallation of Bio_Excel also removes MBF installed DLLs

Repro Steps,
Install MBF.msi
Install Bio_Excel.msi
Uninstall Bio_Excel.msi

Actual result :
Uninstalltion of Bio_Excel also removes MBF installer DLLs. It removes the below DLls,
\MBF\Add_Ins\MBF.PaDeNA.dll
\MBF\Add_Ins\MBF.PAMSAM.DLL
\MBF\MBF.DLL
\MBF\MBF.WebServiceHandlers.dll

Expected result : Uninstall of Bio_Excel should not remove MBF installer DLLs. Should remove only \MBF\Excel Biology Extension.

Commented Feature: Sequence Assembler : PaDeNA always returns contigs even if it runs by enabling Scaffold generation checkBox. [11298]

abhisheks — Tue, 04 Oct 2011 11:38:37 GMT

PaDeNA always returns contigs even if it runs by clicking Scaffold generation checkBox.
It doesn't return scaffold sequences. Should return scaffold sequence.
Repro steps,

1.       Open sequence assembler
2.       Load sequence reads.
3.       Click on Assemble button, select PaDeNA.
4.       Check Scaffold Generation checkbox.
5.       Assemble sequence
(Run PaDeNA for the reads attached in this bug with parameters
Kmer :6,DanglingThreshold:3,RedundantThreshold -7,Redundancy :1,Depth -3.

Actual result : PaDeNA returns Contigs not scaffolds.
PaDeNa returns following contigs if it runs with or without enabling scaffold generation checkBox for the attached file
GCGCGC
TAGCGCGCTA
AGCGCGC
GCGCGCCGCGCG
Expected result : PaDeNA should return proper scffold sequences if it runs by enabling Scaffold generation checkbox.
Comments: ** Comment from web user: abhisheks **

Hi LeonardoBio,

You can use PaDeNa on the HPCS 2008.

We need more specific information about your requirements. This will helps us to answer your query better regarding the use of PaDeNa on the HPCS 2008. Can you please update us on the same.

Regards,
MSR ER Support Team

Commented Feature: Sequence Assembler : PaDeNA always returns contigs even if it runs by enabling Scaffold generation checkBox. [11298]

leonardoBio — Fri, 30 Sep 2011 03:54:27 GMT

i'm starting to using PaDeNA in cluster in windows HPC 2008, any ideas?

Commented Feature: Padenautil FASTQ support [14114]

sjmercer — Wed, 17 Aug 2011 21:31:25 GMT

The Padena algorithm supports FASTQ assembly (insofar as it needs only bases and makes no use of quality values) but it seems that PadenaUtil does not. We do have a parser for FASTQ.
Comments: ** Comment from web user: sjmercer **

Agreed. Since MBF also parses BAM and SAM formats as well, it would make the most sense to modify PadenaUtil to automatically detect file type and invoke the appropriate parser, supporting FASTA, FASTQ (all types), BAM and SAM.

Created Feature: Padenautil FASTQ support [14114]

Rickbe — Wed, 17 Aug 2011 20:46:41 GMT

The Padena algorithm supports FASTQ assembly (insofar as it needs only bases and makes no use of quality values) but it seems that PadenaUtil does not. We do have a parser for FASTQ.

Commented Issue: QualitativeSequence.GetSubSequence(): ID and metadata are not copied to the returned object [13978]

reach2raziq — Thu, 28 Jul 2011 09:24:47 GMT

When calling QualitativeSequence.GetSubSequence(), the new QualitativeSequence object being returned does not retain the original information stored in the properties ID and metadata.

For example:
QualitativeSequence qseq = new QualitativeSequence(Alphabets.DNA, FastQFormatType.Sanger, "ATGC", "ABCA");
qseq.ID = "my fastq sequence";
var newqseq = qseq.GetSubSequence(0, 2);
Console.WriteLine(newqseq.ID); // empty
Comments: ** Comment from web user: reach2raziq **

Hi,

Thanks for reporting this. This is a bug. The QualitativeSequence.GetSubSequence() method is correct. We will fix the issue related to Sequence.GetSubSequence() in future releases/patches.

Thanks,
MSR Support Team

Commented Issue: QualitativeSequence.GetSubSequence(): ID and metadata are not copied to the returned object [13978]

kch — Tue, 26 Jul 2011 22:58:34 GMT

I see your point. However, the equivalent GetSubSequence() in the Sequence class already copies ID and metadata to the subsequence. So there is a some inconsistency.

Commented Issue: QualitativeSequence.GetSubSequence(): ID and metadata are not copied to the returned object [13978]

reach2raziq — Tue, 26 Jul 2011 11:34:34 GMT

I'm not sure I'd consider the proposal to be completely valid though.. GetSubSequence returns a new sequence, related but not identical to the original (it actually returns a SubSequence of the original sequence with the same Alphabet and FormatType).. it might be the complete sequence but it also might be a portion (even in the middle).. so the ID probably shouldn't be the same.. and I'm not sure why I'd want the metadata with it..

But that said, it would be trivial to implement. I'd probably put a flag onto the method (with an optional parameter as input set to false to indicate whether to copy the metadata). The problem with copying metadata is it would end up being a shallow copy; changing the original on the original sequence would alter the value on the subsequence too.. probably unexpected by most I'd guess.

Thanks,
MSR Support Team

Created Issue: QualitativeSequence.GetSubSequence(): ID and metadata are not copied to the returned object [13978]

kch — Fri, 22 Jul 2011 22:55:53 GMT

Created Issue: verify NUCmer alignment results [13633]

dourada — Thu, 02 Jun 2011 01:48:27 GMT

verify that the results of a NUCmer alignment are correct. Do a multiple alignment on 4 sequences. You will receive 3 actual alignment objects containing an AlignedSequence object and a list of two Sequences (the sequences that generated the alignment). It's the list of two Sequences that do not seem to be correct. After alignment the sequence list looks like:

seq1
seq1

seq1
seq2

seq1
seq3

but should look like (I think):

seq1
seq2

seq1
seq3

seq1
seq4

Commented Issue: Getting original sequence names and IDs in aligned sequences [13534]

FadiF — Tue, 24 May 2011 21:57:40 GMT

Greetings.
I have a couple of issues I would like to discuss ( I am not sure if these are bug or unfinished items - a roadmap of your progress in this regards will be useful). Sorry for the long description.

FIRST: I noticed that both in SequenceAssembler and the Bio.dll that I am using to implement aligners to do sequence alignment, the original sequence names and IDs are missing. Consequently, I cannot tell which original sequence corresponds to which aligned sequence. An example will make this clear, and help you understand the issue (I am using NUCmer aligner here):

Original sequences named: Seq-1, Seq-2, Seq-3, Seq-4
The result is:
Alignments:
Alignment1
Sequence1
Sequence2
Alignment2
Sequence1
Sequence2
Alignment3
Sequence1
Sequence2

How can I tell for sure, without looking at the actual aligned sequences, that Sequence1 in the result corresponds to Seq-1 in the original sequence list? Or Sequence2 in the result of aligned sequences corresponds to Seq-2, Seq-3 or Seq-4 of the input sequences, and in that order? Is it guarenteed that Sequence1 corresponds to Seq-1, and that Sequence2 corresponds to Seq-2, Seq-3 and Seq-4 respectively in the aligned sequences? Is the order in the returned aligned sequences preserved and guarenteed?

If I use PAMSAM, again original sequence names (Seq-1, Seq-2, Seq-3, Seq-4) are translated to Sequences1, Sequences2, Sequences3 and Sequences4. Is the order preserved in the aligned sequences?
Why not update ID in the aligned sequences to the original ID?

SECOND: The Metadata object of the aligned sequences is not being updated, at least for PAMSAM, consequently, there is no staistics available from PAMSAM. Is there a way to obtain these statistics? An example, using AlignedSequences will be helpful.

THIRD: I need Consensus sequences for PAMSAM alinment data. Is there a way to get this? I noticed that Metadata object is not populated. An example, using AlignedSequences will be helpful. For example, I get Consensus like:
MUMmer: Encoding.ASCII.GetString(alignedList[0].PairwiseAlignedSequences[0].Consensus.ToArray()); <--- from Consensus property
NUCmer: Encoding.ASCII.GetString(((Bio.Sequence)(alseq.Metadata["Consensus"])).ToArray()); <--- from Consensus item of Metadata dictionary

Your help in this regards will be highly appreciated.
KPOnCodeplex2011
Comments: ** Comment from web user: FadiF **

Hi KPOnCodeplex2011

We confirm that Issue 1 and 2 are fixed, so if you have a an elisment on TFS, please update to the latest and verify.

Regarding the third issue: "PAMSAM is not giving consensus… "
PAMSAM’s output is SequenceAlignment but for MUMmer and NUCmer it is PairwiseSequenceAlignment. SequenceAlignment will contain only the aligned sequences and not the consensus.. Currently this is a limitation of PAMSAM.

I hope that resolves your questions... and thanks for using MBF.

Fadi Fakhouri, on behalf of the MBF Team

Commented Issue: Getting original sequence names and IDs in aligned sequences [13534]

FadiF — Tue, 24 May 2011 21:51:54 GMT

Hi KPonCodeplex2011
Our developer confirmed that Item 1 and 2 you reported are fixed,
Regarding Issue 3 you report above....
"PAMSAM is not giving consensus:… PAMSAM’s output is SequenceAlignment but for MUMmer and NUCmer it is PairwiseSequenceAlignment. SequenceAlignment will contain only the aligned sequences and not the consensus.. Currently this is a limitation of PAMSAM.

For the fix, they will be part of the next release, or if you are a committer on TFS, you can sync to the latest and verify.

Please let me know if you need anything further, and thank you for using MBF!

Fadi Fakhouri on behalf of the MBF Team

Commented Issue: GenBank Parser: Incorrect parse when qualifier contains embedded '/' at start of a line. [13552]

FadiF — Mon, 23 May 2011 17:38:29 GMT

Self-contained archive containing solution and data to reproduce this bug can be downloaded at
http://bio.mquter.qut.edu.au/Downloads/GenBankParserBugReport.zip (5.5MB)

When parsing a “/note” qualifier, if there are multiple lines of note text, sometimes a line break will happen such that a "/" which is part of the text will start a continuation line. This causes the parser to treat the following text on that line as a qualifier and any following text lines as values for the qualifier. This happened in MBF v1 and still happens in v2.
An example of this is in ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
Acaryochloris_marina_MBIC11017_uid58167/NC_009925.gbk:
misc_feature 948729..949922
/gene="kmo"
/locus_tag="AM1_0975"
/note="2-polyprenyl-6-methoxyphenol hydroxylase and
related FAD-dependent oxidoreductases [Coenzyme metabolism
/ Energy production and conversion]; Region: UbiH;
COG0654"

The parser identifies the following qualifiers for this feature. Observe that the /note has been truncated and a spurious qualifier has been introduced based on the tail of the /note.

Qualifier: { Energy production and conversion]; Region: UbiH;}
Value : { COG0654"}

Qualifier: {db_xref}
Value : {"CDD:30999"}

Qualifier: {gene}
Value : {"kmo"}

Qualifier: {locus_tag}
Value : {"AM1_0975"}

Qualifier: {note}
Value : {"2-polyprenyl-6-methoxyphenol hydroxylase and\nrelated FAD-dependent oxidoreductases [Coenzyme metabolism}
Comments: ** Comment from web user: FadiF **

Hi lbuckingham,
We confirm that we can reproduce this. We will Look at possible solutions, It is currently being tracked in our TFS (If you are a committer, please view item TFS work item 31432).
I will respond to you once we have a resolution / conclusion of our investigations.
Thanks
Fadi Fakhouri
On Behalf of MBF Team

Commented Issue: GenBank Parser: Incorrect parse when qualifier contains embedded '/' at start of a line. [13552]

FadiF — Mon, 23 May 2011 16:49:47 GMT

Hi lbuckingham,

Thanks for this, I have forwaded this information to our Testers to try to reproduce this, and we will get back to you very shortly.

Fadi Fakhouri
on behalf of the MBF team

Created Issue: GenBank Parser: Incorrect parse when qualifier contains embedded '/' at start of a line. [13552]

lbuckingham — Fri, 20 May 2011 23:58:04 GMT

Commented Issue: Getting original sequence names and IDs in aligned sequences [13534]

FadiF — Fri, 20 May 2011 09:24:10 GMT

We are still looking into this, I will update you once we have an answer.
If the fix for above passes code review, then yes, I think this will be in the released bits of 2.0, and will be in the DevelopmentBranch of TFS... I will let you know as soon as I hear back from our developrs.

Fadi Fakhouri, on behalf of the MBF Team

Commented Issue: Getting original sequence names and IDs in aligned sequences [13534]

KPonCodeplex2011 — Thu, 19 May 2011 22:53:43 GMT

Hi Fadi,
Thanks very much. Yes, I am enjoying using MBF library.
Your prompt response is greatly appreciated. Your changes will be really useful for us. Also, please check out the same on Smith-Waterman and Needleman aligners. Will you be able to include it in 2.0 release?

Any update on issue SECOND and THIRD above?
KPOnCodeplex2011

Commented Issue: Getting original sequence names and IDs in aligned sequences [13534]

FadiF — Thu, 19 May 2011 16:59:57 GMT

Hi KPonCodeplex2011

Thanks for reporting this, Aldo, one of our developers had a look at this, and this is his report back:

I see two issues here:
1. Nucmer, Mumer and PAMSAM is not setting sequence ID on the output sequences.
This looks like we missed out to update the ID on the output sequences while we ported Bio to new OM. According to current OM, ID has to be set explicitly. Earlier this was not the case.
2. Sequence assembler is not showing sequence ID in the tree view, instead showing Seq1, Seq2 etc…
This was designed and implemented so from day 1, but showing the ID seems to be more relevant than showing just ordered numbers..

He has a fix for both of these, once the fix passes code review, I will update you with the information.

Thanks again for reporting this, and hope you are enjoying using MBF.

Fadi Fakhouri, on behalf of The MBF Team

Created Issue: Getting original sequence names and IDs in aligned sequences [13534]

KPonCodeplex2011 — Wed, 18 May 2011 17:58:35 GMT