gmane.comp.python.bio.general

Re: [Biopython] Legacy blast XML parser returns prematurelyStopIteration

Peter Cock — 2012-05-16T09:48:10

On Wed, May 16, 2012 at 10:32 AM, Martin Mokrejs
<mmokrejs< at >fold.natur.cuni.cz> wrote:

Could you file a bug here and attach the complete XML test case please?
http://redmine.open-bio.org/projects/biopython

Our XML parser should handle both NCBI  'legacy' BLAST and BLAST+

Thanks,

Peter

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[Biopython] Legacy blast XML parser returns prematurelyStopIteration

Martin Mokrejs — 2012-05-16T09:32:34

Hi,
  I am parsing some blast 2.2.24 XML output and the last record I get is the one from
iteration 124. I see that entry is followed by a new <Iteration_iter-num> section which
is probably the culprit. I will try newer legacy blast but still, biopython could maybe
overcome this bug in XML input?



blastall -p blastn -A 4 -i SRR068315.fasta -d my_targets.fasta -F 0 -S 1 -r 2 -e 10e-30 -m 7

<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
  <BlastOutput_program>blastn</BlastOutput_program>
  <BlastOutput_version>blastn 2.2.24 [Aug-08-2010]</BlastOutput_version>
  <BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~&quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs&quot;,  Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
  <BlastOutput_db>my_targets

Re: [Biopython] parsing genbank file

Lapointe, David — 2012-05-14T14:00:20

You might try looking for sequences here

ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Deinococcus_radiodurans_R1_uid57665/

David

-----Original Message-----
From: biopython-bounces< at >lists.open-bio.org [mailto:biopython-bounces< at >lists.open-bio.org] On Behalf Of Peter Cock
Sent: Monday, May 14, 2012 9:49 AM
To: Anubrata Das
Cc: biopython< at >lists.open-bio.org
Subject: Re: [Biopython] parsing genbank file

On Mon, May 14, 2012 at 1:03 PM, Anubrata Das <anubratadas< at >gmail.com> wrote:

Probably your GenBank file only contains one record (for the
whole of chr1). You could use Bio.SeqIO.read(...) in this case:

from Bio import SeqIO
record = SeqIO.parse(r"C:\Dr1.gb","genbank")
print record.id
print len(record.features)

Peter
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Re: [Biopython] parsing genbank file

Peter Cock — 2012-05-14T13:48:39

Probably your GenBank file only contains one record (for the
whole of chr1). You could use Bio.SeqIO.read(...) in this case:

from Bio import SeqIO
record = SeqIO.parse(r"C:\Dr1.gb","genbank")
print record.id
print len(record.features)

Peter
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[Biopython] parsing genbank file

Anubrata Das — 2012-05-14T12:03:29

i am new to biopython. i wanted to parse through individual records
from the genbank file of deinococcus radiodurans chromosome 1
sequence.for e.g i wanted the list of identifiers for each record
['NC_001263.1']
but i would get only one master entry. then if i wanted to parse thru
individual records
SeqRecord(seq=UnknownSeq(2648638, alphabet = IUPACAmbiguousDNA(),
character = 'N'), id='NC_001263.1', name='NC_001263',
description='Deinococcus radiodurans R1 chromosome 1, complete
sequence.', dbxrefs=['Project:57665'])

Traceback (most recent call last):
  File "<pyshell#25>", line 1, in <module>
   record.next()
StopIteration
i get this output.
please tell me the correct method
regards

Re: [Biopython] .ent versus .pdb files?

João Rodrigues — 2012-05-13T09:16:00

Hi Mark,

Nope, not at all.

Cheers,

João
No dia 13 de Mai de 2012 08:55, "Mark Livingstone" <
livingstonemark< at >gmail.com> escreveu:


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[Biopython] .ent versus .pdb files?

Mark Livingstone — 2012-05-13T06:54:28

Hi Guys,

I have a bunch of files which appear to be pdb file-like but have the
.ent file extension. Is there any difference of significance to
Bio.PDB?

Thanks in advance,

MarkL
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[Biopython] Superposition

Mark Livingstone — 2012-05-12T02:06:07

Hi Guys,

Thanks to Andrew and others for help in my previous message. I have
gone through various incarnations of my code, and suddenly found this
simple code works for the small test I have done.

I am using the datafiles from:

Kellogg, E. H., Leaver-Fay, A., & Baker, D. (2011). Role of
conformational sampling in computing mutation-induced changes in
protein structure and stability. Proteins, 79(3), 830–838.
doi:10.1002/prot.22921

These files have been modified so that there are matched PDBs which
vary only by one mutated residue, and I am trying to  carbon alpha
superimpose the PDB which is the Mutanttype over the Wildtype and save
to a PDB - which I seem to have fluked how to do. I am still working
on the code for directory traversal so I have not tried it on the
hundreds of matched PDBs yet.

Is there anything in this code which is going to bite me? How can I improve it?

------------------------------------------------------------------------------------
#!/usr/bin/env python

# Wildtype (wt) = ref

Re: [Biopython] Fwd: BlastParsing gives Value Error: Invalid header?

Martin Mokrejs — 2012-05-09T18:48:19

Hi Peter,

Peter Cock wrote:

No, not yet.


Yes, "blastall -p blastn ...", the default plaintext pairwise output (-m 0),
version 2.2.24.


Its great that we have GSoC students, would I have some spare time I would mentor
one. Good luck and thanks for your care, Peter!
Martin

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Re: [Biopython] Fwd: BlastParsing gives Value Error: Invalid header?

Peter Cock — 2012-05-09T18:25:36

On Wed, May 9, 2012 at 7:01 PM, Martin Mokrejs
<mmokrejs< at >fold.natur.cuni.cz> wrote:

Have you contacted the NCBI about this possible regression?


Could you clarify if you are talking about documentation for calling
the 'legacy'
BLAST command line tools (e.g. blastall), or documentation for parsing the
plain text human readable output (which still exists in BLAST+)?

On a related point, Bow's just done a bit of work updating our plain
text parser to
cope with BLAST+ (specifically changes in BLAST 2.2.25+ and/or 2.2.26+).

One of the aims of Bow's GSoC project will make dealing with the different
BLAST formats a lot simpler.

Peter

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Re: [Biopython] Fwd: BlastParsing gives Value Error: Invalid header?

Martin Mokrejs — 2012-05-09T18:01:08

Hi Brad,
  I just got bitten by this myself as well. Could be the legacy blast parser
improved to give clearer error message? E.g. that it failed to find the LOCUS
line or whatever was it looking for? With the legacy BLAST documentation being
gone from current Tutorial it is easy to pick the wrong parser. ;)
  And BTW, please do not drop support for legacy BLAST. I just cannot make BLAST+
give me same alignment, no matter what arguments I use to adjust for the (it gives me
wider alignment than wanted and I can make it a look shorter, but shortening it just
a bit like legacy BLAST output .. is not doable).
  And, took me a while to find old biopython-1.52.tar.gz to lookup the old docs.
Could there be a hyperlink from Tutorial to these unpacked, browseable sources? ;)
I am speaking about http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc85 .
Thanks,
Martin
  

Brad Chapman wrote:
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[Biopython] GSoC Project Update -- 1

Wibowo Arindrarto — 2012-05-09T16:24:43

Hi everyone,

I just posted my latest blog updated here:
http://bow.web.id/blog/2012/05/warming-up-for-the-coding-period/

To summarize, I've spent most of my time getting to know the programs
I will support better. This has been done by:

1. Playing around with the programs to see how many different outputs
I can generate.
2. Writing scripts to automate test case generation for each of the programs.
3. Writing wrappers (for programs not yet wrapped by Biopython: FASTA,
HMMER, and BLAT) to ease writing the test case generators.
4. Continuing to complete my proposed SearchIO object naming scheme
(http://bit.ly/searchio-terms)

The test cases, their generators, and the wrappers I've written are
available in my non-Biopython gsoc repo here:
http://github.com/bow/gsoc/. Additionally, I've used the generated
test case to improve a recent bug report and submitted a fix for the
next release.

For the coming weeks prior to coding start, I'm planning to play
around more with XML and SQLite as I will use them in the c

Re: [Biopython] PDBParser-chain breaks

Eric Talevich — 2012-05-09T14:31:34

Oh, there's a caveat to the warnings module -- if a given warning isn't
captured this way the first time, it's never issued again. So, parsing 3BEG
once normally, and again with the setup I gave, won't trigger the warning
again and therefore won't raise an error.

On Wed, May 9, 2012 at 1:39 AM, João Rodrigues <anaryin< at >gmail.com> wrote:


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Re: [Biopython] PDBParser-chain breaks

João Rodrigues — 2012-05-09T05:39:40

For some reason however, I didn't get the discontinuous error .. That's why
I proposed this alternative.

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



2012/5/9 Eric Talevich <eric.talevich< at >gmail.com>


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Re: [Biopython] PDBParser-chain breaks

Eric Talevich — 2012-05-09T01:59:13

The warnings module also lets you convert any warning to an error (or
ignore it, etc.). Use a regular expression to match the warning message:

from Bio import PDB
import warnings
warnings.filterwarnings('error', message='.*discontinuous at.*')
p = PDB.PDBParser()
s = p.get_structure("", "3BEG.pdb")


On Tue, May 8, 2012 at 3:39 PM, João Rodrigues <anaryin< at >gmail.com> wrote:


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Re: [Biopython] PDBParser-chain breaks

João Rodrigues — 2012-05-08T19:39:02

Of course. Since they throw a warning just make sure to count the warnings,
parse the chain break ones, and if they are more than 0, you have chain
breaks.

Cheers,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



2012/5/8 George Devaniranjan <devaniranjan< at >gmail.com>


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Re: [Biopython] PDBParser-chain breaks

George Devaniranjan — 2012-05-08T19:37:47

Hi João,

Is there a way though to find PDB's with chain breaks? using biopython?

Thank you,
George

On Tue, May 8, 2012 at 3:34 PM, João Rodrigues <anaryin< at >gmail.com> wrote:


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Re: [Biopython] PDBParser-chain breaks

João Rodrigues — 2012-05-08T19:34:26

Hi George,

Chain breaks are pretty "harmless" and usually do not represent a faulty
PDB file. The PERMISSIVE flag is for "features" like missing b-factors.

Cheers,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



2012/5/8 George Devaniranjan <devaniranjan< at >gmail.com>


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[Biopython] PDBParser-chain breaks

George Devaniranjan — 2012-05-08T19:12:22

Hi,

I thought using PERMISSIVE=0 would raise an exception if I pass a PDB with
chain breaks.
However, nothing like that seems to happen.....

For instance

P=PDBParser(PERMISSIVE=0)
structure=P.get_structure('test', '7ODC.pdb')


7ODC has 3 chain breaks but it does not raise an exception.

Thank you
George
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Re: [Biopython] PDBParser

George Devaniranjan — 2012-05-08T12:44:09

Thank you everyone,

I just need the coordinates of certain fragments from PDB files and this
works for me.
I was trying to use the PDBParser only, but thank you for pointing out
PDBIO to me.

Thank you,
George

On Tue, May 8, 2012 at 4:16 AM, João Rodrigues <anaryin< at >gmail.com> wrote:


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Re: [Biopython] PDBParser

João Rodrigues — 2012-05-08T08:16:44

Hello George,

You want to write only a part of the PDB file? What do you mean by 'all the
info'? If it is header information as well, then this is not possible, but
coordinates it is. You can do it in two ways:

1. Delete all residues/chains/models that are not part of your region of
interest and then write the structure with PDBIO.

2. Use the 'Select' class from PDBIO.py and trim the region of interest.
For example, for residues 1-10 you could do something like this:

from Bio.PDB import PDBIO
from Bio.PDB import Select

class ResidueFilter(Select):
    def accept_residue(self, residue):
        if residue.id[1] in range(1,11):
            return 1

P = PDBParser()
s = P.get_structure('dummy', 'foo.pdb')

io = PDBIO()

io.set_structure(s)
io.save('foo_1-10.pdb', ResidueFilter())


Check the FAQ for a more detailed explanation:

http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf

Cheers,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



2012/5/8 George Devaniranjan <devaniranjan< at >gmail.com>


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