gmane.comp.python.bio.general

Re: [Biopython] pass a variable to a blast cmd

Willis, Jordan R — 2013-06-18T15:29:21

Just literally put the variable right in there.

On Jun 18, 2013, at 10:15 AM, Frederico Moraes Ferreira <ferreirafm< at >usp.br> wrote:




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Re: [Biopython] pass a variable to a blast cmd

Frederico Moraes Ferreira — 2013-06-18T15:15:39

I'm sorry for this stupid question.
Best,
Fred

Em 18-06-2013 11:12, Frederico Moraes Ferreira escreveu:

[Biopython] pass a variable to a blast cmd

Frederico Moraes Ferreira — 2013-06-18T14:12:33

Hi there,
Is there a clever way of passing a variable to the blast_cline command like:

  blast_cline = NcbiblastpCommandline((cmd = "blastp", task = 
"blastp-short",
                                         query = inf, matrix = "PAM30",
                                         outfmt = "5", db = "%s",
                                         remote = True, comp_based_stats 
= "0",
                                          out = "blast_out.xml") % database)

or should I have to have one command to each option.
Best,
Fred






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Re: [Biopython] Eftech and db='bioproject'... DTD problem?

Nicolas Joannin — 2013-06-18T10:41:38

Hi again,

I got a reply from Scott at NCBI:

"Yes this is the "normal" but it is an oversight as a dtd was never created
for this database. I will have to open a ticket to the developers to create
this and have it included in the XML and on the DTD web page."

Hopefully it will be updated soon!
Best regards,

Nicolas



Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Thu, Jun 13, 2013 at 9:45 PM, Nicolas Joannin
<nicolas.joannin< at >gmail.com>wrote:

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Re: [Biopython] OrthoXML parser?

Eric Talevich — 2013-06-14T16:12:22

Hi guys,

Biopython has SeqXML support in SeqIO in recent releases thanks to Thomas
Schmidt. We don't parse OrthoXML yet, mainly because there's no special
support for ortholog groups as an object type yet in Biopython. But you can
get the raw information from an OrthoXML file using the ElementTree module:
http://docs.python.org/2/library/xml.etree.elementtree.html

Cheers,
Eric



On Fri, Jun 14, 2013 at 10:33 AM, Philipp Schiffer <
philipp.schiffer< at >gmail.com> wrote:

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Re: [Biopython] OrthoXML parser?

Philipp Schiffer — 2013-06-14T14:33:36

Hi! 

Thanks a lot (actually should have seen this myself). Just checked out the latest (I think) biopython from git, but only seem to find SeqXML there:
- seqxml  - SeqXML, simple XML format described in Schmitt et al (2011).
But no OrthoXML. Or am I not seeing it?

Best

Philipp

Re: [Biopython] OrthoXML parser?

Nick Lindberg — 2013-06-14T14:08:52

Looks like there is a patch for Biopython that will give you OrthoXLM and
SeqXML support, but you'll have to do it yourself:

http://seqxml.org/xml/Biopython_Old.html


Perhaps it's already in the latest release?  I'm not at my machine so I
can't check.

Nick Lindberg
Sr. Consulting Engineer, HPC
Milwaukee Institute
414.727.6413 (W)
http://www.mkei.org











On 6/14/13 5:36 AM, "Philipp Schiffer" <philipp.schiffer< at >gmail.com> wrote:



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Re: [Biopython] OrthoXML parser?

Philipp Schiffer — 2013-06-14T10:36:59

Hi there!

Does anybody now if there is a module to parse the OrthoXML format in/with biopython?

Thanks

Philipp

Re: [Biopython] NCBIXML module: missing sgi, qlen, slen,mismacth and others

Wibowo Arindrarto — 2013-06-13T19:36:36

Hi Frederico,

This isn't exactly using NCBIXML (SearchIO instead;
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc100), but
you can indeed access them:

from Bio import SearchIO

for query_result in SearchIO.parse('your_blast.xml', 'blast-xml'):
    print 'query length is', query_result.seq_len
    for hit in query_result:
        print 'sgi is', hit.id
        for hsp in hit:
            print 'mismatch is',
hsp.aln_annotation['homology'].count(' ')  # mismatch == no match at
all, so we count the gaps in the consensus sequence

All the other attributes are of course available as well:
- identities == hsp.ident_num
- score == hsp.bitscore_raw
- bits == hsp.bitscore
- expect == hsp.evalue

Hope that helps :),
Bow

On Thu, Jun 13, 2013 at 4:07 PM, Frederico Moraes Ferreira
<ferreirafm< at >usp.br> wrote:
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[Biopython] NCBIXML module: missing sgi, qlen, slen,mismacth and others

Frederico Moraes Ferreira — 2013-06-13T14:07:37

Biopythoneers,
How do I get sgi, qlen, mismacth from a blastp xml record?
I've got hsp.identities, hsp.score, hsp.bits, and hsp.expect, but also 
need those mentioned. Don't they were implemented?
Thanks in advance.
Best

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Re: [Biopython] Eftech and db='bioproject'... DTD problem?

Nicolas Joannin — 2013-06-13T12:45:12

Hi Michiel,

Thanks for the suggestion. Will do so and post any response I'll get!

Best regards,
Nicolas




On Thu, Jun 13, 2013 at 12:32 AM, Michiel de Hoon <mjldehoon< at >yahoo.com>wrote:

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Re: [Biopython] Eftech and db='bioproject'... DTD problem?

Michiel de Hoon — 2013-06-12T15:32:22

The XML returned by Entrez for this query starts like this:
<?xml version="1.0"?>
<RecordSet><DocumentSummary>
    <Project>
        <ProjectID>
...
so it does not contain any information regarding the relevant DTD needed to parse this XML.
I would suggest to check with NCBI to find out what to appropriate way is to access the bioproject database through Entrez.

Best,
-Michiel.




________________________________
 From: Nicolas Joannin <nicolas.joannin< at >gmail.com>
To: Biopython Mailing List <biopython< at >lists.open-bio.org> 
Sent: Wednesday, June 12, 2013 12:04 PM
Subject: [Biopython] Eftech and db='bioproject'... DTD problem?
 

Hello,

I'm trying to use Entrez.efetch to retrieve info about a BioProject.
However, I get DTD error (see ouput below).
Using "validate=False" avoids the error, but results in an empty string
output..

Any idea as to how I can read BioProject data from Entrez?

Best regards,
Nicolas

Example output:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/Bio/Entrez/__init__.py",
line 368, in read
    record = handler.read(handle)
  File
"/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/Bio/Entrez/Parser.py",
line 184, in read
    self.parser.ParseFile(handle)
  File
"/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/Bio/Entrez/Parser.py",
line 300, in startElementHandler
    raise ValidationError(name)
Bio.Entrez.Parser.ValidationError: Failed to find tag 'RecordSet' in the
DTD. To skip all tags that are not represented in the DTD, please call
Bio.Entrez.read or Bio.Entrez.parse with validate=False.


Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan
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[Biopython] Eftech and db='bioproject'... DTD problem?

Nicolas Joannin — 2013-06-12T03:04:31

Hello,

I'm trying to use Entrez.efetch to retrieve info about a BioProject.
However, I get DTD error (see ouput below).
Using "validate=False" avoids the error, but results in an empty string
output..

Any idea as to how I can read BioProject data from Entrez?

Best regards,
Nicolas

Example output:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/Bio/Entrez/__init__.py",
line 368, in read
    record = handler.read(handle)
  File
"/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/Bio/Entrez/Parser.py",
line 184, in read
    self.parser.ParseFile(handle)
  File
"/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/Bio/Entrez/Parser.py",
line 300, in startElementHandler
    raise ValidationError(name)
Bio.Entrez.Parser.ValidationError: Failed to find tag 'RecordSet' in the
DTD. To skip all tags that are not represented in the DTD, please call
Bio.Entrez.read or Bio.Entrez.parse with validate=False.


Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan
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Re: [Biopython] writing sequences one by one using SeqIO

Peter Cock — 2013-06-08T09:53:52


Hi Iddo,

For simple sequential files (without any headers etc to worry about),
open the handle, call SeqIO.write multiple times, close the handle.

Although I would agree with Lenna that if you can refactor the
code to use an iterator approach, it is often more pleasing.

Peter
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Re: [Biopython] writing sequences one by one using SeqIO

Lenna Peterson — 2013-06-07T19:48:22

In my opinion, iterator functions are one of Python's most powerful tools.
In the linked example, you could replace the generator comprehension with
the following function::

def short_seq_gen():
    for record in input_seq_iterator:
        if len(record.seq) < 300:
            yield record

output_handle = open("short_seqs.fasta", "w")
SeqIO.write(short_seq_gen(), output_handle, "fasta")  # note parentheses to
call function


I don't think there's a better way to do this.

Cheers,

Lenna



On Fri, Jun 7, 2013 at 3:15 PM, Iddo Friedberg <idoerg< at >gmail.com> wrote:

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[Biopython] writing sequences one by one using SeqIO

Iddo Friedberg — 2013-06-07T19:15:02

Hi,

Probably has been asked & answered on this list, but I cannot find it.

My problem is doing a SeqIO read and SeqIO.write of sequences one by one
instead of in bulk to save memory. The wiki  as an example of generating an
iterator in a single shot. .
http://biopython.org/wiki/SeqIO#Input.2FOutput_Example_-_Filtering_by_sequence_length

However, my processing of sequences is a bit more involved than that, and
requires several lines of code. Do I have to resorlt to calling an iterator
function, or is there a way to read a single sequence, process, & then
write it before the next iteration?

Thanks,

Iddo

[Biopython] GO terms

Mic — 2013-06-05T08:12:04

Hello,
Suppose I have a gene ID such as Q8L9A8. How can I get a list of GO terms
with which this ID is associated?

Thank you in advance

Mic
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Re: [Biopython] Custom Distance Matrices using Custom Scoring Matrices

Willis, Jordan R — 2013-05-31T22:59:26

Hello,

I think my solution is to use a neighbor joining from the PHYLIP package. You can define distance matrices yourself, which I will write using biopython, but I don't think that it has been done before. If I get something nice and stable, I will contribute to the devel branch of biopython.

Jordan

On May 31, 2013, at 4:15 PM, "Willis, Jordan R" <jordan.r.willis< at >Vanderbilt.Edu> wrote:




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[Biopython] Custom Distance Matrices using Custom Scoring Matrices

Willis, Jordan R — 2013-05-31T21:15:48

Hello Bio,

I know I asked something like this a while ago but didn't really know what I needed to do. Now I think I know exactly the path, however the solution is unclear.

The goal is to compare sequences all of the same length and view them in a dendrogram. In one tree I would like it to be scored with something simple like a PAM250 matrix. In another dendrogram, I would like the tree to be scored with my own custom position-specific scoring matrix.

So it looks like I can use a neighbor-joining method using a distance matrix where the distance matrix will be all my sequences scored against each other using either the PAM250 or my custom matrix.

Now, does Biopython have the means to do this? I can quickly write a method to score all my sequences against each other using PAM250 or my PSSM and store it in some sort of dictionary. Can I then convert that dictionary to a distance matrix to be used in neighbor joining? Is there a method to write out a newick tree using neighbor joining? Should I even be using Biopython? 

Thanks so much!

Jordan




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Re: [Biopython] Problem parsing embl files

Jaime Tovar — 2013-05-31T19:12:32

Thanks Peter,

I found gff3 files I can easily parse for the data I need. So will leave 
this strange embl files alone. If someone with more experience with embl 
files wants to take a look at them to check the parser let me know and I 
will forward some sample files.

I asked the people who gave me the files if they know what kind of 
software they used to generate them. But since they are third party data 
they have no information. I was lucky they had also gff3 files to get 
gene annotation data.

Jaime.

On 31/05/2013 09:43, Peter Cock wrote:

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Re: [Biopython] Versions of Python 3 to support in Biopython?

c0d3g33k — 2013-05-31T16:31:05

Hi Martin,

On 5/30/2013 2:39 PM, Martin Mokrejs wrote:

I fully understand the sentiment - change for the sake of change is 
unwelcome.  Bear in mind, though, that this is a discussion about 
versions of Python to support in *future* releases of Biopython.  A 
developer as conservatively paranoid as you describe isn't going to be 
tracking the bleeding edge of Biopython unless he really enjoys being 
self-contradictory.

These days, if stability is a high priority and you aren't using 
virtualenv (http://www.virtualenv.org), "You're Doing It Wrong".  Set up 
a stable virtual environment for that application that's been working 
for years and tested within an inch of it's life and have done with it.

Let the Biopython developers move carefully forward without having to 
drag the chains of sins past along with them forever like Jacob Marley 
in A Christmas Carol.


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