Carlos Pena | 28 Jul 15:21 2015
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[Biopython] Is there any Biopython tool to degenerate a nucleotide sequence

Dear Biopython members,

I want to take a nucleotide string and degenerate those bases that can
undergo synonymous change.

For example, a string of just one codon.

* Input:  AAC
* Output:  AAY

Since both AAC and AAT are translated to Asparagine (N) we can
degenerate this codon to AAY (because the third position could produce a
synonymous change).

This is already solved in the Perl library Degen
http://www.phylotools.com/ptdegendocumentation.htm

I could use some glue to execute this Perl code from Python but
I cannot include this library in my project because they are using the
GPL license while I use BSD.

So I thought asking around before writing a Python script to do this for me.

thanks for any pointers,

carlos

--

-- 
Dr. Carlos Peña
Laboratory of Genetics
(Continue reading)

Peter Cock | 21 Jul 13:04 2015

[Biopython] BOSC slides: Biopython Project Update - 2015

Hello all,

I'm still catching up on emails etc from my conference trip,
but I want to publicly thank João Rodrigues for presenting
the "Biopython Project Update - 2015" talk at BOSC 2015.

The slides are available on F1000 Research as part of the
BOSC "channel" http://f1000research.com/channels/BOSC
which has the bonus of being formally cited with a DOI:

Rodrigues J, et al. Biopython Project Update – 2015
http://dx.doi.org/10.7490/f1000research.1110022.1

Thanks to continued generous sponsorship from Google,
we were again able to record the talks at BOSC and hope
to have the videos online shortly. Keep an eye on this page:

http://www.open-bio.org/wiki/BOSC_2015_Schedule

Also, of course, thank you to all the contributors to Biopython
during the last year - even thought unfortunately we could
only highlight some of these efforts in the short talk.

It was also great meeting some of you in person (again),
and speaking as the BOSC co-chair, I hope for another
strong turnout at BOSC 2016.

Thank you all,

Peter
(Continue reading)

sunwm9 | 17 Jul 11:50 2015

[Biopython] Concatenate all the sequences with same gene name


Dear all,I am new self-educator of Biopython. I would like to concatenate fasta sequences (file attached) with same gene name using SeqIO.parse() function. Here is a snippet from my code:
seq_all = ' 'for cur_record in SeqIO.parse('nucleotide_seq.fasta', "fasta") : if cur_record.name == 'B103': seq_all = seq_all + str(cur_record.seq) print seq_all
It need to change the gene name every time. How can I concatenate all the sequences with same gene name automatically.<ribozyme <at> ioz.ac.cn>
Best regards,Weiming Sun
Attachment (nucleotide_seq.fasta): application/octet-stream, 11 KiB
_______________________________________________
Biopython mailing list  -  Biopython <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biopython
Karin Lagesen | 10 Jul 10:46 2015
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Picon

[Biopython] creating simple genome database

Hi!

I am in need of creating a simple genomics database, basically one that 
contains the information found in a genbank record. However, I need one 
that contains info for multiple genomes, and thus I need several tables, 
an organism table, a feature table, etc. I have been looking around for 
something like this, because I couldn't imagine that this wasn't already 
a solved problem. I imagined that this would be useful for loads of 
researchers out there. However, nothing found yet.

Hence this email. Do any of you know of something like this already 
existing, or if not, do you have any suggestions for how I go about 
making my own?

Thanks a lot in advance,

Karin

--

-- 
Karin Lagesen, PhD
Institute of Informatics
University of Oslo
_______________________________________________
Biopython mailing list  -  Biopython <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biopython

WU | 10 Jul 03:40 2015
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Re: [Biopython] Biopython Digest, Vol 151, Issue 6

Nice book. congratulations Tiago.

在2015-07-09 21:03:35,WU<ribozyme <at> ioz.ac.cn>写道:
> Send Biopython mailing list submissions to
> 	biopython <at> mailman.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://mailman.open-bio.org/mailman/listinfo/biopython
> or, via email, send a message with subject or body 'help' to
> 	biopython-request <at> mailman.open-bio.org
> 
> You can reach the person managing the list at
> 	biopython-owner <at> mailman.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biopython digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: Biopython Digest, Vol 151, Issue 4 (Bj?rn Johansson)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 9 Jul 2015 13:45:12 +0100
> From: Bj?rn Johansson <bjorn_johansson <at> bio.uminho.pt>
> To: biopython <at> mailman.open-bio.org
> Subject: Re: [Biopython] Biopython Digest, Vol 151, Issue 4
> Message-ID:
> 	<CAG_4V=YtBGVNRFePzCpJ8O3_zUfHo9tYEvNWZPiqo7WKougJiA <at> mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hello,
> Very nice book!
> I you run the welcome link through nbviewer, the links work:
> 
> http://nbviewer.ipython.org/github/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb
> 
> 
> /bjorn
> 
> On Thu, Jul 9, 2015 at 4:29 AM, <biopython-request <at> mailman.open-bio.org>
> wrote:
> 
> > Send Biopython mailing list submissions to
> >         biopython <at> mailman.open-bio.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >         http://mailman.open-bio.org/mailman/listinfo/biopython
> > or, via email, send a message with subject or body 'help' to
> >         biopython-request <at> mailman.open-bio.org
> >
> > You can reach the person managing the list at
> >         biopython-owner <at> mailman.open-bio.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Biopython digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Re: Bioinformatics with Python cookbook (Iddo Friedberg)
> >    2. Re: Bioinformatics with Python cookbook (Wibowo Arindrarto)
> >    3. Entrez EFetch Options (Zach Gayk)
> >    4. Re: Bioinformatics with Python cookbook (Chris Mitchell)
> >    5. Re: Entrez EFetch Options (Joshua Klein)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 8 Jul 2015 13:02:37 -0500
> > From: Iddo Friedberg <idoerg <at> gmail.com>
> > To: Tiago Antao <tra <at> popgen.net>
> > Cc: Biopython Mailing List <biopython <at> biopython.org>
> > Subject: Re: [Biopython] Bioinformatics with Python cookbook
> > Message-ID:
> >         <CABm4-MQxTm6x_fS-_91R40y=ME0=
> > pJQgnCGo15RqvwKfYn-DHA <at> mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Wow, nice going, Tiago. Will buy!
> >
> > On Tue, Jul 7, 2015 at 6:26 AM, Tiago Antao <tra <at> popgen.net> wrote:
> >
> > > Dear all,
> > >
> > >
> > > I would like to announce "Bioinformatics with Python Cookbook" which I
> > > authored. As you might imagine Biopython is discussed heavily in the
> > > book.
> > >
> > > This book is slightly different from the standard books on
> > > Bioinformatics and Python. It is not about teaching Bioinformatics
> > > algorithms, but about solving practical day-to-day problems with
> > > Python, for example:
> > >
> > > Next-Generation Sequencing: FASTQ, BAM and VCF processing. Along with
> > > filtering of datasets.
> > >
> > > Genomics: processing reference genomes of both high-quality references
> > > of model species and low-quality non-model species. Also discussed are
> > > genome annotations and gene ontologies.
> > >
> > > Population Genetics: doing PCA, Admixture/Structure, computing FSTs, ...
> > >
> > > Genome simulation: mostly forward-time simulations, but also a bit of
> > > coalescent
> > >
> > > Phylogenetics: tree reconstruction and tree drawing
> > >
> > > Proteins: PDB processing and visualization.
> > >
> > > Other topics like processing map data, GBIF, interfacing with
> > > Cytoscape, accessing lots of online databases, ...
> > >
> > > There is a bit on interacting with R/Bioconductor via Python.
> > >
> > > Finally we discuss high-performance in Python: faster algorithms,
> > > clusters, Numba and Cython. Also related technologies like Docker
> > >
> > > The book discusses the usual Python Libraries in the field: Biopython,
> > > PyVCF, Pysam, simuPOP, DendroPy, Pymol and also scientific libraries
> > > like NumPy, SciPy, matplotlib and scikit-learn.
> > >
> > > The code is fully available for free at github
> > >
> > >
> > https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb
> > >
> > > I am keen on maintaining the book code, so if you find any issues
> > > please do contact me.
> > >
> > > The book is available in the usual places (Amazon, etc.) in paperback
> > > and e-book format. The web page of the book is
> > >
> > >
> > https://www.packtpub.com/application-development/bioinformatics-python-cookbook
> > >
> > > Regards,
> > > Tiago
> > > _______________________________________________
> > > Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> > > http://mailman.open-bio.org/mailman/listinfo/biopython
> > >
> >
> >
> >
> > --
> > Iddo Friedberg
> > http://iddo-friedberg.net/contact.html
> > ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
> > ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
> > .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
> > >>----.<--.>++++++.<<<<------------------------------------.
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> > http://mailman.open-bio.org/pipermail/biopython/attachments/20150708/65038d9c/attachment-0001.html
> > >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 9 Jul 2015 01:35:44 +0200
> > From: Wibowo Arindrarto <w.arindrarto <at> gmail.com>
> > To: Iddo Friedberg <idoerg <at> gmail.com>
> > Cc: Biopython Mailing List <biopython <at> biopython.org>
> > Subject: Re: [Biopython] Bioinformatics with Python cookbook
> > Message-ID:
> >         <
> > CADEGkF512cv2G07iwgAETt3m0Oc-c8nHUivaKgNvyONN+n7tjQ <at> mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi Tiago,
> >
> > Congratulations on publishing the book! +1 as well for using notebooks
> > and putting them on GitHub (and using many of the up-and-coming
> > libraries ~ I see e.g. numba and spark there :) ).
> >
> > One small note, apparently the direct links to the other notebooks in
> > the Welcome.ipynb notebook is not working properly in the
> > GitHub-rendered page. Looks like this is something from GitHub, though
> > (i.e. the way they render notebook links in notebooks). Anyway, just
> > in case you haven't noticed :).
> >
> > Cheers,
> >
> > On Wed, Jul 8, 2015 at 8:02 PM, Iddo Friedberg <idoerg <at> gmail.com> wrote:
> > > Wow, nice going, Tiago. Will buy!
> > >
> > > On Tue, Jul 7, 2015 at 6:26 AM, Tiago Antao <tra <at> popgen.net> wrote:
> > >>
> > >> Dear all,
> > >>
> > >>
> > >> I would like to announce "Bioinformatics with Python Cookbook" which I
> > >> authored. As you might imagine Biopython is discussed heavily in the
> > >> book.
> > >>
> > >> This book is slightly different from the standard books on
> > >> Bioinformatics and Python. It is not about teaching Bioinformatics
> > >> algorithms, but about solving practical day-to-day problems with
> > >> Python, for example:
> > >>
> > >> Next-Generation Sequencing: FASTQ, BAM and VCF processing. Along with
> > >> filtering of datasets.
> > >>
> > >> Genomics: processing reference genomes of both high-quality references
> > >> of model species and low-quality non-model species. Also discussed are
> > >> genome annotations and gene ontologies.
> > >>
> > >> Population Genetics: doing PCA, Admixture/Structure, computing FSTs, ...
> > >>
> > >> Genome simulation: mostly forward-time simulations, but also a bit of
> > >> coalescent
> > >>
> > >> Phylogenetics: tree reconstruction and tree drawing
> > >>
> > >> Proteins: PDB processing and visualization.
> > >>
> > >> Other topics like processing map data, GBIF, interfacing with
> > >> Cytoscape, accessing lots of online databases, ...
> > >>
> > >> There is a bit on interacting with R/Bioconductor via Python.
> > >>
> > >> Finally we discuss high-performance in Python: faster algorithms,
> > >> clusters, Numba and Cython. Also related technologies like Docker
> > >>
> > >> The book discusses the usual Python Libraries in the field: Biopython,
> > >> PyVCF, Pysam, simuPOP, DendroPy, Pymol and also scientific libraries
> > >> like NumPy, SciPy, matplotlib and scikit-learn.
> > >>
> > >> The code is fully available for free at github
> > >>
> > >>
> > https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb
> > >>
> > >> I am keen on maintaining the book code, so if you find any issues
> > >> please do contact me.
> > >>
> > >> The book is available in the usual places (Amazon, etc.) in paperback
> > >> and e-book format. The web page of the book is
> > >>
> > >>
> > https://www.packtpub.com/application-development/bioinformatics-python-cookbook
> > >>
> > >> Regards,
> > >> Tiago
> > >> _______________________________________________
> > >> Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> > >> http://mailman.open-bio.org/mailman/listinfo/biopython
> > >
> > >
> > >
> > >
> > > --
> > > Iddo Friedberg
> > > http://iddo-friedberg.net/contact.html
> > > ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
> > > ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
> > > .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
> > >>>----.<--.>++++++.<<<<------------------------------------.
> > >
> > > _______________________________________________
> > > Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> > > http://mailman.open-bio.org/mailman/listinfo/biopython
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Wed, 8 Jul 2015 21:12:46 -0400
> > From: "Zach Gayk" <zgayk <at> nmu.edu>
> > To: biopython <at> mailman.open-bio.org
> > Subject: [Biopython] Entrez EFetch Options
> > Message-ID:
> >         <1a6578a08666733c24564622fe2f8dc2.squirrel <at> webmail.nmu.edu>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > Hello,
> >
> > I would like to use the following code from the biopython tutorial to
> > retrieve gi numbers for a number of sequences that matched to scaffolds on
> > a genome assembly:
> >
> > import os
> > os.chdir('/Users/zachgayk/Desktop/GAVIABioinformatics/')
> > from Bio import Entrez # this is the most likely script modified
> > from Bio import SeqIO
> > Entrez.email = "zgayk <at> nmu.edu"
> > handle = Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", \
> >                        id="gi|50254217|gb|`, gi|50254217|gb|AY567890.1|,
> > gi|559028|gb|L33375.1|GVSMTDGI,
> > gi|559028|gb|L33375.1|GVSMTDGI")
> > for seq_record in SeqIO.parse(handle, "gb"):
> >     print seq_record.description[:100] + "..." # the :100 specifies no.
> > characters and "..." says this comes after specified character limit
> > handle.close()
> >
> > The problem, however, is that there are a large number of gi numbers I
> > wish to retrieve, and so there are simply too many to manually enter into
> > the id ="" field. What I would like to do is specify a file containing all
> > of the needed gi numbers in a list and then have the code parse all of
> > them. I haven't been able to figure out how to do this yet, and if anyone
> > has any ideas they would be very much appreciated.
> >
> > Thank you,
> > Zach Gayk
> >
> >
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Wed, 8 Jul 2015 21:25:27 -0400
> > From: Chris Mitchell <chris.mit7 <at> gmail.com>
> > To: Wibowo Arindrarto <w.arindrarto <at> gmail.com>
> > Cc: Iddo Friedberg <idoerg <at> gmail.com>, biopython <at> biopython.org
> > Subject: Re: [Biopython] Bioinformatics with Python cookbook
> > Message-ID:
> >         <
> > CAK_U6OCMSuxexTfj3S2zvoY-UkTMERX8sp9vaPpMvwvVU_w0pw <at> mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > I noticed that as well bow, but it's only for pages that are opened in a
> > new tab.
> >
> > Really good stuff all in all.
> >
> > Sent from my phone
> > On Jul 8, 2015 8:07 PM, "Wibowo Arindrarto" <w.arindrarto <at> gmail.com>
> > wrote:
> >
> > > Hi Tiago,
> > >
> > > Congratulations on publishing the book! +1 as well for using notebooks
> > > and putting them on GitHub (and using many of the up-and-coming
> > > libraries ~ I see e.g. numba and spark there :) ).
> > >
> > > One small note, apparently the direct links to the other notebooks in
> > > the Welcome.ipynb notebook is not working properly in the
> > > GitHub-rendered page. Looks like this is something from GitHub, though
> > > (i.e. the way they render notebook links in notebooks). Anyway, just
> > > in case you haven't noticed :).
> > >
> > > Cheers,
> > >
> > > On Wed, Jul 8, 2015 at 8:02 PM, Iddo Friedberg <idoerg <at> gmail.com> wrote:
> > > > Wow, nice going, Tiago. Will buy!
> > > >
> > > > On Tue, Jul 7, 2015 at 6:26 AM, Tiago Antao <tra <at> popgen.net> wrote:
> > > >>
> > > >> Dear all,
> > > >>
> > > >>
> > > >> I would like to announce "Bioinformatics with Python Cookbook" which I
> > > >> authored. As you might imagine Biopython is discussed heavily in the
> > > >> book.
> > > >>
> > > >> This book is slightly different from the standard books on
> > > >> Bioinformatics and Python. It is not about teaching Bioinformatics
> > > >> algorithms, but about solving practical day-to-day problems with
> > > >> Python, for example:
> > > >>
> > > >> Next-Generation Sequencing: FASTQ, BAM and VCF processing. Along with
> > > >> filtering of datasets.
> > > >>
> > > >> Genomics: processing reference genomes of both high-quality references
> > > >> of model species and low-quality non-model species. Also discussed are
> > > >> genome annotations and gene ontologies.
> > > >>
> > > >> Population Genetics: doing PCA, Admixture/Structure, computing FSTs,
> > ...
> > > >>
> > > >> Genome simulation: mostly forward-time simulations, but also a bit of
> > > >> coalescent
> > > >>
> > > >> Phylogenetics: tree reconstruction and tree drawing
> > > >>
> > > >> Proteins: PDB processing and visualization.
> > > >>
> > > >> Other topics like processing map data, GBIF, interfacing with
> > > >> Cytoscape, accessing lots of online databases, ...
> > > >>
> > > >> There is a bit on interacting with R/Bioconductor via Python.
> > > >>
> > > >> Finally we discuss high-performance in Python: faster algorithms,
> > > >> clusters, Numba and Cython. Also related technologies like Docker
> > > >>
> > > >> The book discusses the usual Python Libraries in the field: Biopython,
> > > >> PyVCF, Pysam, simuPOP, DendroPy, Pymol and also scientific libraries
> > > >> like NumPy, SciPy, matplotlib and scikit-learn.
> > > >>
> > > >> The code is fully available for free at github
> > > >>
> > > >>
> > >
> > https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb
> > > >>
> > > >> I am keen on maintaining the book code, so if you find any issues
> > > >> please do contact me.
> > > >>
> > > >> The book is available in the usual places (Amazon, etc.) in paperback
> > > >> and e-book format. The web page of the book is
> > > >>
> > > >>
> > >
> > https://www.packtpub.com/application-development/bioinformatics-python-cookbook
> > > >>
> > > >> Regards,
> > > >> Tiago
> > > >> _______________________________________________
> > > >> Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> > > >> http://mailman.open-bio.org/mailman/listinfo/biopython
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Iddo Friedberg
> > > > http://iddo-friedberg.net/contact.html
> > > > ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
> > > > ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
> > > > .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
> > > >>>----.<--.>++++++.<<<<------------------------------------.
> > > >
> > > > _______________________________________________
> > > > Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> > > > http://mailman.open-bio.org/mailman/listinfo/biopython
> > > _______________________________________________
> > > Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> > > http://mailman.open-bio.org/mailman/listinfo/biopython
> > >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> > http://mailman.open-bio.org/pipermail/biopython/attachments/20150708/08f11293/attachment-0001.html
> > >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Wed, 8 Jul 2015 23:29:01 -0400
> > From: Joshua Klein <mobiusklein <at> gmail.com>
> > To: Zach Gayk <zgayk <at> nmu.edu>
> > Cc: biopython <at> mailman.open-bio.org
> > Subject: Re: [Biopython] Entrez EFetch Options
> > Message-ID:
> >         <
> > CAFZWoGbwDtfzFe02p3qtAyVEjBdSo-oLTzOaOqRkeTuCqKJqkA <at> mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > If you store your list of identifiers in a file given by the variable
> > 'file_path', with one identifier per line, you can use:
> >
> > ids_to_fetch = ",".join(open(file_path))
> >
> > This code will open the file, and use the default iteration behavior for
> > file objects to yield a line at a time to the join method of the string
> > ",". This will create a long string of comma-separated identifiers to use
> > in your efetch call.
> >
> > On Wed, Jul 8, 2015 at 9:12 PM, Zach Gayk <zgayk <at> nmu.edu> wrote:
> >
> > > Hello,
> > >
> > > I would like to use the following code from the biopython tutorial to
> > > retrieve gi numbers for a number of sequences that matched to scaffolds
> > on
> > > a genome assembly:
> > >
> > > import os
> > > os.chdir('/Users/zachgayk/Desktop/GAVIABioinformatics/')
> > > from Bio import Entrez # this is the most likely script modified
> > > from Bio import SeqIO
> > > Entrez.email = "zgayk <at> nmu.edu"
> > > handle = Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", \
> > >                        id="gi|50254217|gb|`, gi|50254217|gb|AY567890.1|,
> > > gi|559028|gb|L33375.1|GVSMTDGI,
> > > gi|559028|gb|L33375.1|GVSMTDGI")
> > > for seq_record in SeqIO.parse(handle, "gb"):
> > >     print seq_record.description[:100] + "..." # the :100 specifies no.
> > > characters and "..." says this comes after specified character limit
> > > handle.close()
> > >
> > > The problem, however, is that there are a large number of gi numbers I
> > > wish to retrieve, and so there are simply too many to manually enter into
> > > the id ="" field. What I would like to do is specify a file containing
> > all
> > > of the needed gi numbers in a list and then have the code parse all of
> > > them. I haven't been able to figure out how to do this yet, and if anyone
> > > has any ideas they would be very much appreciated.
> > >
> > > Thank you,
> > > Zach Gayk
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> > > http://mailman.open-bio.org/mailman/listinfo/biopython
> > >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> > http://mailman.open-bio.org/pipermail/biopython/attachments/20150708/f83d063f/attachment.html
> > >
> >
> > ------------------------------
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython
> >
> > End of Biopython Digest, Vol 151, Issue 4
> > *****************************************
> >
> 
> 
> 
> -- 
> ______O_________oO________oO______o_______oO__
> Bj?rn Johansson
> Assistant Professor
> Departament of Biology
> University of Minho
> Campus de Gualtar
> 4710-057 Braga
> PORTUGAL
> www.bio.uminho.pt
> Google profile <https://profiles.google.com/bjornjobb>
> Google Scholar Profile
> <http://scholar.google.com/citations?user=7AiEuJ4AAAAJ>
> my group <https://sites.google.com/site/metabolicengineeringgroup/>
> Office (direct) +351-253 601517 | (PT) mob.  +351-967 147 704 | (SWE) mob.
>  +46 739 792 968
> Dept of Biology (secr) +351-253 60 4310  | fax +351-253 678980
> -------------- next part --------------
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> http://mailman.open-bio.org/mailman/listinfo/biopython
> 
> End of Biopython Digest, Vol 151, Issue 6
> *****************************************


_______________________________________________
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http://mailman.open-bio.org/mailman/listinfo/biopython
Björn Johansson | 9 Jul 14:45 2015
Picon

Re: [Biopython] Biopython Digest, Vol 151, Issue 4

Hello,
Very nice book!
I you run the welcome link through nbviewer, the links work:



/bjorn

On Thu, Jul 9, 2015 at 4:29 AM, <biopython-request <at> mailman.open-bio.org> wrote:
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Today's Topics:

   1. Re: Bioinformatics with Python cookbook (Iddo Friedberg)
   2. Re: Bioinformatics with Python cookbook (Wibowo Arindrarto)
   3. Entrez EFetch Options (Zach Gayk)
   4. Re: Bioinformatics with Python cookbook (Chris Mitchell)
   5. Re: Entrez EFetch Options (Joshua Klein)


----------------------------------------------------------------------

Message: 1
Date: Wed, 8 Jul 2015 13:02:37 -0500
From: Iddo Friedberg <idoerg <at> gmail.com>
To: Tiago Antao <tra <at> popgen.net>
Cc: Biopython Mailing List <biopython <at> biopython.org>
Subject: Re: [Biopython] Bioinformatics with Python cookbook
Message-ID:
        <CABm4-MQxTm6x_fS-_91R40y=ME0=pJQgnCGo15RqvwKfYn-DHA <at> mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Wow, nice going, Tiago. Will buy!

On Tue, Jul 7, 2015 at 6:26 AM, Tiago Antao <tra <at> popgen.net> wrote:

> Dear all,
>
>
> I would like to announce "Bioinformatics with Python Cookbook" which I
> authored. As you might imagine Biopython is discussed heavily in the
> book.
>
> This book is slightly different from the standard books on
> Bioinformatics and Python. It is not about teaching Bioinformatics
> algorithms, but about solving practical day-to-day problems with
> Python, for example:
>
> Next-Generation Sequencing: FASTQ, BAM and VCF processing. Along with
> filtering of datasets.
>
> Genomics: processing reference genomes of both high-quality references
> of model species and low-quality non-model species. Also discussed are
> genome annotations and gene ontologies.
>
> Population Genetics: doing PCA, Admixture/Structure, computing FSTs, ...
>
> Genome simulation: mostly forward-time simulations, but also a bit of
> coalescent
>
> Phylogenetics: tree reconstruction and tree drawing
>
> Proteins: PDB processing and visualization.
>
> Other topics like processing map data, GBIF, interfacing with
> Cytoscape, accessing lots of online databases, ...
>
> There is a bit on interacting with R/Bioconductor via Python.
>
> Finally we discuss high-performance in Python: faster algorithms,
> clusters, Numba and Cython. Also related technologies like Docker
>
> The book discusses the usual Python Libraries in the field: Biopython,
> PyVCF, Pysam, simuPOP, DendroPy, Pymol and also scientific libraries
> like NumPy, SciPy, matplotlib and scikit-learn.
>
> The code is fully available for free at github
>
> https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb
>
> I am keen on maintaining the book code, so if you find any issues
> please do contact me.
>
> The book is available in the usual places (Amazon, etc.) in paperback
> and e-book format. The web page of the book is
>
> https://www.packtpub.com/application-development/bioinformatics-python-cookbook
>
> Regards,
> Tiago
> _______________________________________________
> Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>



--
Iddo Friedberg
http://iddo-friedberg.net/contact.html
++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>----.<--.>++++++.<<<<------------------------------------.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20150708/65038d9c/attachment-0001.html>

------------------------------

Message: 2
Date: Thu, 9 Jul 2015 01:35:44 +0200
From: Wibowo Arindrarto <w.arindrarto <at> gmail.com>
To: Iddo Friedberg <idoerg <at> gmail.com>
Cc: Biopython Mailing List <biopython <at> biopython.org>
Subject: Re: [Biopython] Bioinformatics with Python cookbook
Message-ID:
        <CADEGkF512cv2G07iwgAETt3m0Oc-c8nHUivaKgNvyONN+n7tjQ <at> mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi Tiago,

Congratulations on publishing the book! +1 as well for using notebooks
and putting them on GitHub (and using many of the up-and-coming
libraries ~ I see e.g. numba and spark there :) ).

One small note, apparently the direct links to the other notebooks in
the Welcome.ipynb notebook is not working properly in the
GitHub-rendered page. Looks like this is something from GitHub, though
(i.e. the way they render notebook links in notebooks). Anyway, just
in case you haven't noticed :).

Cheers,

On Wed, Jul 8, 2015 at 8:02 PM, Iddo Friedberg <idoerg <at> gmail.com> wrote:
> Wow, nice going, Tiago. Will buy!
>
> On Tue, Jul 7, 2015 at 6:26 AM, Tiago Antao <tra <at> popgen.net> wrote:
>>
>> Dear all,
>>
>>
>> I would like to announce "Bioinformatics with Python Cookbook" which I
>> authored. As you might imagine Biopython is discussed heavily in the
>> book.
>>
>> This book is slightly different from the standard books on
>> Bioinformatics and Python. It is not about teaching Bioinformatics
>> algorithms, but about solving practical day-to-day problems with
>> Python, for example:
>>
>> Next-Generation Sequencing: FASTQ, BAM and VCF processing. Along with
>> filtering of datasets.
>>
>> Genomics: processing reference genomes of both high-quality references
>> of model species and low-quality non-model species. Also discussed are
>> genome annotations and gene ontologies.
>>
>> Population Genetics: doing PCA, Admixture/Structure, computing FSTs, ...
>>
>> Genome simulation: mostly forward-time simulations, but also a bit of
>> coalescent
>>
>> Phylogenetics: tree reconstruction and tree drawing
>>
>> Proteins: PDB processing and visualization.
>>
>> Other topics like processing map data, GBIF, interfacing with
>> Cytoscape, accessing lots of online databases, ...
>>
>> There is a bit on interacting with R/Bioconductor via Python.
>>
>> Finally we discuss high-performance in Python: faster algorithms,
>> clusters, Numba and Cython. Also related technologies like Docker
>>
>> The book discusses the usual Python Libraries in the field: Biopython,
>> PyVCF, Pysam, simuPOP, DendroPy, Pymol and also scientific libraries
>> like NumPy, SciPy, matplotlib and scikit-learn.
>>
>> The code is fully available for free at github
>>
>> https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb
>>
>> I am keen on maintaining the book code, so if you find any issues
>> please do contact me.
>>
>> The book is available in the usual places (Amazon, etc.) in paperback
>> and e-book format. The web page of the book is
>>
>> https://www.packtpub.com/application-development/bioinformatics-python-cookbook
>>
>> Regards,
>> Tiago
>> _______________________________________________
>> Biopython mailing list  -  Biopython <at> mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biopython
>
>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
> ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
> .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>>----.<--.>++++++.<<<<------------------------------------.
>
> _______________________________________________
> Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython


------------------------------

Message: 3
Date: Wed, 8 Jul 2015 21:12:46 -0400
From: "Zach Gayk" <zgayk <at> nmu.edu>
To: biopython <at> mailman.open-bio.org
Subject: [Biopython] Entrez EFetch Options
Message-ID:
        <1a6578a08666733c24564622fe2f8dc2.squirrel <at> webmail.nmu.edu>
Content-Type: text/plain;charset=iso-8859-1

Hello,

I would like to use the following code from the biopython tutorial to
retrieve gi numbers for a number of sequences that matched to scaffolds on
a genome assembly:

import os
os.chdir('/Users/zachgayk/Desktop/GAVIABioinformatics/')
from Bio import Entrez # this is the most likely script modified
from Bio import SeqIO
Entrez.email = "zgayk <at> nmu.edu"
handle = Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", \
                       id="gi|50254217|gb|`, gi|50254217|gb|AY567890.1|,
gi|559028|gb|L33375.1|GVSMTDGI,
gi|559028|gb|L33375.1|GVSMTDGI")
for seq_record in SeqIO.parse(handle, "gb"):
    print seq_record.description[:100] + "..." # the :100 specifies no.
characters and "..." says this comes after specified character limit
handle.close()

The problem, however, is that there are a large number of gi numbers I
wish to retrieve, and so there are simply too many to manually enter into
the id ="" field. What I would like to do is specify a file containing all
of the needed gi numbers in a list and then have the code parse all of
them. I haven't been able to figure out how to do this yet, and if anyone
has any ideas they would be very much appreciated.

Thank you,
Zach Gayk






------------------------------

Message: 4
Date: Wed, 8 Jul 2015 21:25:27 -0400
From: Chris Mitchell <chris.mit7 <at> gmail.com>
To: Wibowo Arindrarto <w.arindrarto <at> gmail.com>
Cc: Iddo Friedberg <idoerg <at> gmail.com>, biopython <at> biopython.org
Subject: Re: [Biopython] Bioinformatics with Python cookbook
Message-ID:
        <CAK_U6OCMSuxexTfj3S2zvoY-UkTMERX8sp9vaPpMvwvVU_w0pw <at> mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

I noticed that as well bow, but it's only for pages that are opened in a
new tab.

Really good stuff all in all.

Sent from my phone
On Jul 8, 2015 8:07 PM, "Wibowo Arindrarto" <w.arindrarto <at> gmail.com> wrote:

> Hi Tiago,
>
> Congratulations on publishing the book! +1 as well for using notebooks
> and putting them on GitHub (and using many of the up-and-coming
> libraries ~ I see e.g. numba and spark there :) ).
>
> One small note, apparently the direct links to the other notebooks in
> the Welcome.ipynb notebook is not working properly in the
> GitHub-rendered page. Looks like this is something from GitHub, though
> (i.e. the way they render notebook links in notebooks). Anyway, just
> in case you haven't noticed :).
>
> Cheers,
>
> On Wed, Jul 8, 2015 at 8:02 PM, Iddo Friedberg <idoerg <at> gmail.com> wrote:
> > Wow, nice going, Tiago. Will buy!
> >
> > On Tue, Jul 7, 2015 at 6:26 AM, Tiago Antao <tra <at> popgen.net> wrote:
> >>
> >> Dear all,
> >>
> >>
> >> I would like to announce "Bioinformatics with Python Cookbook" which I
> >> authored. As you might imagine Biopython is discussed heavily in the
> >> book.
> >>
> >> This book is slightly different from the standard books on
> >> Bioinformatics and Python. It is not about teaching Bioinformatics
> >> algorithms, but about solving practical day-to-day problems with
> >> Python, for example:
> >>
> >> Next-Generation Sequencing: FASTQ, BAM and VCF processing. Along with
> >> filtering of datasets.
> >>
> >> Genomics: processing reference genomes of both high-quality references
> >> of model species and low-quality non-model species. Also discussed are
> >> genome annotations and gene ontologies.
> >>
> >> Population Genetics: doing PCA, Admixture/Structure, computing FSTs, ...
> >>
> >> Genome simulation: mostly forward-time simulations, but also a bit of
> >> coalescent
> >>
> >> Phylogenetics: tree reconstruction and tree drawing
> >>
> >> Proteins: PDB processing and visualization.
> >>
> >> Other topics like processing map data, GBIF, interfacing with
> >> Cytoscape, accessing lots of online databases, ...
> >>
> >> There is a bit on interacting with R/Bioconductor via Python.
> >>
> >> Finally we discuss high-performance in Python: faster algorithms,
> >> clusters, Numba and Cython. Also related technologies like Docker
> >>
> >> The book discusses the usual Python Libraries in the field: Biopython,
> >> PyVCF, Pysam, simuPOP, DendroPy, Pymol and also scientific libraries
> >> like NumPy, SciPy, matplotlib and scikit-learn.
> >>
> >> The code is fully available for free at github
> >>
> >>
> https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb
> >>
> >> I am keen on maintaining the book code, so if you find any issues
> >> please do contact me.
> >>
> >> The book is available in the usual places (Amazon, etc.) in paperback
> >> and e-book format. The web page of the book is
> >>
> >>
> https://www.packtpub.com/application-development/bioinformatics-python-cookbook
> >>
> >> Regards,
> >> Tiago
> >> _______________________________________________
> >> Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> >> http://mailman.open-bio.org/mailman/listinfo/biopython
> >
> >
> >
> >
> > --
> > Iddo Friedberg
> > http://iddo-friedberg.net/contact.html
> > ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
> > ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
> > .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
> >>>----.<--.>++++++.<<<<------------------------------------.
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython
> _______________________________________________
> Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>
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------------------------------

Message: 5
Date: Wed, 8 Jul 2015 23:29:01 -0400
From: Joshua Klein <mobiusklein <at> gmail.com>
To: Zach Gayk <zgayk <at> nmu.edu>
Cc: biopython <at> mailman.open-bio.org
Subject: Re: [Biopython] Entrez EFetch Options
Message-ID:
        <CAFZWoGbwDtfzFe02p3qtAyVEjBdSo-oLTzOaOqRkeTuCqKJqkA <at> mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

If you store your list of identifiers in a file given by the variable
'file_path', with one identifier per line, you can use:

ids_to_fetch = ",".join(open(file_path))

This code will open the file, and use the default iteration behavior for
file objects to yield a line at a time to the join method of the string
",". This will create a long string of comma-separated identifiers to use
in your efetch call.

On Wed, Jul 8, 2015 at 9:12 PM, Zach Gayk <zgayk <at> nmu.edu> wrote:

> Hello,
>
> I would like to use the following code from the biopython tutorial to
> retrieve gi numbers for a number of sequences that matched to scaffolds on
> a genome assembly:
>
> import os
> os.chdir('/Users/zachgayk/Desktop/GAVIABioinformatics/')
> from Bio import Entrez # this is the most likely script modified
> from Bio import SeqIO
> Entrez.email = "zgayk <at> nmu.edu"
> handle = Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", \
>                        id="gi|50254217|gb|`, gi|50254217|gb|AY567890.1|,
> gi|559028|gb|L33375.1|GVSMTDGI,
> gi|559028|gb|L33375.1|GVSMTDGI")
> for seq_record in SeqIO.parse(handle, "gb"):
>     print seq_record.description[:100] + "..." # the :100 specifies no.
> characters and "..." says this comes after specified character limit
> handle.close()
>
> The problem, however, is that there are a large number of gi numbers I
> wish to retrieve, and so there are simply too many to manually enter into
> the id ="" field. What I would like to do is specify a file containing all
> of the needed gi numbers in a list and then have the code parse all of
> them. I haven't been able to figure out how to do this yet, and if anyone
> has any ideas they would be very much appreciated.
>
> Thank you,
> Zach Gayk
>
>
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>
-------------- next part --------------
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------------------------------

_______________________________________________
Biopython mailing list  -  Biopython <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biopython

End of Biopython Digest, Vol 151, Issue 4
*****************************************



--
______O_________oO________oO______o_______oO__
Björn Johansson
Assistant Professor
Departament of Biology
University of Minho
Campus de Gualtar
4710-057 Braga
PORTUGAL
www.bio.uminho.pt
Google profile
Google Scholar Profile
my group
Office (direct) +351-253 601517 | (PT) mob.  +351-967 147 704 | (SWE) mob.  +46 739 792 968
Dept of Biology (secr) +351-253 60 4310  | fax +351-253 678980
_______________________________________________
Biopython mailing list  -  Biopython <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biopython
Zach Gayk | 9 Jul 03:12 2015
Picon

[Biopython] Entrez EFetch Options

Hello,

I would like to use the following code from the biopython tutorial to
retrieve gi numbers for a number of sequences that matched to scaffolds on
a genome assembly:

import os
os.chdir('/Users/zachgayk/Desktop/GAVIABioinformatics/')
from Bio import Entrez # this is the most likely script modified
from Bio import SeqIO
Entrez.email = "zgayk <at> nmu.edu"
handle = Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", \
                       id="gi|50254217|gb|`, gi|50254217|gb|AY567890.1|,
gi|559028|gb|L33375.1|GVSMTDGI,
gi|559028|gb|L33375.1|GVSMTDGI")
for seq_record in SeqIO.parse(handle, "gb"):
    print seq_record.description[:100] + "..." # the :100 specifies no.
characters and "..." says this comes after specified character limit
handle.close()

The problem, however, is that there are a large number of gi numbers I
wish to retrieve, and so there are simply too many to manually enter into
the id ="" field. What I would like to do is specify a file containing all
of the needed gi numbers in a list and then have the code parse all of
them. I haven't been able to figure out how to do this yet, and if anyone
has any ideas they would be very much appreciated.

Thank you,
Zach Gayk

_______________________________________________
Biopython mailing list  -  Biopython <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biopython

Tiago Antao | 7 Jul 13:26 2015
Picon

[Biopython] Bioinformatics with Python cookbook

Dear all,

I would like to announce "Bioinformatics with Python Cookbook" which I
authored. As you might imagine Biopython is discussed heavily in the
book.

This book is slightly different from the standard books on
Bioinformatics and Python. It is not about teaching Bioinformatics
algorithms, but about solving practical day-to-day problems with
Python, for example:

Next-Generation Sequencing: FASTQ, BAM and VCF processing. Along with
filtering of datasets.

Genomics: processing reference genomes of both high-quality references
of model species and low-quality non-model species. Also discussed are
genome annotations and gene ontologies.

Population Genetics: doing PCA, Admixture/Structure, computing FSTs, ...

Genome simulation: mostly forward-time simulations, but also a bit of
coalescent

Phylogenetics: tree reconstruction and tree drawing

Proteins: PDB processing and visualization.

Other topics like processing map data, GBIF, interfacing with
Cytoscape, accessing lots of online databases, ...

There is a bit on interacting with R/Bioconductor via Python.

Finally we discuss high-performance in Python: faster algorithms,
clusters, Numba and Cython. Also related technologies like Docker

The book discusses the usual Python Libraries in the field: Biopython,
PyVCF, Pysam, simuPOP, DendroPy, Pymol and also scientific libraries
like NumPy, SciPy, matplotlib and scikit-learn.

The code is fully available for free at github
https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb

I am keen on maintaining the book code, so if you find any issues
please do contact me.

The book is available in the usual places (Amazon, etc.) in paperback
and e-book format. The web page of the book is
https://www.packtpub.com/application-development/bioinformatics-python-cookbook

Regards,
Tiago
_______________________________________________
Biopython mailing list  -  Biopython <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biopython

Courtenay Godshall | 24 Jun 16:21 2015

[Biopython] ANN: Last Call for SciPy 2015 Registration (Scientific Python Conference - July 8-10)

Last Call to Register for
SciPy 2015!

Main conference July 8-10, tutorials July 6-7 & coding sprints July 11-12!

Here are just a few reasons you don't want to miss this year's SciPy Conference (Online registration closes 7/3/15):

  1. 2 full days of 90 talks + 40 posters on topics specific to Python for science, engineering, and data analysis you won't hear anywhere else.See the full list of talks and posters here.

  2. Meet and talk with over 500 attendees representing diverse backgrounds and industries, gathering to share their Python experience and learn from each other.

  3. Incredible keynote speakers: hear from Wes McKinney, author of Pandas; Chris Wiggins, Chief Data Scientist for The New York Times; and Jake VanderPlas, director of research at the University of Washington's eScience Institute and core contributor to a number of scientific Python libraries including sci-kit learn and AstroML.

  4. Great social events to network and get to know other attendees, including a riverboat cruise on Lady Bird Lake, diversity luncheon, annual reception, and conference kick-off reception.

  5. Attend tutorials from major community contributors. Seats are still available for Software Carpentry, Machine Learning with Sci-Kit Learn (2nd session opened due to massive demand), Manipulating Numerical Data with NumPy, Image Analysis with Sci-Kit Image, Modern Optimization Methods in Python, and more. See tutorial details and the full schedule here.

  6. Participate in coding sprints: Over 200 community members from core developers to Python newcomers will work together to contribute to projects and code during the SciPy sprints. You can make a huge contribution and sharpen your skills at the same time.
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Ian Stavros | 24 Jun 16:39 2015
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[Biopython] Melting Point.TM_NN calculation

Hello,

 

My name is Ian and I am new to the bioinformatics world. I am using the biopython's melting temp TM_NN algorithm to calculate the melting temp differences in wild type sequence with the complementary mutation sequence, using the the the Allawi and SantaLucia (1997), Biochemistry 36: 10581-10594 table. I have attached a small output of the sample program for better understanding, which shows the Key Error I am getting and other times I will get a Value Error, meaning it can find the key but can't find the value, I was wondering if

A) if there is something else out there better suited for this problem

B) if I need to update the table or something to get working and if so how would I go about improving the dictionary being used to address the problems which can be seen here


/Library/Python/2.7/site-packages/Bio/SeqUtils/MeltingTemp.py:931: BiopythonWarning: no data for neighbors 'AT/AG'. Calculation will be wrong
  BiopythonWarning)


Here is the output of the code. I think that the '.' may be equivalent to the regex expression of '.' meaning it could be any character in front of the G. But as you can see it is not a problem for the one up above. 


seq:  ['G', 'A', 'T']
Mutation c_seq:  ['C', 'C', 'A']
/Library/Python/2.7/site-packages/Bio/SeqUtils/MeltingTemp.py:931: BiopythonWarning: no data for neighbors 'AT/AG'. Calculation will be wrong
  BiopythonWarning)
TM:  -262.480685148
seq:  ['G', 'A', 'T', 'A']
Mutation c_seq:  ['C', 'C', 'A', 'T']
Traceback (most recent call last):
  File "PrimerBuilder.py", line 333, in <module>
    switchList = switchBuilder(middle,basepairs,mutation)
  File "PrimerBuilder.py", line 56, in switchBuilder
    tmMismatch = mt.Tm_NN(switch,strict=False,c_seq=mutation,nn_table=mt.DNA_NN3)
  File "/Library/Python/2.7/site-packages/Bio/SeqUtils/MeltingTemp.py", line 856, in Tm_NN
    deltaH += de_table[right_de][dH]
KeyError: '.G/AT'

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Lior Glick | 16 Jun 09:35 2015
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[Biopython] Mapping positions in a pairwise alignment

Hi all,

I have a pairwise alignment of protein sequences, created with Bio.pairwise2, something like this:

C-GGLK-GAPFLAC |||||||||||||| CHG--KTGASFLQC
I would like to know which position in the subject sequence is aligned to which position in the query sequence. In this example if the top sequence is the subject than I would like to know that position 1 in subject is aligned to position 1 in query, 2 is aligned to 3, 5 to 4, 6 to 6 etc...

Does Biopython have this functionality, or do I have to write my own function? Any suggestions?

Thanks!





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Gmane