Sergio Martinez Cuesta | 27 Aug 19:27 2015
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[Biopython] parse header fastqc

Dear all,

How can I use biopython in order to figure out which of the read headers 
in my fastq file do not start with the character " <at> "?

The record and title objects in the SeqIO.parse and FastqGeneralIterator 
functionalities assume headers start with " <at> ".

Thanks in advance.
Sergio
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ning luwen | 7 Aug 04:56 2015
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[Biopython] Error in Querying the KEGG API

Dear All,

I followed the tutorial http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc231 to learn KEGG things in biopython, but without lucky, any suggestion? 

>>> from Bio import KEGG
>>> from Bio.KEGG import Enzyme
>>> request = KEGG.get("ec:5.4.2.2")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'module' object has no attribute 'get'
>>> import Bio
>>> print Bio.__version__
1.65


--
regards,
luwen ning
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Ian Stavros | 5 Aug 19:37 2015
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[Biopython] Tm Mismatch Question

Hello All,

It's me again. I have another question about the results that I am getting back from the Tm Mismatch.

Is it suppose to be returning the Tm Mismatch value or just the Second Seq in comparison to the Original Sequence?

Thanks,
Ian Stavros
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Prakhar Gaur | 5 Aug 06:00 2015
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[Biopython] Regarding Bio.SearchIO Hmmer Use Case

Hello,

Biopython & SearchIO user for over three weeks.

OS - Ubuntu 14,04
Biopython Bio.__version__ 1.65
HMMER -- 3.1b2
Code is here (github) - branch alpha

Briefly, if a hmmer 3 text output is parsed using the 'SearchIO.parse()' and that file has output from more than one searches only the first result is read and rest are ignored.

Details -- Used 'hmmsearch' with pfam models against a database of proteins. Since I wanted to club some domain models together, hence concatenated the result into a single text file. As all the domains concatenated together belong to a single protein.

When I use SearchIO.parse() to read this file, the Queryresult object has only the top entry (first hmm models result), iterating over the Queryresult does not give the other results.

To test this I have split the results file to have the results of a single hmmsearch run in each file, after this parse works fine.
But this use case (single result in one file) is for 'SearchIO.read()'. Consequently I would expect 'SearchIO.parse()' to be able to parse multiple results from a single file.

​​As test case from my repo, first run the script 'hmmer-SearchIO-text-parser.py', the output file 'Q9UP38.out' would be read 
 this represents the use case in which the result file has multiple (2) entries.

Are my expectations from 'SearchIO.parse()' correct ? Or am I missing something ?

Reply, Comments, Pointers etc. are all welcome.

-- 
Thanking you,
--
Prakhar Gaur

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Carlos Pena | 2 Aug 14:24 2015
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Re: [Biopython] Biopython Digest, Vol 152, Issue 2

Thanks Jeremy, Jared,

I will take a better look at your script. I had already come up with a
Python package to do the trick: https://github.com/carlosp420/degenerate-dna

I tried to make it easy to use:

>>> from degenerate_dna import Degenera
>>> dna = 'AGTTCT'
>>> res = Degenera(dna=dna, table=1, method='S')
>>> res.degenerate()
>>> res.degenerated
'AGYAGY'

But so far I have implemented the degenerated sequences for the Standard
Code and the Invertebrate Mitochondrial. In our lab, we don't urgently
need the other translation codes yet.

> "YTN" would also match both of Phe's codons ("TTT" and "TTC")
I just run the original Perl Degen_v1.4.pl script and both TTT and TTC
get degenerated to "TTY" using both translation tables 1 and 5.

cheers,

carlos

On 02.08.2015 15:00, biopython-request <at> mailman.open-bio.org wrote:
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> 
>    1. Re: Is there any Biopython tool to degenerate a nucleotide
>       sequence (Jeremy)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sat, 1 Aug 2015 23:23:23 +0000 (UTC)
> From: Jeremy <Jeremy.molbio <at> gmail.com>
> To: biopython <at> biopython.org
> Subject: Re: [Biopython] Is there any Biopython tool to degenerate a
> 	nucleotide	sequence
> Message-ID: <loom.20150802T011012-309 <at> post.gmane.org>
> Content-Type: text/plain; charset=utf-8
> 
> Sampson, Jared <Jared.Sampson <at> nyumc.org> writes:
> 
>>
>>
>> Hi Jeremy -?
>>
>> Nice work, thanks for sharing.
>>
>>
>> However (and someone please correct me if I'm wrong here!), it looks like 
> the current Leucine substitution, "YTN" would also match both of Phe's 
> codons ("TTT" and "TTC"), and the current Arginine ("MGN") also matches two 
> of Serine's codons ("AGT" and "AGC").
>>  ?FWIW, the?PhyloTools script?also produces the same erroneous degenerate 
> codons. ?I've sent the contact address on that site a bug report.
>>
>> I've updated a?fork?of your original gist to implement fixes for these 
> residues, along with a couple stylistic changes (hope you don't mind). 
> ?Please feel free to incorporate them
>>  into your original. ?If you want to double check the rest of the 
> degen_dict, there's a?nice table on Wikipedia.
>>
>> Also, if you're looking to make other improvements, it might be nice to 
> add a "frame=1" argument to degenerate_sequence() to optionally accommodate 
> the other two reading frames rather than chopping leftover bases.
>>
>> Cheers,
>> Jared
>>
>>
>>
>>
>> --?
>> Jared Sampson
>> Xiangpeng Kong Lab
>> NYU Langone Medical Centerhttp://kong.med.nyu.edu/
>>
>>
>>
>> On Jul 31, 2015, at 1:39 AM, Jeremy <Jeremy.molbio <at> gmail.com> wrote:
>>
>>
>> Carlos Pena <mycalesis <at>?gmail.com> writes:
>>
>> 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 
> Degenhttp://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
>>
>>
>> Hi Carlos,
>> I hacked up something that should return the same output as the Degen 
> 1.4?
>> Perlweb tool. ?
>> The gist can be found here: 
> ?https://gist.github.com/biojerm/6242381eb4ad3ef18ac6
>> I am pretty new to both Python and Biopython, so the please let me know 
> if?
>> you have any feedback on both form, styling, and/or function.?
>> I know the method is currently quite fragile. Below are a few thoughts 
> on?
>> the method's weaknesses
>> 1)The method does not handle sequences that are not evenly divisible by 
> 3.
>> 2)I think the method would be a lot more useful if you could call it on 
> a?
>> single or set of FASTA files or a GB files. ?But, I have not learned 
> ?how?
>> to program that yet. ?
>> 3) I probably should return the degenerate sequences as Seq files, but 
> at?
>> the moment they are simple strings.
>> 4)Tests...need to figure those out too. ?
>> Please let me know if you find this useful or and if there are any must?
>> have features for your purposes.
>> Thanks,
>> Jeremy
>> _______________________________________________
>> Biopython mailing list ?- ?Biopython <at> mailman.open-
> bio.orghttp://mailman.open-bio.org/mailman/listinfo/biopython
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------
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> 
> 
> Hi Jared,
> Thanks for editing the code.  Your improvements in both style and function 
> are greatly appreciated.  I originally  was trying to mimic the output of 
> the bioPerl function.  However, I think your improvements help to maintain 
> accuracy of the original sequence.  I will incorporate your method into the 
> final function.  I will also try and introduce different frames and 
> possibly different codon tables.  
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
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> http://mailman.open-bio.org/mailman/listinfo/biopython
> 
> End of Biopython Digest, Vol 152, Issue 2
> *****************************************
> 

--

-- 
Dr. Carlos Peña
Laboratory of Genetics
Department of Biology
University of Turku
20014 Turku
FINLAND

* Associated Editor, Revista Peruana de Biología
http://revistasinvestigacion.unmsm.edu.pe/index.php/rpb
* The Nymphalidae Systematics Group
http://nymphalidae.net
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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
Department of Biology
University of Turku
20014 Turku
FINLAND

* Associated Editor, Revista Peruana de Biología
http://revistasinvestigacion.unmsm.edu.pe/index.php/rpb
* The Nymphalidae Systematics Group
http://nymphalidae.net
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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

--

Dr. Peter Cock,
BOSC 2015 co-chair with Nomi Harris,
Secretary for the Open Bioinformatics Foundation,
Bioinformatician at The James Hutton Institute, UK

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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
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Karin Lagesen | 10 Jul 10:46 2015
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[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
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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:
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> than "Re: Contents of Biopython digest..."
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> 
> 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 --------------
> An HTML attachment was scrubbed...
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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 6
> *****************************************


_______________________________________________
Biopython mailing list  -  Biopython <at> mailman.open-bio.org
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:
Send Biopython mailing list submissions to
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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
>
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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
>
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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
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