http://blog.gmane.org/gmane.comp.python.bio.devel hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.comp.python.bio.devel/10584 <pre>A new uniprot-GOA parser is available for you to poke around: https://github.com/idoerg/biopython/tree/uniprot-goa/Bio/UniProtGOA More on Uniprot-GOA: http://www.ebi.ac.uk/GOA There are three file formats: GAF (gene association file) , GPA (gene product association) and GPI (gene product information) explained here: http://www.ebi.ac.uk/GOA/downloads Input GAF files can be very large, due to the growth of uniprot GOA. If you would like to test in a timely fashion, I suggest you get historical files, which are smaller. Once you get to the &gt; 40 version numbers, the runtime for the example code in UniProtGOA.py goes over 2 minutes (on my i5 machine). Old GAF files are available here: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/old/UNIPROT/ Current GPI and GPA files are not very large. Thanks to Peter for his help on this. Best, Iddo </pre> Iddo Friedberg 2013-05-08T23:28:17 http://comments.gmane.org/gmane.comp.python.bio.devel/10583 <pre>Hi, Here is a progress follow up to http://lists.open-bio.org/pipermail/biopython-dev/2013-April/010548.html .  I have added a commit to the github branch that adds an option to create claude branch lines using linecollection.  The linecollection objects are stored in a tuple before adding them to the plot.  It’s in Bio/Phylo/_utils.py.  Is this what the last bullet point was requesting in https://redmine.open-bio.org/issues/3336 ?   Thanks! Nate P. S.  I used a tuple to store the linecollection objects instead of a list because that was mentioned in the ticket but if that looks like it should be different let me know.  Also, I got some global variables to work with the code but I was only able to do that after declaring them as globals twice.  If there are suggestions on how to code that differently let me know. _______________________________________________ Biopython-dev mailing list Biopython-dev&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-dev </pre> Nate Sutton 2013-05-07T21:12:59 http://comments.gmane.org/gmane.comp.python.bio.devel/10581 <pre>hi, As promised, I have written a uniprot-goa parser. Very skeletal, has iterators for reading the three uniprot-GOA file types, a write function, and a couple of usage examples. No github write access, so attaching. Cheers, Iddo </pre> Iddo Friedberg 2013-05-07T16:24:00 http://comments.gmane.org/gmane.comp.python.bio.devel/10578 <pre>Hi everyone, I forget to post my gsoc proposal page here. Any comment? http://www.google-melange.com/gsoc/proposal/review/google/gsoc2013/yeyanbo/1# Thanks, Yanbo </pre> Yanbo Ye 2013-05-03T02:19:07 http://comments.gmane.org/gmane.comp.python.bio.devel/10573 <pre>Does anybody have a GOA parser in the works? Currently writing a simple parser for GAF, GPA and GPI formats. Can contribute if there is interest. More on GOA: http://www.ebi.ac.uk/GOA Cheers, Iddo </pre> Iddo Friedberg 2013-05-02T16:12:12 http://comments.gmane.org/gmane.comp.python.bio.devel/10562 <pre>Hi Eric, Again, thanks for your comment. It might be better to discuss here. https://github.com/lijax/gsoc/commit/e969c82a5a0aef45bba1277ce01d6dbee03e6a84#commitcomment-3096321 I have changed my proposal and timeline based on your advice. I think I was too optimistic that I didn't consider about the compatibility with existing code or other potential problem that may exist. After careful consideration, I removed one task from the goal list to make the time more relaxed, the tree comparison&lt;http://www.biopython.org/wiki/Phylo_cookbook#Comparing_trees&gt;(seems I miss understood this). I might be able to complete all of them. But it's better to make it as an extra task, to make sure this coding experience is not a burden. According to your comment: 1. I didn't know PyCogent and DendroPy. I'll refer to them for useful solutions. 2. For distance-based tree and consensus tree, I think there is no need to use NumPy. And for consensus tree, my original plan is to implement a binary class to count the clade with th</pre> Yanbo Ye 2013-04-30T07:20:59 http://comments.gmane.org/gmane.comp.python.bio.devel/10558 <pre>Hi All, I am a Fourth Year Undergraduate studying Chemical Engineering at IIT Bombay, India. As a warmup, I have been working upon NGS analysis this sem. Besides playing around with NGS pipelines, scripting one on my own, I have lately been plying around with the PSSM approach for BWA . https://github.com/pkerpedjiev/bwa-pssm/ . So far my contributions to this project have been only at testing level, I havent really contributed to the code as such, just reported some bugs. I have been using BioPython for my Computational Biology Course that I am doing this semester. I have also been using BIoPython for NGS analysis, modifying fastq formats and all. I recently contributed to the BWA wrapper for BioPython (https://github.com/biopython/biopython/pull/167). I am also working on the samtools wrapper. I was a Google Summer of Code 2012 Student for Connexions(http://cnx.org) and contributed towards SlideImporter Module(Pyramid/Python): That allows the user to upload SlideShows to SlideShare and Google Driv</pre> Saket Choudhary 2013-04-28T14:13:43 http://comments.gmane.org/gmane.comp.python.bio.devel/10551 <pre> Issue #3430 has been reported by Paulo Nuin. ---------------------------------------- Bug #3430: Error parsing PubMedCentral XML files https://redmine.open-bio.org/issues/3430 Author: Paulo Nuin Status: New Priority: Normal Assignee: Biopython Dev Mailing List Category: Main Distribution Target version: URL: It seems that there is an error parsing locally downloaded PubMedCentral xml (extension nxml) files. Using the code &lt; at &gt; from Bio import Entrez handle = open('nihms83342.nxml') records = Entrez.parse(handle) for record in records: print record &lt; at &gt; the following error occurs (copied from iPython), even though the XML header contains the declaration --------------------------------------------------------------------------- NotXMLError Traceback (most recent call last) &lt;ipython-input-5-e78d8d3c3888&gt; in &lt;module&gt;() 2 handle = open('nihms83342.nxml') 3 records = Entrez.parse(handle) ----&gt; 4 for record in records: 5 print record /Library/Python/2.</pre> redmine< at >redmine.open-bio.org 2013-04-27T19:46:51 http://comments.gmane.org/gmane.comp.python.bio.devel/10547 <pre> Hi Zhigang, It isn't too late to write up a proposal for GSoC 2013, but please also introduce yourself on the NESCent Phyloinformatics Summer of Code community on Google Plus: https://plus.google.com/communities/105828320619238393015 The GSoC program is a great chance to spend a few months focussed just on one programming project - which can be really fun. However, the fact that you're interested in making contributions outside of GSoC is great. I wrote some more about the lazy-loading sequence parsers and indexing idea on the biopython-dev mailing list last month: http://lists.open-bio.org/pipermail/biopython-dev/2013-March/010469.html However, lazy-parsing can also be done separately from the indexing. This is something I was trying in my experimental SAM/BAM parser mentioned on this thread: http://lists.open-bio.org/pipermail/biopython-dev/2013-April/010492.html The basic idea here was that the raw data for each record was loaded into memory as a (bytes) string, but not all of it was parsed into the</pre> Peter Cock 2013-04-27T11:20:57 http://comments.gmane.org/gmane.comp.python.bio.devel/10545 <pre>Sorry I forget to introduce myself. My name is Zheng Ruan, currently a first year graduate students at the University of Georiga. I have a background in biology and now pursue a PhD in Bioinformatics. I taught myself many programming language and finally python became my favorite. I use biopython a lot for everyday sequence manipulation and format conversion. For example, I use Bio.Phylo class for reroot tree and visualization functionality in the sever http://bioinformatics.publichealth.uga.edu/SpeciesTreeAnalysis/index.php, which has just been accepted by NAR. I really hope to contribute the the Open Source Project and GSoC seems to be a good start point. I think the codon alignment proposal suitable to me because it requires medium programming skills and I've already finished the Computational Molecular Evolution by Zihen g Yang and also have a phylogenetics course this spring semester. Thanks for all. Best, Zheng Ruan ------------------ Original ------------------ From: "Zheng Ruan"&lt;rz1991&lt; at &gt;foxmail.</pre> 阮铮 2013-04-27T08:18:56 http://comments.gmane.org/gmane.comp.python.bio.devel/10544 <pre>Hi Biopython developers, I hope it's not too late to inform you my interest in Biopython GSoC, but I talked to Eric Talevich several weeks before that I would like to apply the Codon Alignment proposal. As a simple trial, I've already got a simple implementation of codon alignment script as can be found in https://github.com/zruan/CodonAlignment. It doesn't account for frame shift and mismatches between protein sequences and nucleotide sequences. But as least it works if the protein sequences can be exactly translated by nucleotide sequences. Hopefully I will finish my proposal this week. Is there any suggestions? Sincerely, Ruan _______________________________________________ Biopython-dev mailing list Biopython-dev&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-dev </pre> 阮铮 2013-04-27T02:12:11 http://comments.gmane.org/gmane.comp.python.bio.devel/10543 <pre>Hi guys, My name is Yanbo Ye. I'm a third-year master student in bioinformatics(mainly phylogenetics) in China. My master project is about the genome evolution of baculovirus and a bioinformatics tool development. The tool is a java program named BlastGraph&lt;https://github.com/bigwiv/BlastGraph&gt;that can be used for sequence clustering, genome tree construction and gene gain and loss estimation. This involves a range of phylogenetics algorithms commonly used. So based on my experice, I'd like to contribute to the Phylo package of Biopython for some unimplemented methods during the Google Summer of Code this year, which will be under the direction of Eric Talevich. I have been using python and Biopython for nearly a year to do some sequence file parsing and tree manipulation. But I must say I'm still new to python about the design convention or any popular python packages, etc. Anyway, I'm a fast learner and would like to improve my python programming skills through this project. I'd like to discuss with you</pre> Yanbo Ye 2013-04-27T03:16:22 http://comments.gmane.org/gmane.comp.python.bio.devel/10540 <pre>To all the Biopythoneers, For the last few years Biopython has participated in the Google Summer of Code (GSoC) program under the umbrella of the Open Bioinformatics Foundation (OBF): https://developers.google.com/open-source/soc/ https://github.com/OBF/GSoC Unfortunately like quite a few previously accepted organisations, this year the OBF not accepted. Google has kept the total about the same year on year, so this is probably simply a slot rotation to get some new organisations involved. The good news (for those not following the Biopython-dev mailing list) is we have an alternative option agreed with the good people at NESCent, as we did back in 2009: http://biopython.org/wiki/Google_Summer_of_Code http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2013 I'd like to thank Eric for co-ordinating this, and encourage any interested potential students to sign up to the Biopython development list and NESCent's Google+ group as soon as possible (if you haven't done so already): http://list</pre> Peter Cock 2013-04-24T19:19:48 http://comments.gmane.org/gmane.comp.python.bio.devel/10536 <pre>The following script: import sys import Bio from Bio.PDB.DSSP import DSSP from Bio.PDB.PDBParser import PDBParser pdb_filename = sys.argv[1] p = PDBParser() structure = p.get_structure('chupacabra', pdb_filename) model = structure[0] biodssp = DSSP(model, pdb_filename, dssp="dssp") will fail on files without HEADER with traceback: Traceback (most recent call last): File "testdssp_fail.py", line 13, in &lt;module&gt; biodssp = DSSP(model, pdb_filename, dssp="dssp") File "/home/modorama_dev/modorama/ENV_INI/lib/python2.7/site-packages/Bio/PDB/DSSP.py", line 200, in __init__ dssp_dict, dssp_keys = dssp_dict_from_pdb_file(pdb_file, dssp) File "/home/modorama_dev/modorama/ENV_INI/lib/python2.7/site-packages/Bio/PDB/DSSP.py", line 101, in dssp_dict_from_pdb_file out_dict, keys = make_dssp_dict(out_file.name) File "/home/modorama_dev/modorama/ENV_INI/lib/python2.7/site-packages/Bio/PDB/DSSP.py", line 121, in make_dssp_dict if sl[1] == "RESIDUE": IndexError: list index out of range This is bec</pre> Jan Kosinski 2013-04-23T08:09:30 http://comments.gmane.org/gmane.comp.python.bio.devel/10533 <pre>Dear BioPython Devs, Probably a strange request, but I was wondering if it might be a good idea to make the fasta parser raise an error when it is asked to parse incorrectly formatted files. I ask, because a while ago, I made a simple command line utility to convert sequence files to/from various formats, using SeqIO.parser. It's attached if anyone's interested. My supervisor's now using it to filter fastq formatted sequences by length, but keeps forgetting to add a '-format fastq' option. The script by default assumes fasta formatted sequences, which, like SeqIO.parser is by design, but the problem is that the parser doesn't mind at all when a fastq file doesn't contain a single "&gt;" character. Are there any interfaces to make the fasta parser stricter? This error is completely silent until picked up by external programs; hmmer, in this instance. Ideally, an error would be raised much earlier in the process, especially as the department's NFS servers take ages to retrieve and conv</pre> Alex Leach 2013-04-19T11:29:28 http://comments.gmane.org/gmane.comp.python.bio.devel/10527 <pre> Issue #3427 has been reported by Ben Morris. ---------------------------------------- Feature #3427: Cache paths in Bio.Phylo trees for later use https://redmine.open-bio.org/issues/3427 Author: Ben Morris Status: New Priority: Normal Assignee: Category: Target version: URL: I'm doing some analyses using Bio.Phylo in which I need to find many distances between pairs of taxa, and have found that this can be quite slow as currently implemented. My current solution is to extend Newick.Tree objects and cache the result of the get_path function. This way, after finding the distance between species A and B, finding the distance between A and C doesn't require recomputing the path from A to the root. Example: &lt;pre&gt; class CachingTree(bp.Newick.Tree): _paths = {} def __init__(self, tree): self.__dict__.update(tree.__dict__) def get_path(self, target, **kwargs): if not target in self._paths: self._paths[target] = bp.Newick.Tree.get_path(self, target=target, </pre> redmine< at >redmine.open-bio.org 2013-04-15T14:29:45 http://comments.gmane.org/gmane.comp.python.bio.devel/10520 <pre>Hi all, We've have Python 3 coverage on the Travis continuous integration tests &amp; the nightly builtbot tests for quite some time now. http://travis-ci.org/biopython/biopython http://testing.open-bio.org/biopython/tgrid There have been a few Python 3 specific issues reported (which have been fixed), but I think we should probably go ahead and say we support Python 3.1 or later (with the exception of some minor C code which has not been ported). Does this seem like a good move for the next release? We've already said that this (Biopython 1.62) will be the final release to support Python 2.5, which will help make some bits of the 2/3 compatibility code much simpler. Regards, Peter </pre> Peter Cock 2013-04-14T20:10:02 http://comments.gmane.org/gmane.comp.python.bio.devel/10511 <pre>Hi everyone, I've been doing a ton of mpileup work recently with samtools so I made a python daemon to parallelize the process. Is there any interest in a generic SamTools package for BioPython? I know pysam exists, but it'd be an added dependency as well as not threaded. In my experience, for querying a ton of positions threading mpileup is the best way to go (much faster than -l bed_file in my use cases). If there's interest, I'll package it as a general SamTools command line wrapper with the added bonuses that for certain operations you can input a list and thread those parts. Chris </pre> Chris Mitchell 2013-04-11T02:57:41 http://comments.gmane.org/gmane.comp.python.bio.devel/10508 <pre>Hi all, As a phd student in bioinformatics, I found in Biopython a useful tool. Actually, I work on NGS, differential gene expression, alternative splicing and conservationa analysis of transposable elements. Therefore, would like to introduce myself and say that I would like to contribute. Best regards, </pre> Andrei Rozanski 2013-04-10T16:16:02 http://comments.gmane.org/gmane.comp.python.bio.devel/10507 <pre>Hi all, I've suspected for a some time that there is some subtle bug in run_tests.py or a limitation in the Python warnings module - although our code tries to reset the filters between tests this doesn't seem to be working all the time. The obvious effect of this is getting loads of ResourceWarning messages under Python 3.3, e.g. http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.3/builds/130/steps/shell/logs/stdio Sometimes theses warnings can manifest as real bugs, in particular on Windows where you cannot delete a file when there is still an open handle to it which will not be closed until the garbage collection runs. i.e. Bugs which tend to only show under Windows with PyPy or Jython. e.g. https://github.com/biopython/biopython/commit/943fffe2835dca4a996a6a171f026f6374ecaaa9 After fixing most of the handle leaks (which is a good thing to do anyway), the remainder of being shown are in the documentation tests (where fixing them can make the examples harder to follow): http://t</pre> Peter Cock 2013-04-10T11:17:34 http://comments.gmane.org/gmane.comp.python.bio.devel/10503 <pre>Hi all, First a general reminder that the BOSC 2013 abstract deadline is this coming Friday 12 April, http://www.open-bio.org/wiki/BOSC_2013 Second, we need to prepare an abstract for the traditional Biopython Project update. Both Brad and I should be there for BOSC 2013, and the preceding mini hackathon/codefest to which everyone is welcome: http://www.open-bio.org/wiki/Codefest_2013 Who else is planning to be at BOSC 2013 (and the Codefest), and is there anyone keen to present the update? I'm happy to give the talk, but this is a nice chance for someone else to present and give a more rounded impression of the Biopython developers ;) According to http://biopython.org/wiki/Documentation#Presentations the recent Biopython presenters at BOSC have been: BOSC 2013, Berlin, Germany - ??? BOSC 2012, Long beach, USA - Eric BOSC 2011, Vienna, Austria - Peter BOSC 2010, Boston, USA - Brad BOSC 2009, Stockholm, Sweden - Peter BOSC 2008, Toronto, Canada - Tiago BOSC 2007, Vienna, Austria - Peter BOSC 2006, Fortal</pre> Peter Cock 2013-04-09T13:36:27 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.python.bio.devel