From m.ebert at umontreal.ca Tue Feb 2 21:11:33 2016 From: m.ebert at umontreal.ca (Ebert Maximilian) Date: Tue, 2 Feb 2016 21:11:33 +0000 Subject: [Biopython] How does pairwise2 alignement returns begin on first matching amino acid? Message-ID: <6381E031-5A23-41A8-B257-09A9AD512366@umontreal.ca> Hi there, I aligned two sequences using the following: from Bio import pairwise2 from Bio.pairwise2 import format_alignment from Bio.SubsMat import MatrixInfo as matlist seq1="SKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNST" seq2="HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPLTSTFKVLLCGAVLSRVDAGQEQLGRRI" matrix = matlist.blosum62 gap_open = -11 gap_extend = -1 alns = pairwise2.align.localds(seq1, seq2, matrix, gap_open, gap_extend) for a in alns: print(format_alignment(*a)) So the result is (hard to see in text mode here is a link to biostars forum entry https://www.biostars.org/p/175229/): SKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWD-YNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNST- |||||||||||||||||||||||||||||||||||||||||||||||||||||||| --HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPLTSTFKVLLCGAVLSRVDAGQEQLGRRI Score=98 And hence the begin is 9 but I want the beginning to be 2. Also for the end I want it to be the T/R combination and not K/Q. Any idea how to do this? Thanks! From p.j.a.cock at googlemail.com Thu Feb 11 09:51:45 2016 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 11 Feb 2016 09:51:45 +0000 Subject: [Biopython] How does pairwise2 alignement returns begin on first matching amino acid? In-Reply-To: <6381E031-5A23-41A8-B257-09A9AD512366@umontreal.ca> References: <6381E031-5A23-41A8-B257-09A9AD512366@umontreal.ca> Message-ID: Hi Ebert, I just replied on BioStars: Have you calculated the score of the preferred alignment (starting from the first letter of the second sequence, F/H, though to the last letter of the first sequence, T/R)? Can you see how to adjust the scoring to make this win? Peter On Tue, Feb 2, 2016 at 9:11 PM, Ebert Maximilian wrote: > Hi there, > I aligned two sequences using the following: > > from Bio import pairwise2 > from Bio.pairwise2 import format_alignment > from Bio.SubsMat import MatrixInfo as matlist > > seq1="SKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNST" > seq2="HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPLTSTFKVLLCGAVLSRVDAGQEQLGRRI" > matrix = matlist.blosum62 > gap_open = -11 > gap_extend = -1 > alns = pairwise2.align.localds(seq1, seq2, matrix, gap_open, gap_extend) > for a in alns: > print(format_alignment(*a)) > So the result is (hard to see in text mode here is a link to biostars forum entry https://www.biostars.org/p/175229/): > > SKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWD-YNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNST- > |||||||||||||||||||||||||||||||||||||||||||||||||||||||| > --HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPLTSTFKVLLCGAVLSRVDAGQEQLGRRI > Score=98 > And hence the begin is 9 but I want the beginning to be 2. Also for the end I want it to be the T/R combination and not K/Q. Any idea how to do this? > > Thanks! > > _______________________________________________ > Biopython mailing list - Biopython at mailman.open-bio.org > http://mailman.open-bio.org/mailman/listinfo/biopython From cgodshall at enthought.com Fri Feb 26 18:11:18 2016 From: cgodshall at enthought.com (Courtenay Godshall (Enthought)) Date: Fri, 26 Feb 2016 12:11:18 -0600 Subject: [Biopython] ANN: SciPy (Scientific Python) 2016 Conference Call for Talk / Tutorial Proposals Open Until 3/25 Message-ID: <006f01d170c1$17790060$466b0120$@enthought.com> **SciPy 2016 Conference (Scientific Computing with Python) Announcement** *Call for Proposals: Submit Your Tutorial and Talk Ideas by March 25, 2015 at http://scipy2016.scipy.org. SciPy 2016, the 15th annual Scientific Computing with Python conference, will be held July 11-17, 2016 in Austin, Texas. SciPy is a community dedicated to the advancement of scientific computing through open source Python software for mathematics, science, and engineering. The annual SciPy Conference brings together over 650 participants from industry, academia, and government to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. The full program will consist of 2 days of tutorials (July 11-12), 3 days of talks (July 13-15), and 2 days of developer sprints (July 16-17). More info is available on the conference website at http://scipy2016.scipy.org (where you can sign up for the mailing list); or follow @scipyconf on Twitter. We hope you'll join us - early bird registration is open until May 22, 2016 at http://scipy2016.scipy.org/ehome/146062/332936/?&& We encourage you to submit tutorial or talk proposals in the categories below; please also share with others who you'd like to see participate! Submit via the conference website: http://scipy2016.scipy.org. ---------------------------------------------------------------------------- ------------------------- *SUBMIT A SCIPY 2016 TUTORIAL PROPOSAL - DUE MARCH 21, 2016* ---------------------------------------------------------------------------- ------------------------- Details and submission here: http://scipy2016.scipy.org/ehome/146062/332967/?&& These sessions provide extremely affordable access to expert training, and consistently receive fantastic feedback from participants. We're looking for submissions on topics from introductory to advanced - we'll have attendees across the gamut looking to learn. Whether you are a major contributor to a scientific Python library or an expert-level user, this is a great opportunityto share your knowledge and stipends are available. ---------------------------------------------------------------------------- --------------------------------- **SUBMIT A SCIPY 2016 TALK / POSTER PROPOSAL - DUE MARCH 25, 2016* ---------------------------------------------------------------------------- --------------------------------- Details and submission here: http://scipy2016.scipy.org/ehome/146062/332968/?&& SciPy 2016 will include 3 major topic tracks and 8 mini-symposia tracks. Major topic tracks include: - Scientific Computing in Python - Python in Data Science (Big data and not so big data) - High Performance Computing Mini-symposia will include the applications of Python in: - Earth and Space Science - Engineering - Medicine and Biology - Social Sciences - Special Purpose Databases - Case Studies in Industry - Education - Reproducibility If you have any questions or comments, feel free to contact us at: scipy-organizers at scipy.org ----------------------------------------------------------- **SCIPY 2016 REGISTRATION IS OPEN** ----------------------------------------------------------- Please register early. SciPy early bird registration until May 22, 2016! Register at http://scipy2016.scipy.org. Plus, enter our t-shirt design contest to win a free registration. (Send a vector art file to scipy at enthought.com by March 31 to enter). -------------- next part -------------- An HTML attachment was scrubbed... URL: From ulrich.melcher at okstate.edu Sat Feb 27 23:39:59 2016 From: ulrich.melcher at okstate.edu (Melcher, Ulrich) Date: Sat, 27 Feb 2016 23:39:59 +0000 Subject: [Biopython] Installing Biopython on Mac Message-ID: I need help interpreting the instruction "You will need to have installed Apple's XCode tools from the App Store ..., and then the optional command line tools from within the XCode GUI's options menu." from http://biopython.org/wiki/Download I have no trouble installing the Xcode package, but am unable to locate either the tools or the options menu. I am not a developer. Ulrich Melcher Regents & RJ Sirny Professor Department of Biochemistry & Molecular Biology Oklahoma State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From ericmajinglong at gmail.com Sun Feb 28 02:31:02 2016 From: ericmajinglong at gmail.com (Eric Ma) Date: Sat, 27 Feb 2016 21:31:02 -0500 Subject: [Biopython] Installing Biopython on Mac In-Reply-To: References: Message-ID: Hi Ulrich, To solve your immediate problem, you can try a few things, in order: 1. Go to your Terminal and type (without quotations) "gcc". You might get a pop-up that says, "The 'gcc' command requires the command line tools." Accept and proceed from there. 2. If you get a message "clang: error: no input files", then you have gcc installed. You can double-confirm that gcc is installed by doing "which gcc" at the command line; it'll likely show something along the lines of "/usr/bin/gcc". 3. Alternative to steps 1 and 2: type "xcode-select --install" in Terminal, then follow the prompts. If you're starting out with Python and BioPython, then I would recommend installing a distribution of Python that is separate from your system Python. I have written on my own blog recommending the Anaconda distribution of Python . There are some benefits to doing this: (1) You don't risk breaking the Python that Apple ships with your Mac; I have nuked my environment before and wreaked iPhoto on older versions of Mac OS X, totally unexpected. (2) Anaconda solves the software packaging problem pretty nicely, and you don't have to type "sudo" when installing packages, with biopython being a simple "conda install biopython" away, and (3) if you or your group members progress really far with Python, it'll be a great thing to have isolated "environments", which Anaconda solves nicely as well. If you need help getting set up, I can attempt to give more detailed instructions via email. Cheers, Eric ??? This email was written with recycled electrons. w: http://www.ericmajinglong.com/ a: http://about.me/ericmjl f: https://www.facebook.com/ericmjl On Sat, Feb 27, 2016 at 6:39 PM, Melcher, Ulrich wrote: > I need help interpreting the instruction "You will need to have installed > Apple's XCode tools from the App Store ?, and then the optional command > line tools from within the XCode GUI's options menu." from > http://biopython.org/wiki/Download > I have no trouble installing the Xcode package, but am unable to locate > either the tools or the options menu. I am not a developer. > Ulrich Melcher > Regents & RJ Sirny Professor > Department of Biochemistry & Molecular Biology > Oklahoma State University > > > _______________________________________________ > 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: