SeqXML Biopython support

Installation on UNIX and MacOSX

   Download and unpack seqxml patch

cd
wget http://seqxml.org/download/SeqXML/biopython-seqxml-patch.tar.gz
tar -xzf biopython-seqxml-patch.tar.gz

   Checkout a copy of the Biopython codebase form github. Requires git
git clone git://github.com/biopython/biopython.git 

    Patch the copy to add the SeqXML parser/writer.

cd biopython
git am ../biopython-seqxml.patch

    Install the patched Biopython. More details about the Biopython installation.

python setup.py install
http://biopython.orghttp://git-scm.com/downloadhttp://biopython.org/DIST/docs/install/Installation.htmlshapeimage_2_link_0shapeimage_2_link_1shapeimage_2_link_2

Usage

   

    Reading with the standard BioPython Bio.SeqIO function:


  1. from Bio import SeqIO   

  2. fileHandle = open("SEQXML_FILE","r")

  3. records = list(SeqIO.parse(fileHandle, "seqxml"))

   


    Writing with the standard BioPython Bio.SeqIO function:


  1. from Bio import SeqIO

  2. import sys

  3. SeqIO.write(records,sys.stdout,"seqxml")