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

Download


    biopython-seqxml-patch.tar.gz

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")