Hello, I am using Linux version 2.6 and python version 2.6.6 (gcc version 4.4.5). I have a list of protein names and am trying to get their sequences. I thought I would download Biopython, and am having troubles. I first downloaded and installed easyinstall from http://pypi.python.org/pypi/setuptools I followed the instructions and it seemed to work (see below error messages).
This is the error I get when I try to install biopython: root@debbie-VirtualBox:/usr/local/bin# easy_install biopython Searching for biopython Reading http://pypi.python.org/simple/biopython/ Reading http://www.biopython.org/ Reading http://biopython.org/DIST/ Best match: biopython 1.59 Downloading http://biopython.org/DIST/biopython-1.59.zip Processing biopython-1.59.zip Running biopython-1.59/setup.py -q bdist_egg --dist-dir /tmp/easy_install-qMfJsF/biopython-1.59/egg-dist-tmp-W4L1YX warning: no previously-included files found matching 'Tests/Graphics/*' warning: no previously-included files matching '.cvsignore' found under directory '*' warning: no previously-included files matching '*.pyc' found under directory '*' Bio/cpairwise2module.c:12: fatal error: Python.h: No such file or directory compilation terminated. error: Setup script exited with error: command 'gcc' failed with exit status 1 *I also tried it in the directory Downloads, because this is where the easyinstall was downloaded to. Same message. Then I tried downloading Biopython from http://pypi.python.org/pypi/biopython I downloaded biopython-1.59.tar.gz<http://pypi.python.org/packages/source/b/biopython/biopython-1.59.tar.gz#md5=c83b26cc1bc2b2ecdce28c1b5e49110d>. and extracted it to the folder BLAST-SW in my Documents folder. Here is what I tried: debbie@debbie-VirtualBox:~/Documents/BLAST-SW$ sh biopython-1.59.tar.gz sh: Can't open biopython-1.59.tar.gz debbie@debbie-VirtualBox:~$ sh biopython-1.59.tar.gz sh: Can't open biopython-1.59.tar.gz debbie@debbie-VirtualBox:~/Documents/BLAST-SW$ sh biopython-1.59 *This had no error message, but I think that Biopython is not installed because: >>> import Bio Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named Bio The end goal is to use ncbi Eutils to get protein sequences, so if anyone has experience with this please let me know. Thanks! Laura Scearce
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