I see. Yes, that makes sense now. My match is at the beginning of the read so there's nothing to the left of it (and thus empty).
Thanks!
Thanks!
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running install running build running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/cutadapt copying cutadapt/seqio.py -> build/lib.linux-x86_64-2.7/cutadapt copying cutadapt/compat.py -> build/lib.linux-x86_64-2.7/cutadapt copying cutadapt/xopen.py -> build/lib.linux-x86_64-2.7/cutadapt copying cutadapt/qualtrim.py -> build/lib.linux-x86_64-2.7/cutadapt copying cutadapt/adapters.py -> build/lib.linux-x86_64-2.7/cutadapt copying cutadapt/align.py -> build/lib.linux-x86_64-2.7/cutadapt copying cutadapt/modifiers.py -> build/lib.linux-x86_64-2.7/cutadapt copying cutadapt/report.py -> build/lib.linux-x86_64-2.7/cutadapt copying cutadapt/colorspace.py -> build/lib.linux-x86_64-2.7/cutadapt copying cutadapt/__init__.py -> build/lib.linux-x86_64-2.7/cutadapt creating build/lib.linux-x86_64-2.7/cutadapt/scripts copying cutadapt/scripts/cutadapt.py -> build/lib.linux-x86_64-2.7/cutadapt/scripts copying cutadapt/scripts/__init__.py -> build/lib.linux-x86_64-2.7/cutadapt/scripts running build_ext building 'cutadapt._align' extension creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/cutadapt gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c cutadapt/_align.c -o build/temp.linux-x86_64-2.7/cutadapt/_align.o gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/cutadapt/_align.o -o build/lib.linux-x86_64-2.7/cutadapt/_align.so building 'cutadapt._qualtrim' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c cutadapt/_qualtrim.c -o build/temp.linux-x86_64-2.7/cutadapt/_qualtrim.o gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/cutadapt/_qualtrim.o -o build/lib.linux-x86_64-2.7/cutadapt/_qualtrim.so building 'cutadapt._seqio' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c cutadapt/_seqio.c -o build/temp.linux-x86_64-2.7/cutadapt/_seqio.o gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/cutadapt/_seqio.o -o build/lib.linux-x86_64-2.7/cutadapt/_seqio.so running build_scripts creating build/scripts-2.7 copying and adjusting bin/cutadapt -> build/scripts-2.7 changing mode of build/scripts-2.7/cutadapt from 664 to 775 running install_lib copying build/lib.linux-x86_64-2.7/cutadapt/_seqio.so -> /home/<username>/.local/lib/python2.7/site-packages/cutadapt copying build/lib.linux-x86_64-2.7/cutadapt/_qualtrim.so -> /home/<username>/.local/lib/python2.7/site-packages/cutadapt copying build/lib.linux-x86_64-2.7/cutadapt/_align.so -> /home/<username>/.local/lib/python2.7/site-packages/cutadapt running install_scripts copying build/scripts-2.7/cutadapt -> /home/<username>/.local/bin changing mode of /home/<username>/.local/bin/cutadapt to 775 running install_egg_info Removing /home/<username>/.local/lib/python2.7/site-packages/cutadapt-1.7.1.egg-info Writing /home/<username>/.local/lib/python2.7/site-packages/cutadapt-1.7.1.egg-info
/home/<username>/.local/bin/cutadapt --version
pip install --user cutadapt
Requirement already satisfied (use --upgrade to upgrade): cutadapt in /usr/local/lib/python2.7/dist-packages Cleaning up...
head -n 1 $HOME/.local/bin/cutadapt python -c 'import sys; print sys.path' python -c 'import cutadapt; print cutadapt.__file__'
pip install --user cutadapt==1.7.1
>$ head -n 1 $HOME/.local/bin/cutadapt #!/usr/bin/python
>$ python -c 'import sys; print sys.path' ['', '/usr/local/lib/python2.7/dist-packages/screed-0.7-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/pbcore-0.8.0-py2.7.egg', '/usr/local/lib/python2.7/dist-packages', '/usr/local/lib/python2.7/dist-packages/distribute-0.6.34-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/ete2-2.2rev1056-py2.7.egg', '/usr/local/lib/python2.7/dist-packages/pbtools.pbdagcon-0.2.3-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/dist-packages/MAVR-1.0-py2.7.egg', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-linux2', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/home/<username>/.local/lib/python2.7/site-packages', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PIL', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7']
>$ python -c 'import cutadapt; print cutadapt.__file__' cutadapt/__init__.pyc
>$ pip install --user cutadapt==1.7.1 Downloading/unpacking cutadapt==1.7.1 Downloading cutadapt-1.7.1.tar.gz (451Kb): 451Kb downloaded Running setup.py egg_info for package cutadapt Installing collected packages: cutadapt Found existing installation: cutadapt 1.2.1 Uninstalling cutadapt: Exception: Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 126, in main self.run(options, args) File "/usr/lib/python2.7/dist-packages/pip/commands/install.py", line 228, in run requirement_set.install(install_options, global_options) File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1089, in install requirement.uninstall(auto_confirm=True) File "/usr/lib/python2.7/dist-packages/pip/req.py", line 476, in uninstall paths_to_remove.remove(auto_confirm) File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1391, in remove renames(path, new_path) File "/usr/lib/python2.7/dist-packages/pip/util.py", line 248, in renames shutil.move(old, new) File "/usr/lib/python2.7/shutil.py", line 300, in move os.unlink(src) OSError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/dist-packages/cutadapt-1.2.1.egg-info' Storing complete log in /home/<username>/.pip/pip.log
cd /; python -c 'import cutadapt; print cutadapt.__file__'
pip --version
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