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lpantano / seqcluster

small RNA analysis from NGS data
http://seqcluster.readthedocs.io
MIT License
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NameError: global name 'gzip' is not defined #11

Closed sung closed 9 years ago

sung commented 9 years ago

Hi,

I followed the instruction manual, but could not manage to run 'seqcluster': [ssg29@login-sand1 ~]$ which seqcluster ~/Install/seqcluster/linuxbrew/bin/seqcluster [ssg29@login-sand1 ~]$ seqcluster Traceback (most recent call last): File "/home/ssg29/Install/seqcluster/linuxbrew/bin/seqcluster", line 4, in from seqcluster.command_line import main File "/home/ssg29/Install/seqcluster/anaconda/lib/python2.7/site-packages/seqcluster/command_line.py", line 4, in from prepare_data import prepare File "/home/ssg29/Install/seqcluster/anaconda/lib/python2.7/site-packages/seqcluster/prepare_data.py", line 8, in from libs.classes import sequence_unique File "/home/ssg29/Install/seqcluster/anaconda/lib/python2.7/site-packages/seqcluster/libs/classes.py", line 6, in import numpy as np File "/home/ssg29/.local/lib/python2.7/site-packages/numpy/init.py", line 170, in from . import add_newdocs File "/home/ssg29/.local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in from numpy.lib import add_newdoc File "/home/ssg29/.local/lib/python2.7/site-packages/numpy/lib/init.py", line 8, in from .type_check import * File "/home/ssg29/.local/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in import numpy.core.numeric as _nx File "/home/ssg29/.local/lib/python2.7/site-packages/numpy/core/init.py", line 6, in from . import multiarray ImportError: /home/ssg29/.local/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyUnicodeUCS2_AsASCIIString

It seems anaconda tries to pick up local numpy package as shown below.

If I manually export PYTHONPATH like: PYTHONPATH=$HOME/Install/seqcluster/anaconda/lib/python2.7/site-packages:$PYTHONPATH

Then, seqcluster seems to work: [ssg29@login-sand1 ~]$ seqcluster use ['stats', 'collapse', 'prepare', 'predict', 'cluster', 'explore', 'report']

I wanted to use 'collapse', but with no luck:

[ssg29@login-sand1 ~]$ seqcluster collapse -f ~/results/SLX-9176.Homo_sapiens.v1/Trim/NEBsmRNA01/SLX-9176.NEBsmRNA01.C7TWVANXX.s_6.r_1_trimmed.fq.gz -o ~/results/SLX-9176.Homo_sapiens.v1/Trim/NEBsmRNA01/SLX-9176.NEBsmRNA01.C7TWVANXX.s_6.r_1_trimmed.collapsed 07/30/2015 03:31:13 PM INFO: Run collapse Traceback (most recent call last): File "/home/ssg29/Install/seqcluster/linuxbrew/bin/seqcluster", line 6, in sys.exit(main()) File "/home/ssg29/Install/seqcluster/anaconda/lib/python2.7/site-packages/seqcluster/command_line.py", line 40, in main collapse_fastq(kwargs["args"]) File "/home/ssg29/Install/seqcluster/anaconda/lib/python2.7/site-packages/seqcluster/collapse.py", line 14, in collapse_fastq seqs = collapse(args.fastq) File "/home/ssg29/Install/seqcluster/anaconda/lib/python2.7/site-packages/seqcluster/libs/fastq.py", line 10, in collapse with open_fastq(in_file) as handle: File "/home/ssg29/Install/seqcluster/anaconda/lib/python2.7/site-packages/seqcluster/libs/fastq.py", line 30, in open_fastq return gzip.open(in_file, 'rb') NameError: global name 'gzip' is not defined

Any idea?

Sung

lpantano commented 9 years ago

thanks so much!

please let me know if the devel version doesn't work!

fixed by e06ec0d

lpantano commented 9 years ago

@sung, I will update the conda binary this afternoon. In case you want to try first with the code in github.

thanks for your patient!

lpantano commented 9 years ago

Hi @sung, conda binary is updated.

please let me know if the issue got away.

thanks!