Comments (1)
This issue cropped up again when referencing the latest version of cohorts
:
E.g.
running from cohorts.functions import *
ImportErrorTraceback (most recent call last)
<ipython-input-1-c5376ccc9100> in <module>()
9 import numpy as np
10 import pandas as pd
---> 11 from cohorts.functions import *
12 get_ipython().magic(u'matplotlib inline')
/mnt/ssd0/env/local/lib/python2.7/site-packages/cohorts/__init__.py in <module>()
13 # limitations under the License.
14
---> 15 from .load import *
16
17 from ._version import get_versions
/mnt/ssd0/env/local/lib/python2.7/site-packages/cohorts/load.py in <module>()
35 from topiary import predict_epitopes_from_variants, epitopes_to_dataframe
36 from topiary.sequence_helpers import contains_mutant_residues
---> 37 from isovar.protein_sequence import variants_to_protein_sequences_dataframe
38 from pysam import AlignmentFile
39
ImportError: No module named protein_sequence
Here is the output when installing cohorts
from git (note that isovar
is not mentioned):
$ pip install git+git://github.com/hammerlab/cohorts --upgrade
Collecting git+git://github.com/hammerlab/cohorts
Cloning git://github.com/hammerlab/cohorts to /tmp/pip-lrdXz6-build
Requirement already up-to-date: pandas>=0.15 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: seaborn>=0.7.0 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: scipy>=0.17.0 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: topiary>=0.0.20 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: mhctools>=0.2.3 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: varcode>=0.4.12 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: pyensembl>=0.8.12 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: six>=1.10.0 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: lifelines>=0.9.1.0 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: scikit-learn>=0.17.1 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: vcf-annotate-polyphen>=0.1.2 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: patsy>=0.4.1 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: pytz>=2011k in /mnt/ssd0/env/lib/python2.7/site-packages (from pandas>=0.15->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: numpy>=1.7.0 in /mnt/ssd0/env/lib/python2.7/site-packages (from pandas>=0.15->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: python-dateutil in /mnt/ssd0/env/lib/python2.7/site-packages (from pandas>=0.15->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: matplotlib in /mnt/ssd0/env/lib/python2.7/site-packages (from seaborn>=0.7.0->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: gtfparse>=0.0.4 in /mnt/ssd0/env/lib/python2.7/site-packages (from topiary>=0.0.20->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: nose>=1.3.6 in /mnt/ssd0/env/lib/python2.7/site-packages (from topiary>=0.0.20->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: mhcnames in /mnt/ssd0/env/lib/python2.7/site-packages (from topiary>=0.0.20->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: memoized-property>=1.0.2 in /mnt/ssd0/env/lib/python2.7/site-packages (from varcode>=0.4.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: biopython>=1.64 in /mnt/ssd0/env/lib/python2.7/site-packages (from varcode>=0.4.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: pyvcf>=0.6.7 in /mnt/ssd0/env/lib/python2.7/site-packages (from varcode>=0.4.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: datacache>=0.4.16 in /mnt/ssd0/env/lib/python2.7/site-packages (from pyensembl>=0.8.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: typechecks>=0.0.2 in /mnt/ssd0/env/lib/python2.7/site-packages (from pyensembl>=0.8.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: sqlalchemy in /mnt/ssd0/env/lib/python2.7/site-packages (from vcf-annotate-polyphen>=0.1.2->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: cycler in /mnt/ssd0/env/lib/python2.7/site-packages (from matplotlib->seaborn>=0.7.0->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: pyparsing!=2.0.0,!=2.0.4,>=1.5.6 in /mnt/ssd0/env/lib/python2.7/site-packages (from matplotlib->seaborn>=0.7.0->cohorts==0.1.1+103.g71e0082)
Collecting setuptools (from pyvcf>=0.6.7->varcode>=0.4.12->cohorts==0.1.1+103.g71e0082)
Downloading setuptools-24.1.0-py2.py3-none-any.whl (441kB)
100% |████████████████████████████████| 450kB 2.8MB/s
Requirement already up-to-date: progressbar33>=2.4 in /mnt/ssd0/env/lib/python2.7/site-packages (from datacache>=0.4.16->pyensembl>=0.8.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: requests>=2.5.1 in /mnt/ssd0/env/lib/python2.7/site-packages (from datacache>=0.4.16->pyensembl>=0.8.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: appdirs>=1.4.0 in /mnt/ssd0/env/lib/python2.7/site-packages (from datacache>=0.4.16->pyensembl>=0.8.12->cohorts==0.1.1+103.g71e0082)
Installing collected packages: cohorts, setuptools
Found existing installation: cohorts 0.1.1+103.g71e0082
Uninstalling cohorts-0.1.1+103.g71e0082:
Successfully uninstalled cohorts-0.1.1+103.g71e0082
Running setup.py install for cohorts ... done
Found existing installation: setuptools 24.0.3
Uninstalling setuptools-24.0.3:
Successfully uninstalled setuptools-24.0.3
Successfully installed cohorts-0.1.1+103.g71e0082 setuptools-24.1.0
from cohorts.
Related Issues (20)
- Support easy Cohort creation
- Annoying conflicts between patient-attributes & variables in `additional_data`
- Invalid RGBA argument error using `plot_survival` HOT 3
- Make cohorts more workflow-engine and cloud storage friendly
- Help with creating a cohort HOT 14
- Error using median_vaf_purity on a combined-polyphen-snpeff.vcf HOT 6
- StopIteration error results in cached empty VariantCollection
- ImportError: cannot import name 'AlleleParseError' HOT 2
- Update README & documentation to match current usage
- Explain why predicted neoantigens are NaN when HLA types missing
- Set mhcflurry as the default MHC binding predictor
- plot_survival for the whole cohort, not "on" something
- logging does not respond to user-configured level
- KeyError when predicting neoantigens
- Capture logger output when caching a result
- Test new parameters - fail_on_missing_bams, etc
- Refactor `_load_single_patient_variants` function
- Don't cache after only top-priority effects; post-filter instead HOT 3
- all_effects caches, but does not return, all effects HOT 1
- ExonicSpliceSite with Subsitution/etc. alternate_effect is not included in filtering
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from cohorts.