How Numpy was installed:
git clone [email protected]:numpy/numpy
git clone [email protected]:scipy/scipy
cd numpy
cp ~/.numpy.site.cfg .
emacs numpy/distutils/intelccompiler.py
# In "IntelEM64TCCompiler", changed:
Olga Botvinnik olgabot
olgabot
/ (home-yeo) ssh -4 -vvv tscc-login1 7710:localhost::7710
Last active
August 29, 2015 13:58
Debugging ssh tunneling into TSCC
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| debug3: load_hostkeys: loading entries for host "tscc-login1" from file "/home/obotvinnik/.ssh/known_hosts" | |
| debug3: load_hostkeys: loaded 0 keys | |
| debug3: load_hostkeys: loading entries for host "tscc-login1" from file "/etc/ssh/ssh_known_hosts" | |
| debug3: load_hostkeys: found key type DSA in file /etc/ssh/ssh_known_hosts:341 | |
| debug3: load_hostkeys: found key type RSA in file /etc/ssh/ssh_known_hosts:342 | |
| debug3: load_hostkeys: loaded 2 keys | |
| debug3: load_hostkeys: loading entries for host "10.1.255.90" from file "/home/obotvinnik/.ssh/known_hosts" | |
| debug3: load_hostkeys: loaded 0 keys | |
| debug3: load_hostkeys: loading entries for host "10.1.255.90" from file "/etc/ssh/ssh_known_hosts" | |
| debug3: load_hostkeys: found key type DSA in file /etc/ssh/ssh_known_hosts:341 |
olgabot
/ matplotlib_axes_set_ticks_position_ticklabels_disappear.ipynb
Last active
August 29, 2015 14:00
matplotlib ticklabels text disappears when set to non-default position
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olgabot
/ pandas_groupby_operate_on_specific_columns.py
Last active
August 29, 2015 14:00
pandas groupby operate on specific columns and sub-columns
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| json = '{"chrom":{"4010":"chr2","4011":"chr2","4012":"chr2","4013":"chr2","4014":"chr2","4015":"chr2","4016":"chr2","4017":"chr2","4018":"chr2","4019":"chr2","4020":"chr2","4021":"chr2","4022":"chr2","4023":"chr2","4024":"chr2","4025":"chr2"},"first_bp_intron":{"4010":50149390,"4011":50170930,"4012":50280729,"4013":50318633,"4014":50464109,"4015":50692700,"4016":50693626,"4017":50699610,"4018":50723234,"4019":50724853,"4020":50733756,"4021":50755790,"4022":50758569,"4023":50765775,"4024":51012497,"4025":51015345},"last_bp_intron":{"4010":50170841,"4011":50280408,"4012":50318460,"4013":50463926,"4014":50692579,"4015":50693598,"4016":50699435,"4017":50723042,"4018":50724470,"4019":50733632,"4020":50755762,"4021":50758364,"4022":50765390,"4023":50779724,"4024":51017681,"4025":51017681},"unique_junction_reads":{"4010":1,"4011":3,"4012":6,"4013":6,"4014":15,"4015":8,"4016":8,"4017":5,"4018":40,"4019":86,"4020":85,"4021":64,"4022":81,"4023":53,"4024":12,"4025":9}}' | |
| sj = pd.read_json(json) | |
| five_prime_reads = sj. |
olgabot
/ pandas_make_new_rows_from_other_cols.py
Last active
August 29, 2015 14:00
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| import pandas as pd | |
| json = '{"chrom":{"18716":"chrM","28459":"chrM","41509":"chrM","22813":"chrM"},"first_bp_intron":{"18716":728,"28459":728,"41509":728,"22813":728},"last_bp_intron":{"18716":5369,"28459":5295,"41509":5295,"22813":5295},"strand":{"18716":2,"28459":2,"41509":2,"22813":2},"intron_motif":{"18716":"CT\\/AC","28459":"CT\\/GC","41509":"CT\\/GC","22813":"CT\\/GC"},"annotated":{"18716":false,"28459":false,"41509":false,"22813":false},"unique_junction_reads":{"18716":99,"28459":1407,"41509":1,"22813":139},"multimap_junction_reads":{"18716":0,"28459":0,"41509":0,"22813":0},"max_overhang":{"18716":49,"28459":50,"41509":34,"22813":45},"sample_id":{"18716":"M4_9","28459":"M6_4","41509":"M6_6","22813":"M1_08"},"multimap_junction_reads_filtered":{"18716":0,"28459":0,"41509":0,"22813":0},"unique_junction_reads_filtered":{"18716":99,"28459":1407,"41509":0,"22813":139},"total_filtered_reads":{"18716":99,"28459":1407,"41509":0,"22813":139},"psi5":{"18716":1.0,"28459":1.0,"41509":null,"22813":1.0},"psi3":{"18 |
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| [obotvinnik@tscc-login2 ~]$ conda -h | |
| Traceback (most recent call last): | |
| File "/projects/ps-yeolab/software/anaconda/bin/conda", line 3, in <module> | |
| from conda.cli import main | |
| File "/projects/ps-yeolab/software/anaconda/lib/python2.7/site-packages/conda/cli/__init__.py", line 8, in <module> | |
| from conda.cli.main import main | |
| File "/projects/ps-yeolab/software/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 47, in <module> | |
| from conda.cli import main_create | |
| File "/projects/ps-yeolab/software/anaconda/lib/python2.7/site-packages/conda/cli/main_create.py", line 11, in <module> | |
| from conda.cli import common, install |
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| (olga)[obotvinnik@tscc-login2 flotilla]$ conda info -a | |
| Current conda install: | |
| platform : linux-64 | |
| conda version : 3.5.5 | |
| python version : 2.7.7.final.0 | |
| root environment : /projects/ps-yeolab/software/anaconda (writable) | |
| default environment : /projects/ps-yeolab/software/anaconda/envs/olga | |
| envs directories : /projects/ps-yeolab/software/anaconda/envs | |
| package cache : /projects/ps-yeolab/software/anaconda/pkgs |
olgabot
/ test_predict.py
Created
June 25, 2014 20:28
How to check for raising an error within a test class using pytest?
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| import numpy as np | |
| import numpy.testing as npt | |
| import pandas as pd | |
| import pandas.util.testing as pdt | |
| import pytest | |
| from sklearn.ensemble import ExtraTreesRegressor, ExtraTreesClassifier | |
| from sklearn.preprocessing import LabelEncoder | |
| class TestPredictorBase: |
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| def binify(df, bins): | |
| """Makes a histogram of each row the provided binsize | |
| Parameters | |
| ---------- | |
| data : pandas.DataFrame | |
| A samples x features dataframe. Each feature will be binned into the | |
| provided bins | |
| bins : iterable | |
| Bins you would like to use for this data. Must include the final bin |
olgabot
/ flotilla_neural_diff_modalities.ipynb
Created
July 5, 2014 20:15
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