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sr320 / paper-pano-go

Draft manuscript describing Panopea gonad transcriptome
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CpG again!! #25

Closed lafarga13 closed 7 years ago

lafarga13 commented 8 years ago

@sr320

Hi Steven!!! Finally I am trying to reproduce what you did in the 05-Geoduck-CpG.ipynb and perl is running in the new computer using Anaconda.

but my jupiter does not recognize this command lines (from 84 step)

import pandas as pd %matplotlib inline import matplotlib.pyplot as plt

What Should I do to run does commands?

this is the message I got…

AttributeError Traceback (most recent call last)

in () ----> 1 import pandas as pd /Users/miguelangeldelrio/anaconda/lib/python3.5/site-packages/pandas/**init**.py in () 42 import pandas.core.config_init 43 ---> 44 from pandas.core.api import * 45 from pandas.sparse.api import * 46 from pandas.stats.api import * /Users/miguelangeldelrio/anaconda/lib/python3.5/site-packages/pandas/core/api.py in () 7 from pandas.core.common import isnull, notnull 8 from pandas.core.categorical import Categorical ----> 9 from pandas.core.groupby import Grouper 10 from pandas.core.format import set_eng_float_format 11 from pandas.core.index import Index, CategoricalIndex, Int64Index, Float64Index, MultiIndex /Users/miguelangeldelrio/anaconda/lib/python3.5/site-packages/pandas/core/groupby.py in () 15 from pandas.core.base import PandasObject 16 from pandas.core.categorical import Categorical ---> 17 from pandas.core.frame import DataFrame 18 from pandas.core.generic import NDFrame 19 from pandas.core.index import Index, MultiIndex, CategoricalIndex, _ensure_index /Users/miguelangeldelrio/anaconda/lib/python3.5/site-packages/pandas/core/frame.py in () 39 create_block_manager_from_arrays, 40 create_block_manager_from_blocks) ---> 41 from pandas.core.series import Series 42 from pandas.core.categorical import Categorical 43 import pandas.computation.expressions as expressions /Users/miguelangeldelrio/anaconda/lib/python3.5/site-packages/pandas/core/series.py in () 33 from pandas.core.internals import SingleBlockManager 34 from pandas.core.categorical import Categorical, CategoricalAccessor ---> 35 import pandas.core.strings as strings 36 from pandas.tseries.common import (maybe_to_datetimelike, 37 CombinedDatetimelikeProperties) AttributeError: module 'pandas' has no attribute 'core'
mdelrio1 commented 8 years ago

@lafarga13 @sr320 Faby close all notebooks, stop the terminal (Ctrl-C), close the terminal session and then anaconda. open a new terminal window and run a) conda install pandas b) conda install -c https://conda.anaconda.org/anaconda biopython this last one installs biopython. After installation run anaconda and then the notebook, if this does not work, we'll see it tomorrow.

lafarga13 commented 8 years ago

no quizo correrlo al final :-1:

lafarga13 commented 8 years ago

so, how to install pandas ???

lafarga13 commented 8 years ago

Logre usar pandas pero en Wakari!!!! no pude desde anaconda

mdelrio1 commented 8 years ago

@sr320 @lafarga13 Steven, sorry I couldn't find the file 'analyses/Geoduck-transcriptome-v2_CpG-GOSlim.tab' from the 05-Geoduck-CpG.ipynb. I think I have mange to reproduce the CpG data using biopython and I would like to compare the results. I uploaded a notebook with the information in my repository https://github.com/mdelrio1/mdelrio-panopea1/blob/master/CpG-Geo.ipynb It may need some clean up, but I think it gives the results we need, I'll check tomorrow with Fabiola her problem with pandas Thank you Miguel

lafarga13 commented 8 years ago

@sr320 I already upload the files Geoduck-transcriptome-v2_CpG-GOSlim.tab (all sequences) Geoduck-transcriptome-v3_CpG-GOSlim.tab (without bacteria)

I didn´t see to much changes..