Comments (10)
Looks like my first intuition was wrong. I missed a case in implementing support for GTFs with entries in the order that yours are... I'll see what I can do. Thanks for being a great beta tester!
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Thank @fairliereese for your quick response. I will re-add it and will proceed fresh.
Thanks again.
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I'm assuming this is with the data you've already shared with me? I'll try running it on my end.
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Yah I am having it in that dataset also.
Thanks
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It looks like this is a pandas version issue. What version of pandas are you running? You can find out by running the following in Python.
import pandas as pd
print(pd.__version__)
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Its 0.25.2
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@fairliereese on which version it's working? I can install that specific version.
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I am still trying to figure it out. I just got it to work on version 1.0.5 but I'm having trouble recreating the error that I got the first time around.
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Thanks @fairliereese
Bellow is the list version of pandas dependencies I am having. If it helps anyways
INSTALLED VERSIONS
------------------
commit : None
python : 3.7.0.final.0
python-bits : 64
OS : Linux
OS-release : 2.6.32-754.23.1.el6.x86_64
machine : x86_64
processor : x86_64
byteorder : little
LC_ALL : None
LANG : en_US.UTF-8
LOCALE : en_US.UTF-8
pandas : 0.25.2
numpy : 1.17.3
pytz : 2019.3
dateutil : 2.8.0
pip : 19.1.1
setuptools : 41.4.0
Cython : 0.29.7
pytest : None
hypothesis : None
sphinx : None
blosc : None
feather : None
xlsxwriter : None
lxml.etree : 4.3.3
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 2.10.3
IPython : 7.8.0
pandas_datareader: None
bs4 : None
bottleneck : None
fastparquet : None
gcsfs : None
lxml.etree : 4.3.3
matplotlib : 3.1.1
numexpr : None
odfpy : None
openpyxl : None
pandas_gbq : None
pyarrow : None
pytables : None
s3fs : None
scipy : 1.4.1
sqlalchemy : None
tables : None
xarray : None
xlrd : None
xlwt : None
xlsxwriter : None
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Okay, I think everything should be in working order for you now. I was able to run everything with your data!
Unfortunately after installing the new version you will have to re-add all your datasets to the SwanGraph. I hope this works!
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Related Issues (18)
- swanvis broken? HOT 3
- Intron retention and exon skipping analysis HOT 22
- Missing transcripts HOT 3
- AttributeError: 'SwanGraph' object has no attribute 'ass_transcriptome' HOT 2
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- plot a transcript with all transcripts as background HOT 8
- relation between splicing in/out sites and exons HOT 5
- Issues differential expression HOT 3
- Differential isoform usage multiple conditions HOT 1
- find_es_genes returns duplicated entries
- Example code problem HOT 1
- MemoryError: Unable to allocate 113. GiB for an array with shape (9992, 3033596) and data type float32 HOT 5
- cannot load swan into python using recommended installation method
- self.create_dfs_db(fname, annot, whitelist, 'hepg2_1') HOT 2
- ValueError HOT 10
- Missing case for plottedgraph init HOT 2
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