Closed seboles closed 4 years ago
Hi @seboles, you likely need to install pandas into your environment. If you have a dammit environment (e.g. dammit-env
from before), you should conda activate dammit-env
to enter into that conda environment, where pandas should already be available. Alternatively, you can use conda install pandas
to install pandas into your current environment.
Hi Tessa,
I'll give that a shot and let you know how it goes. As always, thank you for your help.
Sara
On Wed, Jul 10, 2019 at 11:56 AM Tessa Pierce notifications@github.com wrote:
Hi @seboles https://github.com/seboles, you likely need to install pandas into your environment. If you have a dammit environment (e.g. dammit-env from before), you should conda activate dammit-env to enter into that conda environment, where pandas should already be available. Alternatively, you can use conda install pandas to install pandas into your current environment.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dib-lab/dammit/issues/149?email_source=notifications&email_token=AEHDXAFZOMMFOOITQFHUTXDP6YWGZA5CNFSM4H7IDL4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZUNDJA#issuecomment-510185892, or mute the thread https://github.com/notifications/unsubscribe-auth/AEHDXAG4FGJW5FBGCREYNGDP6YWGZANCNFSM4H7IDL4A .
-- Sara E. Boles, MS PhD Candidate | Whitehead Lab Pharmacology and Toxicology Graduate Group Department of Environmental Toxicology University of California, Davis, CA 95616 http://whiteheadresearch.wordpress.com/ https://sites.google.com/a/ucdavis.edu/sara-e-boles/
That worked. Thanks a bunch!
On Mon, Jul 15, 2019 at 12:50 PM Sara Boles seboles@ucdavis.edu wrote:
Hi Tessa,
I'll give that a shot and let you know how it goes. As always, thank you for your help.
Sara
On Wed, Jul 10, 2019 at 11:56 AM Tessa Pierce notifications@github.com wrote:
Hi @seboles https://github.com/seboles, you likely need to install pandas into your environment. If you have a dammit environment (e.g. dammit-env from before), you should conda activate dammit-env to enter into that conda environment, where pandas should already be available. Alternatively, you can use conda install pandas to install pandas into your current environment.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dib-lab/dammit/issues/149?email_source=notifications&email_token=AEHDXAFZOMMFOOITQFHUTXDP6YWGZA5CNFSM4H7IDL4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZUNDJA#issuecomment-510185892, or mute the thread https://github.com/notifications/unsubscribe-auth/AEHDXAG4FGJW5FBGCREYNGDP6YWGZANCNFSM4H7IDL4A .
-- Sara E. Boles, MS PhD Candidate | Whitehead Lab Pharmacology and Toxicology Graduate Group Department of Environmental Toxicology University of California, Davis, CA 95616 http://whiteheadresearch.wordpress.com/ https://sites.google.com/a/ucdavis.edu/sara-e-boles/
-- Sara E. Boles, MS PhD Candidate | Whitehead Lab Pharmacology and Toxicology Graduate Group Department of Environmental Toxicology University of California, Davis, CA 95616 http://whiteheadresearch.wordpress.com/ https://sites.google.com/a/ucdavis.edu/sara-e-boles/
Hello!
I have hit another bump in the dammit pipeline and am having an issue parsing the dammit output. Thank you for any suggestions.
Sara
Here is my code:
cd /home/seboles/annotation/developmental_annotation
source ~/.bashrc
python3
import pandas as pd
from dammit.fileio.gff3 import GFF3Parser
gff_file = "Trinitydevelopment.fasta.dammit.gff3"
annotations = GFF3Parser(filename=gff_file).read()
names = annotations.sort_values(by=['seqid', 'score'], ascending=True).query('score < 1e-05').drop_duplicates(subset='seqid')[['seqid', 'Name']]
new_file = names.dropna(axis=0,how='all')
new_file.head()
new_file.to_csv("abalone_development_gene_name_id.csv")
exit()
Here is the error message I receive.
Python 3.6.4 |Anaconda, Inc.| (default, Jan 16 2018, 18:10:19) [GCC 7.2.0] on linux Type "help", "copyright", "credits" or "license" for more information.