dputhier/pygtftk issues and pull requests

#186 - failed installation

Issue - State: closed - Opened by rongrongy 3 months ago - 2 comments

#185 - [Snyk] Security upgrade urllib3 from 2.0.7 to 2.2.2

Pull Request - State: open - Opened by dputhier 4 months ago

#184 - AttributeError: 'Series' object has no attribute 'append'

Issue - State: open - Opened by gyanmishra 6 months ago - 1 comment

#183 - Need a python 3.9 or 3.10

Issue - State: open - Opened by dputhier 6 months ago

#182 - [Snyk] Security upgrade fonttools from 4.38.0 to 4.43.0

Pull Request - State: open - Opened by dputhier 10 months ago

#180 - ERROR-get_tx_seq : No genes were found on chromosomes defined in fasta file.

Issue - State: open - Opened by yaskermezli over 1 year ago - 6 comments

#179 - Segmentation fault core dumped error when reading GTF in python script

Issue - State: closed - Opened by almart7 over 1 year ago - 2 comments

#178 - fixed dash server problem with adding name argument to dash instance

Pull Request - State: closed - Opened by Ouertani95 over 2 years ago

#177 - get_5p_3p_coordsusing the --more-names argument

Issue - State: closed - Opened by yaskermezli over 2 years ago - 3 comments

#176 - Pygtftk version is unsync in pip and bioconda

Issue - State: closed - Opened by dputhier over 2 years ago - 1 comment

#175 - Install error on ubuntu 20.04

Issue - State: closed - Opened by samanthaconte over 2 years ago - 2 comments

#174 - Due to issue with htslib force pysam to at least 0.17.0

Issue - State: closed - Opened by dputhier over 2 years ago - 1 comment

#173 - Develop an argument to add a column with a particular text (col_from_tab)

Issue - State: closed - Opened by dputhier over 2 years ago
Labels: enhancement

#172 - add output field separator to col_from_tab

Issue - State: closed - Opened by dputhier over 2 years ago
Labels: enhancement

#171 - gtftk get_tx_seq: issue with chromosome names

Issue - State: open - Opened by dputhier almost 3 years ago - 1 comment

#170 - Unable to change directory to 'release-106

Issue - State: closed - Opened by dputhier almost 3 years ago - 1 comment

#169 - Need to synchronize requirement.txt and meta.yaml

Issue - State: open - Opened by dputhier almost 3 years ago

#168 - Issue with build on bioconda docker image

Issue - State: closed - Opened by dputhier almost 3 years ago

#167 - Change python version prequirements in README

Issue - State: closed - Opened by dputhier almost 3 years ago

#166 - Error with pyparsing

Issue - State: closed - Opened by dputhier almost 3 years ago - 1 comment

#165 - Support for Python 3.9

Issue - State: closed - Opened by dputhier about 3 years ago - 1 comment

#164 - section "Writing your own commands" from doc is deprecated.

Issue - State: closed - Opened by dputhier about 3 years ago

#163 - segmentation fault on a SLURM cluster for 'gtftk short_long' command

Issue - State: closed - Opened by mickey-spongebob about 3 years ago - 6 comments

#162 - Bioconda build

Issue - State: closed - Opened by dputhier over 3 years ago - 6 comments

#161 - |-- 11:03-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times

Issue - State: open - Opened by dputhier over 3 years ago - 2 comments

#160 - Documentation failed due to ologram issue

Issue - State: closed - Opened by dputhier over 3 years ago - 14 comments

#159 - Found conflicts! Looking for incompatible packages. This can take several minutes. UnsatisfiableError:

Issue - State: closed - Opened by samanthaconte over 3 years ago - 4 comments

#158 - gtf.tail(): local variable 'gtf_sub' referenced before assignment

Issue - State: closed - Opened by dputhier over 3 years ago

#157 - OLOGRAM: exclusive combinations

Issue - State: closed - Opened by dputhier over 3 years ago - 3 comments
Labels: ologram

#156 - The default value of -j/--sort-features in OLOGRAM should be summed_bp_overlaps_true

Issue - State: closed - Opened by dputhier over 3 years ago - 1 comment
Labels: ologram

#155 - tp_vectorcall

Issue - State: closed - Opened by dputhier over 3 years ago - 1 comment

#154 - if ((1 == 0)) abort();

Issue - State: closed - Opened by dputhier over 3 years ago - 4 comments

#153 - ImportError: libhts.so.2

Issue - State: closed - Opened by yaskermezli over 3 years ago - 4 comments

#152 - TypeError: a bytes-like object is required, not 'tuple'

Issue - State: closed - Opened by dputhier over 3 years ago - 1 comment

#151 - dlopen: cannot load any more object with static TLS

Issue - State: closed - Opened by dputhier over 3 years ago - 6 comments

#150 - OLOGRAM: write the name of the query file somewhere in the he report.

Issue - State: closed - Opened by dputhier over 3 years ago - 3 comments

#149 - OLOGRAM: Add an argument to hide bars undefined pvalue

Issue - State: closed - Opened by dputhier over 3 years ago - 2 comments

#148 - some typo and remarks and ologram

Issue - State: closed - Opened by dputhier over 3 years ago - 2 comments

#147 - merge_attr

Issue - State: closed - Opened by dputhier over 3 years ago

#146 - --chom-file should support ensembl format

Issue - State: closed - Opened by dputhier over 3 years ago

#145 - UnsatisfiableError: The following specifications were found to be incompatible with each other:

Issue - State: closed - Opened by dputhier over 3 years ago - 4 comments

#144 - Pb when using chromosome without 'chr' prefix

Issue - State: closed - Opened by dputhier over 3 years ago - 3 comments

#143 - User should be warned not to install pygtftk under unsupported python version

Issue - State: closed - Opened by dputhier over 3 years ago

#142 - AttributeError: module 'yaml' has no attribute 'dump' installing pygtftk

Issue - State: closed - Opened by Norisad over 3 years ago - 4 comments

#141 - Tests on arguments not performed when using Python API

Issue - State: closed - Opened by dputhier almost 4 years ago - 3 comments

#140 - Conda installation not working

Issue - State: closed - Opened by amathelier about 4 years ago - 8 comments

#139 - Issue in nose test (./stats/intersect/modl/dict_learning.py)

Issue - State: closed - Opened by dputhier about 4 years ago - 29 comments

#138 - FAIL: Doctest: pygtftk.stats.intersect.modl.dict_learning.squish_matrix

Issue - State: closed - Opened by dputhier about 4 years ago - 4 comments