dputhier/pygtftk

Issues

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

  #180 opened 2 years ago by yaskermezli
  6

• failed installation

  #186 opened 4 months ago by rongrongy
  2

• AttributeError: 'Series' object has no attribute 'append'

  #184 opened 7 months ago by gyanmishra
  1

• Need a python 3.9 or 3.10

  #183 opened 8 months ago by dputhier
  0

• Segmentation fault core dumped error when reading GTF in python script

  #179 opened 2 years ago by almart7
  2

• get_5p_3p_coordsusing the --more-names argument

  #177 opened 3 years ago by yaskermezli
  3

• ImportError: libhts.so.2

  #153 opened 4 years ago by yaskermezli
  4

• Issue with build on bioconda docker image

  #168 opened 3 years ago by dputhier
  0

• Install error on ubuntu 20.04

  #175 opened 3 years ago by samanthaconte
  2

• Pygtftk version is unsync in pip and bioconda

  #176 opened 3 years ago by dputhier
  1

• warning upon installation

  #135 opened 3 years ago by dputhier
  2

• Support for Python 3.9

  #165 opened 3 years ago by dputhier
  1

• add output field separator to col_from_tab

  #172 opened 3 years ago by dputhier
  0

• Develop an argument to add a column with a particular text (col_from_tab)

  #173 opened 3 years ago by dputhier
  0

• Unable to change directory to 'release-106

  #170 opened 3 years ago by dputhier
  1

• Due to issue with htslib force pysam to at least 0.17.0

  #174 opened 3 years ago by dputhier
  1

• gtftk get_tx_seq: issue with chromosome names

  #171 opened 3 years ago by dputhier
  1

• Need to synchronize requirement.txt and meta.yaml

  #169 opened 3 years ago by dputhier
  0

• Error with pyparsing

  #166 opened 3 years ago by dputhier
  1

• section "Writing your own commands" from doc is deprecated.

  #164 opened 3 years ago by dputhier
  0

• Change python version prequirements in README

  #167 opened 3 years ago by dputhier
  0

• segmentation fault on a SLURM cluster for 'gtftk short_long' command

  #163 opened 3 years ago by mickey-spongebob
  6

• Found conflicts! Looking for incompatible packages. This can take several minutes. UnsatisfiableError:

  #159 opened 3 years ago by samanthaconte
  4

• Bioconda build

  #162 opened 3 years ago by dputhier
  6

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

  #161 opened 3 years ago by dputhier
  2

• Documentation failed due to ologram issue

  #160 opened 3 years ago by dputhier
  14

• AttributeError: module 'yaml' has no attribute 'dump' installing pygtftk

  #142 opened 3 years ago by Norisad
  4

• if ((1 == 0)) abort();

  #154 opened 3 years ago by dputhier
  4

• tp_vectorcall

  #155 opened 3 years ago by dputhier
  1

• User should be warned not to install pygtftk under unsupported python version

  #143 opened 3 years ago by dputhier
  0

• UnsatisfiableError: The following specifications were found to be incompatible with each other:

  #145 opened 3 years ago by dputhier
  4

• gtf.tail(): local variable 'gtf_sub' referenced before assignment

  #158 opened 3 years ago by dputhier
  0

• OLOGRAM: write the name of the query file somewhere in the he report.

  #150 opened 4 years ago by dputhier
  3

• OLOGRAM: exclusive combinations

  #157 opened 4 years ago by dputhier
  3

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

  #156 opened 4 years ago by dputhier
  1

• OLOGRAM: Add an argument to hide bars undefined pvalue

  #149 opened 4 years ago by dputhier
  2

• dlopen: cannot load any more object with static TLS

  #151 opened 4 years ago by dputhier
  6

• some typo and remarks and ologram

  #148 opened 4 years ago by dputhier
  2

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

  #152 opened 4 years ago by dputhier
  1

• Pb when using chromosome without 'chr' prefix

  #144 opened 4 years ago by dputhier
  3

• merge_attr

  #147 opened 4 years ago by dputhier
  0

• --chom-file should support ensembl format

  #146 opened 4 years ago by dputhier
  0

• Tests on arguments not performed when using Python API

  #141 opened 4 years ago by dputhier
  3

• Issue in nose test (./stats/intersect/modl/dict_learning.py)

  #139 opened 4 years ago by dputhier
  29

• Conda installation not working

  #140 opened 4 years ago by amathelier
  8

• FAIL: Doctest: pygtftk.stats.intersect.modl.dict_learning.squish_matrix

  #138 opened 4 years ago by dputhier
  4

• Remaining warnings in doc

  #133 opened 4 years ago by dputhier
  2

• profile: warning in doc

  #134 opened 4 years ago by dputhier
  0

• profile: etst fail with plotnine 0.7.1

  #136 opened 4 years ago by dputhier
  2

• Bio.Alphabet has been removed from Biopython.

  #137 opened 4 years ago by dputhier
  0