dputhier pygtftk issues

dputhier / pygtftk

A python package and a set of shell commands to handle GTF files

GNU General Public License v3.0

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issues

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For test reproducibility chrom_info_as_dict should use an OrderedDict instead of a defaultDict

#37 dputhier closed 5 years ago
1
ArgFormatter.bed6

#36 qferre closed 5 years ago
1
Some temporary files are left

#35 dputhier closed 5 years ago
1
Some functions use mutable arguments as default arg

#34 dputhier closed 5 years ago
1
select_by_key should throw an error when no key/val is available.

#33 dputhier closed 5 years ago
0
Add a command-wise argument to convert (chr)MT into (chr)M

#32 dputhier opened 5 years ago
0
force-tx-class is not supported in profile

#31 dputhier closed 5 years ago
1
get_tx_seq sequence truncated.

#30 dputhier closed 5 years ago
1
get_tx_seq: should accept genome in gz format without complaining.

#29 dputhier closed 5 years ago
1
closest_gn_to_feat output format

#28 dputhier closed 5 years ago
1
Closest_gn_to_feat

#27 dputhier closed 5 years ago
1
Get the closest gene regarding a set of peaks.

#26 dputhier closed 5 years ago
0
Conda dist of pygtftk not available under OSX

#25 dputhier closed 5 years ago
1
.gtftk versioning

#24 dputhier closed 6 years ago
3
Loosen dep requirements

#23 dputhier closed 6 years ago
3
Example file

#22 dputhier closed 6 years ago
5
Hardcoded gcc at some point in setup.py?

#21 guillaumecharbonnier closed 6 years ago
8
Check whether -C is supported with 'retrieve'

#20 dputhier closed 6 years ago
1
Doc: The gtftk.bam.bam_coverage_matrix module

#19 dputhier closed 6 years ago
1
issue with select_by_regexp

#18 dputhier closed 6 years ago
1
Distutils package at installation - 'ftputils'

#17 qferre closed 6 years ago
1
Setup.py could contain an extra_require slot in setup()

#16 dputhier closed 5 years ago
1
ERROR-mk_matrix with conda packaged version of release 0.9.1

#15 guillaumecharbonnier closed 6 years ago
3
Bad extension check for outfile in gtftk coverage

#14 guillaumecharbonnier closed 6 years ago
1
Not meaningful

#13 dputhier closed 6 years ago
0
peak_anno: idea for new argument "-rpm"

#12 dputhier closed 5 years ago
1
divergent / convergent list of transcript

#11 dputhier opened 6 years ago
1
Completion not working under zsh

#10 dputhier closed 6 years ago
1
Improving the detection/annotation of alternative splicing events

#9 dputhier opened 6 years ago
0
Adding test to check wether bigwigs contain the expected chrs

#8 dputhier closed 6 years ago
0
Peak_anno new feature idea: --peak-file taking list instead of only one file

#7 dputhier closed 5 years ago
1
libgtftk.so compilation

#6 dputhier closed 6 years ago
1
Select most common tss among transcript

#5 dputhier opened 6 years ago
0
Blast output to GTF

#4 dputhier opened 6 years ago
1
compatible python3

#3 dputhier closed 6 years ago
3
split command

#2 dputhier opened 6 years ago
0
Library is not dynamic

#1 fafa13 closed 6 years ago
2