diff --git a/changelog.md b/changelog.md index 4af8bed..1b76b1f 100644 --- a/changelog.md +++ b/changelog.md @@ -1,12 +1,33 @@ # Changelog +## v1.5.1 + +### Bug Fixes + +* Fix "Index.ravel() returning a np.ndarray is deprecated" in pandas. + +* Fix pillow requirements (8.4.0). + +* Add requirement for libjpeg-devel installation in build_wheels.sh (pillow requirement). + +* Force --no-cache when building docker image for manylinux package. + +### API/CLI Changes + + +### Code changes + + + +### New Features + + ## v1.5.0 ### Bug Fixes -* ### API/CLI Changes @@ -20,9 +41,6 @@ ### New Features -# Changelog - - ## v1.4.0 ### Bug Fixes diff --git a/docs/_images/example_01.png b/docs/_images/example_01.png index cb7519c..0458c7a 100644 Binary files a/docs/_images/example_01.png and b/docs/_images/example_01.png differ diff --git a/docs/_images/example_02.png b/docs/_images/example_02.png index 6d0d8a9..749e119 100644 Binary files a/docs/_images/example_02.png and b/docs/_images/example_02.png differ diff --git a/docs/_images/example_05.png b/docs/_images/example_05.png index 10269af..7f11837 100644 Binary files a/docs/_images/example_05.png and b/docs/_images/example_05.png differ diff --git a/docs/_images/example_06.png b/docs/_images/example_06.png index 0c9f923..1f9aa2b 100644 Binary files a/docs/_images/example_06.png and b/docs/_images/example_06.png differ diff --git a/docs/_images/example_06b.png b/docs/_images/example_06b.png index de4f8ff..99fc949 100644 Binary files a/docs/_images/example_06b.png and b/docs/_images/example_06b.png differ diff --git a/docs/_images/example_07.png b/docs/_images/example_07.png index a3af2de..038bbdd 100644 Binary files a/docs/_images/example_07.png and b/docs/_images/example_07.png differ diff --git a/docs/_images/example_08.png b/docs/_images/example_08.png index e3c963c..41db7de 100644 Binary files a/docs/_images/example_08.png and b/docs/_images/example_08.png differ diff --git a/docs/_images/example_13.png b/docs/_images/example_13.png index f0ee047..b02d25b 100644 Binary files a/docs/_images/example_13.png and b/docs/_images/example_13.png differ diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index ed885a0..f05a0e8 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '1.5.0', + VERSION: '1.5.1', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/_static/example_01.png b/docs/_static/example_01.png index 0458c7a..cb7519c 100644 Binary files a/docs/_static/example_01.png and b/docs/_static/example_01.png differ diff --git a/docs/_static/example_02.png b/docs/_static/example_02.png index 749e119..6856474 100644 Binary files a/docs/_static/example_02.png and b/docs/_static/example_02.png differ diff --git a/docs/_static/example_05.png b/docs/_static/example_05.png index 7f11837..352b1ae 100644 Binary files a/docs/_static/example_05.png and b/docs/_static/example_05.png differ diff --git a/docs/_static/example_06.png b/docs/_static/example_06.png index 1f9aa2b..3029105 100644 Binary files a/docs/_static/example_06.png and b/docs/_static/example_06.png differ diff --git a/docs/_static/example_06b.png b/docs/_static/example_06b.png index 99fc949..dfeb7d7 100644 Binary files a/docs/_static/example_06b.png and b/docs/_static/example_06b.png differ diff --git a/docs/_static/example_07.png b/docs/_static/example_07.png index 038bbdd..479291b 100644 Binary files a/docs/_static/example_07.png and b/docs/_static/example_07.png differ diff --git a/docs/_static/example_08.png b/docs/_static/example_08.png index 41db7de..f8d3662 100644 Binary files a/docs/_static/example_08.png and b/docs/_static/example_08.png differ diff --git a/docs/_static/example_13.png b/docs/_static/example_13.png index b02d25b..f726499 100644 Binary files a/docs/_static/example_13.png and b/docs/_static/example_13.png differ diff --git a/docs/_static/example_pa_01.pdf b/docs/_static/example_pa_01.pdf index 0e55f58..389a774 100644 Binary files a/docs/_static/example_pa_01.pdf and b/docs/_static/example_pa_01.pdf differ diff --git a/docs/_static/example_pa_02.pdf b/docs/_static/example_pa_02.pdf index 7f71e21..fd35609 100644 Binary files a/docs/_static/example_pa_02.pdf and b/docs/_static/example_pa_02.pdf differ diff --git a/docs/_static/example_pa_03.pdf b/docs/_static/example_pa_03.pdf index f4957b5..18007ef 100644 Binary files a/docs/_static/example_pa_03.pdf and b/docs/_static/example_pa_03.pdf differ diff --git a/docs/_static/example_pa_04.pdf b/docs/_static/example_pa_04.pdf index f63d1d4..316774f 100644 Binary files a/docs/_static/example_pa_04.pdf and b/docs/_static/example_pa_04.pdf differ diff --git a/docs/_static/merge_ologram_stats_01.pdf b/docs/_static/merge_ologram_stats_01.pdf index 337e6c3..cd804a2 100644 Binary files a/docs/_static/merge_ologram_stats_01.pdf and b/docs/_static/merge_ologram_stats_01.pdf differ diff --git a/docs/_static/treeified.pdf b/docs/_static/treeified.pdf index 6298e0f..a7c7447 100644 Binary files a/docs/_static/treeified.pdf and b/docs/_static/treeified.pdf differ diff --git a/docs/about.html b/docs/about.html index 902c901..c40a170 100644 --- a/docs/about.html +++ b/docs/about.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); -
$ gtftk profile -D -i mini_real_promoter.zip -o profile_prom -pf png -if example_01.png
- |-- 10:19-WARNING-profile : --group-by not set. Choosing 'bwig'.
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 16:57-WARNING-profile : --group-by not set. Choosing 'bwig'.
Changing colors and applying color order can be done using the following syntax:
$ gtftk profile -D -i mini_real_promoter.zip -c 'red,blue,violet' -d H3K79me,H3K4me3,H3K36me3 -o profile_prom -pf png -if example_01b.png
- |-- 10:19-WARNING-profile : --group-by not set. Choosing 'bwig'.
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 16:57-WARNING-profile : --group-by not set. Choosing 'bwig'.
Transcript coverage is obtained using the mini_real_tx.zip matrix. This provides a simple overlayed profile of all epigenetic marks along the transcript body extended in 5’ and 3’ regions:
$ gtftk profile -D -i mini_real_tx.zip -o profile_tx -pf png -if example_02.png
- |-- 10:19-WARNING-profile : --group-by not set. Choosing 'bwig'.
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 16:57-WARNING-profile : --group-by not set. Choosing 'bwig'.
$ gtftk profile -D -i mini_real_promoter.zip -f tx_classes -g bwig -t tx_classes.txt -o profile_prom -pf png -if example_05.png -e -V 2 -fc 2
- |-- 10:19-DEBUG-profile : Using pandas version 1.2.5
- |-- 10:19-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
- |-- 10:19-DEBUG-profile : Using numpy version 1.21.0
- |-- 10:19-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
- |-- 10:19-DEBUG-profile : Using plotnine version 0.8.0
- |-- 10:19-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
- |-- 10:19-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk__1mc90ng
- |-- 10:19-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk__1mc90ng
- |-- 10:19-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk__1mc90ng/mini_real_promoter
- |-- 10:19-INFO-profile : Getting configuration info from input file.
- |-- 10:19-INFO-profile : Reading transcript file.
- |-- 10:19-INFO-profile : Deleting duplicates in transcript-file.
- |-- 10:19-INFO-profile : Checking how many transcripts where found in the transcript list.
- |-- 10:19-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
- |-- 10:19-DEBUG-profile : Color order : ['H3K79me', 'H3K4me3', 'H3K36me3']
- |-- 10:19-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
- |-- 10:19-INFO-profile : Searching coverage columns.
- |-- 10:19-INFO-profile : Melting.
- |-- 10:19-INFO-profile : Ceiling
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
- |-- 10:19-INFO-profile : Computing column ordering.
- |-- 10:19-INFO-profile : Preparing diagram
- |-- 10:19-INFO-profile : Theming and ordering. Please be patient...
- |-- 10:19-INFO-profile : Preparing x axis
- |-- 10:19-INFO-profile : facet_col 2
- |-- 10:19-INFO-profile : Page width set to 6
- |-- 10:19-INFO-profile : Page height set to 5.0
- |-- 10:19-INFO-profile : Saving diagram to file : example_05.png
- |-- 10:19-INFO-profile : Be patient. This may be long for large datasets.
- |-- 10:19-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk__1mc90ng
+ |-- 16:57-DEBUG-profile : Using pandas version 1.2.5
+ |-- 16:57-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
+ |-- 16:57-DEBUG-profile : Using numpy version 1.21.0
+ |-- 16:57-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
+ |-- 16:57-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 16:57-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
+ |-- 16:57-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_0sekrk57
+ |-- 16:57-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_0sekrk57
+ |-- 16:57-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_0sekrk57/mini_real_promoter
+ |-- 16:57-INFO-profile : Getting configuration info from input file.
+ |-- 16:57-INFO-profile : Reading transcript file.
+ |-- 16:57-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 16:57-INFO-profile : Checking how many transcripts where found in the transcript list.
+ |-- 16:57-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
+ |-- 16:57-DEBUG-profile : Color order : ['H3K36me3', 'H3K79me', 'H3K4me3']
+ |-- 16:57-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
+ |-- 16:57-INFO-profile : Searching coverage columns.
+ |-- 16:57-INFO-profile : Melting.
+ |-- 16:57-INFO-profile : Ceiling
+ |-- 16:58-INFO-profile : Computing column ordering.
+ |-- 16:58-INFO-profile : Preparing diagram
+ |-- 16:58-INFO-profile : Theming and ordering. Please be patient...
+ |-- 16:58-INFO-profile : Preparing x axis
+ |-- 16:58-INFO-profile : facet_col 2
+ |-- 16:58-INFO-profile : Page width set to 6
+ |-- 16:58-INFO-profile : Page height set to 5.0
+ |-- 16:58-INFO-profile : Saving diagram to file : example_05.png
+ |-- 16:58-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 16:58-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_0sekrk57
Alternatively, the groups can be set to chromosomes or transcript classes:
$ gtftk profile -D -i mini_real_promoter.zip -g tx_classes -f bwig -t tx_classes.txt -o profile_prom -pf png -if example_06.png -V 2 -nm ranging
- |-- 10:19-DEBUG-profile : Using pandas version 1.2.5
- |-- 10:19-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
- |-- 10:19-DEBUG-profile : Using numpy version 1.21.0
- |-- 10:19-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
- |-- 10:19-DEBUG-profile : Using plotnine version 0.8.0
- |-- 10:19-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
- |-- 10:19-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_zquijr44
- |-- 10:19-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_zquijr44
- |-- 10:19-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_zquijr44/mini_real_promoter
- |-- 10:19-INFO-profile : Getting configuration info from input file.
- |-- 10:19-INFO-profile : Reading transcript file.
- |-- 10:19-INFO-profile : Deleting duplicates in transcript-file.
- |-- 10:19-INFO-profile : Checking how many transcripts where found in the transcript list.
- |-- 10:19-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
- |-- 10:19-DEBUG-profile : Color order : ['antisense', 'lincRNA', 'protein_coding']
- |-- 10:19-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
- |-- 10:19-INFO-profile : Searching coverage columns.
- |-- 10:19-INFO-profile : Melting.
- |-- 10:19-INFO-profile : Ceiling
- |-- 10:19-INFO-profile : Normalizing (ranging)
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
- |-- 10:19-INFO-profile : Computing column ordering.
- |-- 10:19-INFO-profile : Preparing diagram
- |-- 10:19-INFO-profile : Theming and ordering. Please be patient...
- |-- 10:19-INFO-profile : Preparing x axis
- |-- 10:19-INFO-profile : facet_col 3
- |-- 10:19-INFO-profile : Page width set to 9
- |-- 10:19-INFO-profile : Page height set to 2.0
- |-- 10:19-INFO-profile : Saving diagram to file : example_06.png
- |-- 10:19-INFO-profile : Be patient. This may be long for large datasets.
- |-- 10:19-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_zquijr44
+ |-- 16:58-DEBUG-profile : Using pandas version 1.2.5
+ |-- 16:58-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
+ |-- 16:58-DEBUG-profile : Using numpy version 1.21.0
+ |-- 16:58-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
+ |-- 16:58-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 16:58-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
+ |-- 16:58-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_0ww9zwp6
+ |-- 16:58-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_0ww9zwp6
+ |-- 16:58-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_0ww9zwp6/mini_real_promoter
+ |-- 16:58-INFO-profile : Getting configuration info from input file.
+ |-- 16:58-INFO-profile : Reading transcript file.
+ |-- 16:58-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 16:58-INFO-profile : Checking how many transcripts where found in the transcript list.
+ |-- 16:58-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
+ |-- 16:58-DEBUG-profile : Color order : ['lincRNA', 'protein_coding', 'antisense']
+ |-- 16:58-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
+ |-- 16:58-INFO-profile : Searching coverage columns.
+ |-- 16:58-INFO-profile : Melting.
+ |-- 16:58-INFO-profile : Ceiling
+ |-- 16:58-INFO-profile : Normalizing (ranging)
+ |-- 16:58-INFO-profile : Computing column ordering.
+ |-- 16:58-INFO-profile : Preparing diagram
+ |-- 16:58-INFO-profile : Theming and ordering. Please be patient...
+ |-- 16:58-INFO-profile : Preparing x axis
+ |-- 16:58-INFO-profile : facet_col 3
+ |-- 16:58-INFO-profile : Page width set to 9
+ |-- 16:58-INFO-profile : Page height set to 2.0
+ |-- 16:58-INFO-profile : Saving diagram to file : example_06.png
+ |-- 16:58-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 16:58-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_0ww9zwp6
$ gtftk profile -D -i mini_real_promoter.zip -g chrom -f bwig -t tx_classes.txt -o profile_prom -pf png -if example_06b.png -V 2 -nm ranging
- |-- 10:19-DEBUG-profile : Using pandas version 1.2.5
- |-- 10:19-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
- |-- 10:19-DEBUG-profile : Using numpy version 1.21.0
- |-- 10:19-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
- |-- 10:19-DEBUG-profile : Using plotnine version 0.8.0
- |-- 10:19-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
- |-- 10:19-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk__k4ofbl4
- |-- 10:19-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk__k4ofbl4
- |-- 10:19-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk__k4ofbl4/mini_real_promoter
- |-- 10:19-INFO-profile : Getting configuration info from input file.
- |-- 10:19-DEBUG-profile : Color order : ['chr10', 'chr14', 'chr6', 'chr15', 'chr21', 'chr9', 'chr1', 'chr12', 'chr19', 'chr22', 'chrX', 'chr16', 'chr5', 'chr4', 'chr18', 'chr13', 'chr17', 'chr2', 'chr11', 'chr8', 'chr7', 'chr3', 'chr20']
- |-- 10:19-DEBUG-profile : Profile color : ['#000000', '#6c007c', '#850096', '#2500a5', '#0000ca', '#0041dd', '#0086dd', '#009fca', '#00aaa1', '#00a76f', '#009c00', '#00bb00', '#00da00', '#00f900', '#88ff00', '#dbf400', '#f7db00', '#ffb500', '#ff6100', '#f60000', '#da0000', '#cc1313', '#cccccc']
- |-- 10:19-INFO-profile : Searching coverage columns.
- |-- 10:19-INFO-profile : Melting.
- |-- 10:19-INFO-profile : Ceiling
- |-- 10:19-INFO-profile : Normalizing (ranging)
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
- |-- 10:20-INFO-profile : Computing column ordering.
- |-- 10:20-INFO-profile : Preparing diagram
- |-- 10:20-INFO-profile : Theming and ordering. Please be patient...
- |-- 10:20-INFO-profile : Preparing x axis
- |-- 10:20-INFO-profile : facet_col 3
- |-- 10:20-INFO-profile : Page width set to 9
- |-- 10:20-INFO-profile : Page height set to 2.0
- |-- 10:20-INFO-profile : Saving diagram to file : example_06b.png
- |-- 10:20-INFO-profile : Be patient. This may be long for large datasets.
- |-- 10:20-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk__k4ofbl4
+ |-- 16:58-DEBUG-profile : Using pandas version 1.2.5
+ |-- 16:58-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
+ |-- 16:58-DEBUG-profile : Using numpy version 1.21.0
+ |-- 16:58-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
+ |-- 16:58-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 16:58-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
+ |-- 16:58-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_pvokf3_t
+ |-- 16:58-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_pvokf3_t
+ |-- 16:58-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_pvokf3_t/mini_real_promoter
+ |-- 16:58-INFO-profile : Getting configuration info from input file.
+ |-- 16:58-DEBUG-profile : Color order : ['chr22', 'chr20', 'chr17', 'chr2', 'chr11', 'chr13', 'chr14', 'chr4', 'chr8', 'chr9', 'chr7', 'chr16', 'chr1', 'chr21', 'chr6', 'chr3', 'chr18', 'chr12', 'chr10', 'chr5', 'chrX', 'chr15', 'chr19']
+ |-- 16:58-DEBUG-profile : Profile color : ['#000000', '#6c007c', '#850096', '#2500a5', '#0000ca', '#0041dd', '#0086dd', '#009fca', '#00aaa1', '#00a76f', '#009c00', '#00bb00', '#00da00', '#00f900', '#88ff00', '#dbf400', '#f7db00', '#ffb500', '#ff6100', '#f60000', '#da0000', '#cc1313', '#cccccc']
+ |-- 16:58-INFO-profile : Searching coverage columns.
+ |-- 16:58-INFO-profile : Melting.
+ |-- 16:58-INFO-profile : Ceiling
+ |-- 16:58-INFO-profile : Normalizing (ranging)
+ |-- 16:58-INFO-profile : Computing column ordering.
+ |-- 16:58-INFO-profile : Preparing diagram
+ |-- 16:58-INFO-profile : Theming and ordering. Please be patient...
+ |-- 16:58-INFO-profile : Preparing x axis
+ |-- 16:58-INFO-profile : facet_col 3
+ |-- 16:58-INFO-profile : Page width set to 9
+ |-- 16:58-INFO-profile : Page height set to 2.0
+ |-- 16:58-INFO-profile : Saving diagram to file : example_06b.png
+ |-- 16:58-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 16:58-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_pvokf3_t
Note that facets may also be associated to epigenetic marks. In this case each the –group-by can be set to tx_classes or chrom.
$ gtftk profile -D -i mini_real_tx.zip -g tx_classes -t tx_classes.txt -f bwig -o profile_tx -pf png -if example_07.png -w -nm ranging
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:890: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
- |-- 10:20-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:890: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 16:58-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
$ gtftk profile -D -i mini_real_tx.zip -g chrom -f bwig -o profile_tx -pf png -if example_08.png -w -nm ranging
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:890: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
- |-- 10:20-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:890: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 16:58-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
$ gtftk join_attr -i simple.gtf -j simple.join_mat -k gene_id -m | gtftk discretize_key -k S1 -d S1_d -n 2 -l A,B | gtftk select_by_key -k feature -v gene
- |-- 10:21-INFO-discretize_key : Categories: ['A', 'B']
+ |-- 16:59-INFO-discretize_key : Categories: ['A', 'B']
chr1 gtftk gene 125 138 . + . gene_id "G0001";
chr1 gtftk gene 180 189 . + . gene_id "G0002";
chr1 gtftk gene 50 61 . - . gene_id "G0003"; S1 "0.2322"; S2 "0.4"; S1_d "A";
@@ -450,7 +450,7 @@ discretize_key$ gtftk join_attr -i mini_real.gtf.gz -H -j mini_real_counts_ENCFF630HEX.tsv -k gene_name -n exprs -t gene | gtftk discretize_key -k exprs -p -d exprs_class -n 10 -l A,B,C,D,E,F,G,H,I,J | gtftk tabulate -k exprs_class -Hn | sort | uniq -c
- |-- 10:21-INFO-discretize_key : Categories: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J']
+ |-- 16:59-INFO-discretize_key : Categories: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J']
96 A
83 B
89 C
@@ -567,7 +567,7 @@ Navigation
previous |
- gtftk 1.5.0 documentation »
+ gtftk 1.5.1 documentation »
Commands from section ‘Editing’
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diff --git a/docs/example_pa_01.pdf b/docs/example_pa_01.pdf
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diff --git a/docs/example_pa_02.pdf b/docs/example_pa_02.pdf
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diff --git a/docs/example_pa_03.pdf b/docs/example_pa_03.pdf
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diff --git a/docs/example_pa_04.pdf b/docs/example_pa_04.pdf
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diff --git a/docs/genindex.html b/docs/genindex.html
index a9c5e99..e5e8ccb 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -16,7 +16,7 @@
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
- Index — gtftk 1.5.0 documentation
+ Index — gtftk 1.5.1 documentation
@@ -36,7 +36,7 @@ Navigation
modules |
- gtftk 1.5.0 documentation »
+ gtftk 1.5.1 documentation »
Index
$ gtftk apropos -k promoter
- |-- 10:21-INFO-apropos : >> Keyword 'promoter' was found in the following command:
+ |-- 16:59-INFO-apropos : >> Keyword 'promoter' was found in the following command:
- divergent.
- - coverage.
- ologram.
+ - coverage.
Arguments:
@@ -724,7 +724,7 @@$ gtftk control_list -i mini_real_counts_ENCFF630HEX.tsv -r mini_real_control_1.txt -D -V 2 -s -l -p 1 -ju -if example_13.png -pf png
- |-- 10:21-INFO-control_list : 0 duplicate lines have been deleted in reference file.
- |-- 10:21-INFO-control_list : Found 50 genes of the reference in the provided signal file
- |-- 10:21-INFO-control_list : All reference genes were found.
- |-- 10:21-INFO-control_list : Searching for genes with matched signal.
- |-- 10:21-INFO-control_list : Preparing a dataframe for plotting.
- |-- 10:21-INFO-control_list : Saving diagram to file : example_13.png
- |-- 10:21-INFO-control_list : Be patient. This may be long for large datasets.
+ |-- 16:59-INFO-control_list : 0 duplicate lines have been deleted in reference file.
+ |-- 16:59-INFO-control_list : Found 50 genes of the reference in the provided signal file
+ |-- 16:59-INFO-control_list : All reference genes were found.
+ |-- 16:59-INFO-control_list : Searching for genes with matched signal.
+ |-- 17:00-INFO-control_list : Preparing a dataframe for plotting.
+ |-- 17:00-INFO-control_list : Saving diagram to file : example_13.png
+ |-- 17:00-INFO-control_list : Be patient. This may be long for large datasets.
$ gtftk ologram -i hg38_chr1.gtf.gz -p ENCFF112BHN_H3K4me3_chr1.bed -c hg38_chr1.genome -u 1500 -d 1500 -D -pf example_pa_01.pdf -k 8 -j summed_bp_overlaps_pvalue
- |-- 10:22-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
- |-- 10:22-WARNING-ologram : Computing log(p-val) for a Neg Binom with mean >= var ; var was set to mean+1 (start_codon)
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+ |-- 17:00-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+ |-- 17:00-WARNING-ologram : Computing log(p-val) for a Neg Binom with mean >= var ; var was set to mean+1 (start_codon)
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
$ gtftk select_by_key -i mini_real.gtf.gz -k gene_biotype -v protein_coding,lincRNA,antisense,processed_transcript | gtftk ologram -m gene_biotype -p ENCFF112BHN_H3K4me3_K562_sub.bed -c hg38 -D -n -pf example_pa_02.pdf -k 8 -j summed_bp_overlaps_pvalue
- |-- 10:23-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 17:01-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
$ gtftk join_attr -i mini_real.gtf.gz -H -j mini_real_counts_ENCFF630HEX.tsv -k gene_name -n exprs -t exon | gtftk discretize_key -k exprs -p -d exprs_class -n 6 -u | gtftk ologram -p ENCFF119BYM_H3K36me3_K562_sub.bed -c hg38 -D -n -m exprs_class -pf example_pa_03.pdf -k 8 -j summed_bp_overlaps_pvalue
- |-- 10:23-INFO-discretize_key : Categories: ['[0.0_183.0]', '(183.0_549.0]', '(549.0_1018.0]', '(1018.0_1631.0]', '(1631.0_3139.0]', '(3139.0_41703.0]']
- |-- 10:23-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.0-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+ |-- 17:01-INFO-discretize_key : Categories: ['[0.0_183.0]', '(183.0_549.0]', '(549.0_1018.0]', '(1018.0_1631.0]', '(1631.0_3139.0]', '(3139.0_41703.0]']
+ |-- 17:01-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.5.1-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
$ gtftk add_exon_nb -k exon_nbr -i mini_real.gtf.gz | gtftk discretize_key -p -d exon_nbr_cat -n 5 -k exon_nbr | gtftk ologram -p ENCFF112BHN_H3K4me3_K562_sub.bed -c hg38 -D -n -m exon_nbr_cat -pf example_pa_04.pdf -k 8 -j summed_bp_overlaps_pvalue
- |-- 10:24-INFO-discretize_key : Categories: ['[1.0_2.0]', '(2.0_4.0]', '(4.0_6.0]', '(6.0_12.0]', '(12.0_107.0]']
- |-- 10:24-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 17:02-INFO-discretize_key : Categories: ['[1.0_2.0]', '(2.0_4.0]', '(4.0_6.0]', '(6.0_12.0]', '(12.0_107.0]']
+ |-- 17:02-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
$ gtftk ologram -z -w -q -c simple_07.chromInfo -p simple_07_peaks.bed --more-bed simple_07_peaks.1.bed simple_07_peaks.2.bed --more-bed-multiple-overlap
- |-- 10:24-WARNING : Converting to bed6 format (simple_07_peaks.bed).
- |-- 10:24-WARNING : Converting to bed6 format (simple_07_peaks.1.bed).
- |-- 10:24-WARNING : Converting to bed6 format (simple_07_peaks.2.bed).
- |-- 10:24-WARNING-ologram : Using only 1 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
- |-- 10:24-WARNING-ologram : --more-bed-labels was not set, automatically defaulting to --more-bed file names.
- |-- 10:24-WARNING-ologram : [Query + simple_07_peaks_1 + ... ]: there may be a poor fit for this feature. Check fit quality in the results. This is likely due to there being too few regions.
- |-- 10:24-WARNING-ologram : [Query + simple_07_peaks_1 + simple_07_peaks_2 + ... ]: there may be a poor fit for this feature. Check fit quality in the results. This is likely due to there being too few regions.
- |-- 10:24-WARNING-ologram : Computing log(p-val) for a Neg Binom with mean >= var ; var was set to mean+1 ([Query + simple_07_peaks_1 + simple_07_peaks_2 + ... ])
+ |-- 17:02-WARNING : Converting to bed6 format (simple_07_peaks.bed).
+ |-- 17:02-WARNING : Converting to bed6 format (simple_07_peaks.1.bed).
+ |-- 17:02-WARNING : Converting to bed6 format (simple_07_peaks.2.bed).
+ |-- 17:03-WARNING-ologram : Using only 1 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 17:03-WARNING-ologram : --more-bed-labels was not set, automatically defaulting to --more-bed file names.
+ |-- 17:03-WARNING-ologram : [Query + simple_07_peaks_1 + ... ]: there may be a poor fit for this feature. Check fit quality in the results. This is likely due to there being too few regions.
+ |-- 17:03-WARNING-ologram : [Query + simple_07_peaks_1 + simple_07_peaks_2 + ... ]: there may be a poor fit for this feature. Check fit quality in the results. This is likely due to there being too few regions.
+ |-- 17:03-WARNING-ologram : Computing log(p-val) for a Neg Binom with mean >= var ; var was set to mean+1 ([Query + simple_07_peaks_1 + simple_07_peaks_2 + ... ])
Detailed example:
@@ -810,7 +810,7 @@$ gtftk random_list -n 3 -i simple.gtf | gtftk count
transcript 3
-exon 6
+exon 5
CDS 4