diff --git a/docs/_images/example_01.png b/docs/_images/example_01.png index cb7519c..1b4d486 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 6856474..bd5e012 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 352b1ae..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 3029105..59d173c 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 dfeb7d7..e9b98e0 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 479291b..7a41f5b 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 f8d3662..ca569cc 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 f726499..a0c48af 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 49e8e26..b859b47 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: '1.5.2', + VERSION: '1.5.3', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/_static/example_02.png b/docs/_static/example_02.png index bd5e012..0631793 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..472bc48 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 59d173c..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 e9b98e0..d3828de 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 7a41f5b..a3af2de 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 ca569cc..e117925 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 a0c48af..6ab41f5 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 641d4c5..0b2f1ff 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 7a1146e..30982b3 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 5e238b5..9dcac00 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 f515fe9..3e6fed2 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 72ae154..6fb2ee4 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 e6db75d..f5f6263 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 58e2a25..3cbff43 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
- |-- 14:39-WARNING-profile : --group-by not set. Choosing 'bwig'.
+ |-- 15:51-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
- |-- 14:39-WARNING-profile : --group-by not set. Choosing 'bwig'.
+ |-- 15:51-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
- |-- 14:39-WARNING-profile : --group-by not set. Choosing 'bwig'.
+ |-- 15:51-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
- |-- 14:39-DEBUG-profile : Using pandas version 1.2.5
- |-- 14:39-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
- |-- 14:39-DEBUG-profile : Using numpy version 1.21.0
- |-- 14:39-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
- |-- 14:39-DEBUG-profile : Using plotnine version 0.8.0
- |-- 14:39-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
- |-- 14:39-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_2df2e72e
- |-- 14:39-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_2df2e72e
- |-- 14:39-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_2df2e72e/mini_real_promoter
- |-- 14:39-INFO-profile : Getting configuration info from input file.
- |-- 14:39-INFO-profile : Reading transcript file.
- |-- 14:39-INFO-profile : Deleting duplicates in transcript-file.
- |-- 14:39-INFO-profile : Checking how many transcripts where found in the transcript list.
- |-- 14:39-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
- |-- 14:39-DEBUG-profile : Color order : ['H3K79me', 'H3K4me3', 'H3K36me3']
- |-- 14:39-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
- |-- 14:39-INFO-profile : Searching coverage columns.
- |-- 14:39-INFO-profile : Melting.
- |-- 14:39-INFO-profile : Ceiling
- |-- 14:39-INFO-profile : Computing column ordering.
- |-- 14:39-INFO-profile : Preparing diagram
- |-- 14:39-INFO-profile : Theming and ordering. Please be patient...
- |-- 14:39-INFO-profile : Preparing x axis
- |-- 14:39-INFO-profile : facet_col 2
- |-- 14:39-INFO-profile : Page width set to 6
- |-- 14:39-INFO-profile : Page height set to 5.0
- |-- 14:39-INFO-profile : Saving diagram to file : example_05.png
- |-- 14:39-INFO-profile : Be patient. This may be long for large datasets.
- |-- 14:39-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_2df2e72e
+ |-- 15:51-DEBUG-profile : Using pandas version 1.2.5
+ |-- 15:51-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
+ |-- 15:51-DEBUG-profile : Using numpy version 1.21.0
+ |-- 15:51-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
+ |-- 15:51-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 15:51-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
+ |-- 15:51-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_u9cnp8xc
+ |-- 15:51-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_u9cnp8xc
+ |-- 15:51-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_u9cnp8xc/mini_real_promoter
+ |-- 15:51-INFO-profile : Getting configuration info from input file.
+ |-- 15:51-INFO-profile : Reading transcript file.
+ |-- 15:51-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 15:51-INFO-profile : Checking how many transcripts where found in the transcript list.
+ |-- 15:51-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
+ |-- 15:51-DEBUG-profile : Color order : ['H3K4me3', 'H3K79me', 'H3K36me3']
+ |-- 15:51-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
+ |-- 15:51-INFO-profile : Searching coverage columns.
+ |-- 15:51-INFO-profile : Melting.
+ |-- 15:51-INFO-profile : Ceiling
+ |-- 15:51-INFO-profile : Computing column ordering.
+ |-- 15:51-INFO-profile : Preparing diagram
+ |-- 15:51-INFO-profile : Theming and ordering. Please be patient...
+ |-- 15:51-INFO-profile : Preparing x axis
+ |-- 15:51-INFO-profile : facet_col 2
+ |-- 15:51-INFO-profile : Page width set to 6
+ |-- 15:51-INFO-profile : Page height set to 5.0
+ |-- 15:51-INFO-profile : Saving diagram to file : example_05.png
+ |-- 15:51-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 15:51-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_u9cnp8xc
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
- |-- 14:39-DEBUG-profile : Using pandas version 1.2.5
- |-- 14:39-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
- |-- 14:39-DEBUG-profile : Using numpy version 1.21.0
- |-- 14:39-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
- |-- 14:39-DEBUG-profile : Using plotnine version 0.8.0
- |-- 14:39-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
- |-- 14:39-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_gwqhgdui
- |-- 14:39-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_gwqhgdui
- |-- 14:39-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_gwqhgdui/mini_real_promoter
- |-- 14:39-INFO-profile : Getting configuration info from input file.
- |-- 14:39-INFO-profile : Reading transcript file.
- |-- 14:39-INFO-profile : Deleting duplicates in transcript-file.
- |-- 14:39-INFO-profile : Checking how many transcripts where found in the transcript list.
- |-- 14:39-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
- |-- 14:39-DEBUG-profile : Color order : ['protein_coding', 'antisense', 'lincRNA']
- |-- 14:39-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
- |-- 14:39-INFO-profile : Searching coverage columns.
- |-- 14:39-INFO-profile : Melting.
- |-- 14:39-INFO-profile : Ceiling
- |-- 14:39-INFO-profile : Normalizing (ranging)
- |-- 14:39-INFO-profile : Computing column ordering.
- |-- 14:39-INFO-profile : Preparing diagram
- |-- 14:39-INFO-profile : Theming and ordering. Please be patient...
- |-- 14:39-INFO-profile : Preparing x axis
- |-- 14:39-INFO-profile : facet_col 3
- |-- 14:39-INFO-profile : Page width set to 9
- |-- 14:39-INFO-profile : Page height set to 2.0
- |-- 14:39-INFO-profile : Saving diagram to file : example_06.png
- |-- 14:39-INFO-profile : Be patient. This may be long for large datasets.
- |-- 14:39-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_gwqhgdui
+ |-- 15:51-DEBUG-profile : Using pandas version 1.2.5
+ |-- 15:51-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
+ |-- 15:51-DEBUG-profile : Using numpy version 1.21.0
+ |-- 15:51-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
+ |-- 15:51-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 15:51-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
+ |-- 15:51-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_mm4ih8uc
+ |-- 15:51-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_mm4ih8uc
+ |-- 15:51-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_mm4ih8uc/mini_real_promoter
+ |-- 15:51-INFO-profile : Getting configuration info from input file.
+ |-- 15:51-INFO-profile : Reading transcript file.
+ |-- 15:51-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 15:51-INFO-profile : Checking how many transcripts where found in the transcript list.
+ |-- 15:51-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
+ |-- 15:51-DEBUG-profile : Color order : ['lincRNA', 'protein_coding', 'antisense']
+ |-- 15:51-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
+ |-- 15:51-INFO-profile : Searching coverage columns.
+ |-- 15:51-INFO-profile : Melting.
+ |-- 15:51-INFO-profile : Ceiling
+ |-- 15:51-INFO-profile : Normalizing (ranging)
+ |-- 15:51-INFO-profile : Computing column ordering.
+ |-- 15:51-INFO-profile : Preparing diagram
+ |-- 15:51-INFO-profile : Theming and ordering. Please be patient...
+ |-- 15:51-INFO-profile : Preparing x axis
+ |-- 15:51-INFO-profile : facet_col 3
+ |-- 15:51-INFO-profile : Page width set to 9
+ |-- 15:51-INFO-profile : Page height set to 2.0
+ |-- 15:51-INFO-profile : Saving diagram to file : example_06.png
+ |-- 15:51-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 15:51-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_mm4ih8uc
$ 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
- |-- 14:39-DEBUG-profile : Using pandas version 1.2.5
- |-- 14:39-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
- |-- 14:39-DEBUG-profile : Using numpy version 1.21.0
- |-- 14:39-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
- |-- 14:39-DEBUG-profile : Using plotnine version 0.8.0
- |-- 14:39-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
- |-- 14:39-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_sxoccetc
- |-- 14:39-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_sxoccetc
- |-- 14:39-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_sxoccetc/mini_real_promoter
- |-- 14:39-INFO-profile : Getting configuration info from input file.
- |-- 14:39-DEBUG-profile : Color order : ['chrX', 'chr3', 'chr21', 'chr9', 'chr8', 'chr5', 'chr10', 'chr19', 'chr2', 'chr1', 'chr18', 'chr14', 'chr22', 'chr11', 'chr16', 'chr17', 'chr13', 'chr20', 'chr6', 'chr4', 'chr15', 'chr12', 'chr7']
- |-- 14:39-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']
- |-- 14:39-INFO-profile : Searching coverage columns.
- |-- 14:39-INFO-profile : Melting.
- |-- 14:39-INFO-profile : Ceiling
- |-- 14:39-INFO-profile : Normalizing (ranging)
- |-- 14:39-INFO-profile : Computing column ordering.
- |-- 14:39-INFO-profile : Preparing diagram
- |-- 14:39-INFO-profile : Theming and ordering. Please be patient...
- |-- 14:39-INFO-profile : Preparing x axis
- |-- 14:39-INFO-profile : facet_col 3
- |-- 14:39-INFO-profile : Page width set to 9
- |-- 14:39-INFO-profile : Page height set to 2.0
- |-- 14:39-INFO-profile : Saving diagram to file : example_06b.png
- |-- 14:39-INFO-profile : Be patient. This may be long for large datasets.
- |-- 14:39-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_sxoccetc
+ |-- 15:51-DEBUG-profile : Using pandas version 1.2.5
+ |-- 15:51-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
+ |-- 15:51-DEBUG-profile : Using numpy version 1.21.0
+ |-- 15:51-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
+ |-- 15:51-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 15:51-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
+ |-- 15:51-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_maz7pwx5
+ |-- 15:51-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_maz7pwx5
+ |-- 15:51-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_maz7pwx5/mini_real_promoter
+ |-- 15:51-INFO-profile : Getting configuration info from input file.
+ |-- 15:51-DEBUG-profile : Color order : ['chrX', 'chr21', 'chr2', 'chr14', 'chr9', 'chr15', 'chr4', 'chr1', 'chr6', 'chr10', 'chr11', 'chr19', 'chr7', 'chr20', 'chr17', 'chr8', 'chr18', 'chr22', 'chr13', 'chr12', 'chr3', 'chr16', 'chr5']
+ |-- 15:51-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']
+ |-- 15:51-INFO-profile : Searching coverage columns.
+ |-- 15:51-INFO-profile : Melting.
+ |-- 15:51-INFO-profile : Ceiling
+ |-- 15:51-INFO-profile : Normalizing (ranging)
+ |-- 15:51-INFO-profile : Computing column ordering.
+ |-- 15:51-INFO-profile : Preparing diagram
+ |-- 15:51-INFO-profile : Theming and ordering. Please be patient...
+ |-- 15:51-INFO-profile : Preparing x axis
+ |-- 15:51-INFO-profile : facet_col 3
+ |-- 15:51-INFO-profile : Page width set to 9
+ |-- 15:51-INFO-profile : Page height set to 2.0
+ |-- 15:51-INFO-profile : Saving diagram to file : example_06b.png
+ |-- 15:51-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 15:51-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_maz7pwx5
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-1.5.2-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.
- |-- 14:39-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-1.5.3-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.
+ |-- 15:51-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-1.5.2-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.
- |-- 14:40-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-1.5.3-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.
+ |-- 15:52-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
- |-- 14:40-INFO-discretize_key : Categories: ['A', 'B']
+ |-- 15:52-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
- |-- 14:40-INFO-discretize_key : Categories: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J']
+ |-- 15:52-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 1.5.2 documentation »
+ gtftk 1.5.3 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_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 7d3f15f..8b8c3f2 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 1.5.2 documentation
+ Index — gtftk 1.5.3 documentation
@@ -36,7 +36,7 @@ Navigation
modules |
- gtftk 1.5.2 documentation »
+ gtftk 1.5.3 documentation »
Index
$ gtftk apropos -k promoter
- |-- 14:40-INFO-apropos : >> Keyword 'promoter' was found in the following command:
+ |-- 15:52-INFO-apropos : >> Keyword 'promoter' was found in the following command:
- ologram.
- - divergent.
- coverage.
+ - divergent.
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
- |-- 14:41-INFO-control_list : 0 duplicate lines have been deleted in reference file.
- |-- 14:41-INFO-control_list : Found 50 genes of the reference in the provided signal file
- |-- 14:41-INFO-control_list : All reference genes were found.
- |-- 14:41-INFO-control_list : Searching for genes with matched signal.
- |-- 14:41-INFO-control_list : Preparing a dataframe for plotting.
- |-- 14:41-INFO-control_list : Saving diagram to file : example_13.png
- |-- 14:41-INFO-control_list : Be patient. This may be long for large datasets.
+ |-- 15:53-INFO-control_list : 0 duplicate lines have been deleted in reference file.
+ |-- 15:53-INFO-control_list : Found 50 genes of the reference in the provided signal file
+ |-- 15:53-INFO-control_list : All reference genes were found.
+ |-- 15:53-INFO-control_list : Searching for genes with matched signal.
+ |-- 15:53-INFO-control_list : Preparing a dataframe for plotting.
+ |-- 15:53-INFO-control_list : Saving diagram to file : example_13.png
+ |-- 15:53-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
- |-- 14:41-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-1.5.2-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-1.5.2-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-1.5.2-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-1.5.2-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
- |-- 14:42-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-1.5.2-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-1.5.2-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-1.5.2-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-1.5.2-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+ |-- 15:53-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-1.5.3-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-1.5.3-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-1.5.3-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-1.5.3-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+ |-- 15:54-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-1.5.3-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-1.5.3-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-1.5.3-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-1.5.3-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
- |-- 14:42-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 15:54-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
- |-- 14:43-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]']
- |-- 14:43-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-1.5.2-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-1.5.2-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-1.5.2-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-1.5.2-py3.8-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+ |-- 15:55-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]']
+ |-- 15:55-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-1.5.3-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-1.5.3-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-1.5.3-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-1.5.3-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
- |-- 14:43-INFO-discretize_key : Categories: ['[1.0_2.0]', '(2.0_4.0]', '(4.0_6.0]', '(6.0_12.0]', '(12.0_107.0]']
- |-- 14:43-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 15:55-INFO-discretize_key : Categories: ['[1.0_2.0]', '(2.0_4.0]', '(4.0_6.0]', '(6.0_12.0]', '(12.0_107.0]']
+ |-- 15:55-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
- |-- 14:44-WARNING : Converting to bed6 format (simple_07_peaks.bed).
- |-- 14:44-WARNING : Converting to bed6 format (simple_07_peaks.1.bed).
- |-- 14:44-WARNING : Converting to bed6 format (simple_07_peaks.2.bed).
- |-- 14:44-WARNING-ologram : Using only 1 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
- |-- 14:44-WARNING-ologram : --more-bed-labels was not set, automatically defaulting to --more-bed file names.
- |-- 14:44-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.
- |-- 14:44-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.
- |-- 14:44-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 + ... ])
+ |-- 15:56-WARNING : Converting to bed6 format (simple_07_peaks.bed).
+ |-- 15:56-WARNING : Converting to bed6 format (simple_07_peaks.1.bed).
+ |-- 15:56-WARNING : Converting to bed6 format (simple_07_peaks.2.bed).
+ |-- 15:56-WARNING-ologram : Using only 1 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 15:56-WARNING-ologram : --more-bed-labels was not set, automatically defaulting to --more-bed file names.
+ |-- 15:56-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.
+ |-- 15:56-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.
+ |-- 15:56-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
-CDS 3
+exon 7
+CDS 5
Arguments:
@@ -479,13 +479,13 @@$ gtftk random_tx -m 1 -i simple.gtf | gtftk select_by_key -k feature -v gene,transcript| gtftk tabulate -k gene_id,transcript_id
gene_id transcript_id
-G0001 G0001T002
+G0001 G0001T001
G0002 G0002T001
G0003 G0003T001
-G0004 G0004T001
+G0004 G0004T002
G0005 G0005T001
-G0006 G0006T002
-G0007 G0007T002
+G0006 G0006T001
+G0007 G0007T001
G0008 G0008T001
G0009 G0009T002
G0010 G0010T001
@@ -805,7 +805,7 @@ Navigation