diff --git a/docs/_images/example_01.png b/docs/_images/example_01.png index 963135a..c3d1644 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 5894045..6100483 100644 Binary files a/docs/_images/example_02.png and b/docs/_images/example_02.png differ diff --git a/docs/_images/example_06.png b/docs/_images/example_06.png index 1b5b76f..a88e57c 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 b5598fe..ea0ce30 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 818934e..4f607a3 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 0c2fe31..ce6b017 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 9b95a65..e6f7e87 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 23ba88f..05df8ae 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: '1.6.1', + VERSION: '1.6.2', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/_static/example_01.png b/docs/_static/example_01.png index c3d1644..a60d784 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 6100483..3fd60ff 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 575c2e8..3d5a7ac 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 a88e57c..1138dfe 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 ea0ce30..fdffe3a 100644 Binary files a/docs/_static/example_06b.png and b/docs/_static/example_06b.png differ diff --git a/docs/_static/example_08.png b/docs/_static/example_08.png index ce6b017..a06bf7d 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 e6f7e87..96af8d8 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 79bce7c..d038e29 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 b5f56fa..85be607 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 b61c7f8..1407384 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 59a43b7..64cd44e 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 2b02ce3..bdeb5fd 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 15d9557..e944be6 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 ca18a38..12bafe3 100644 --- a/docs/about.html +++ b/docs/about.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Warning about supported GTF file formats — gtftk 1.6.1 documentation + Warning about supported GTF file formats — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

Navigation

  • previous |
    • -
  • gtftk 1.6.1 documentation »
    • +
  • gtftk 1.6.2 documentation »
  • Warning about supported GTF file formats
    • @@ -207,13 +207,13 @@

    Navigation

  • previous |
    • -
  • gtftk 1.6.1 documentation »
    • +
  • gtftk 1.6.2 documentation »
  • Warning about supported GTF file formats
    • diff --git a/docs/annotation.html b/docs/annotation.html index 4700cac..b786205 100644 --- a/docs/annotation.html +++ b/docs/annotation.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Commands from section ‘annotation’ — gtftk 1.6.1 documentation + Commands from section ‘annotation’ — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

    Navigation

  • previous |
    • -
  • gtftk 1.6.1 documentation »
    • +
  • gtftk 1.6.2 documentation »
  • Commands from section ‘annotation’
    • @@ -481,13 +481,13 @@

    Navigation

  • previous |
    • -
  • gtftk 1.6.1 documentation »
    • +
  • gtftk 1.6.2 documentation »
  • Commands from section ‘annotation’
    • diff --git a/docs/api.html b/docs/api.html index bed824f..f414fb1 100644 --- a/docs/api.html +++ b/docs/api.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Help on Python package (pygtftk) — gtftk 1.6.1 documentation + Help on Python package (pygtftk) — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

    Navigation

  • previous |
    • -
  • gtftk 1.6.1 documentation »
    • +
  • gtftk 1.6.2 documentation »
  • Help on Python package (pygtftk)
    • @@ -3743,13 +3743,13 @@

    Navigation

  • previous |
    • -
  • gtftk 1.6.1 documentation »
    • +
  • gtftk 1.6.2 documentation »
  • Help on Python package (pygtftk)
    • diff --git a/docs/bwig_coverage.html b/docs/bwig_coverage.html index 6b9fab1..cee7806 100644 --- a/docs/bwig_coverage.html +++ b/docs/bwig_coverage.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - The pygtftk.bwig.bw_coverage module — gtftk 1.6.1 documentation + The pygtftk.bwig.bw_coverage module — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

    Navigation

  • previous |
    • -
  • gtftk 1.6.1 documentation »
    • +
  • gtftk 1.6.2 documentation »
  • The pygtftk.bwig.bw_coverage module
    • @@ -182,13 +182,13 @@

    Navigation

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  • gtftk 1.6.1 documentation »
    • +
  • gtftk 1.6.2 documentation »
  • The pygtftk.bwig.bw_coverage module
    • diff --git a/docs/conversion.html b/docs/conversion.html index 14e1b63..95fb9b1 100644 --- a/docs/conversion.html +++ b/docs/conversion.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Commands from section ‘conversion’ — gtftk 1.6.1 documentation + Commands from section ‘conversion’ — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

    Navigation

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  • gtftk 1.6.1 documentation »
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  • Commands from section ‘conversion’
    • @@ -326,13 +326,13 @@

    Navigation

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  • Commands from section ‘conversion’
    • diff --git a/docs/coordinates.html b/docs/coordinates.html index 8deef16..c5a81e5 100644 --- a/docs/coordinates.html +++ b/docs/coordinates.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Commands from section ‘coordinates’ — gtftk 1.6.1 documentation + Commands from section ‘coordinates’ — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

    Navigation

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    • @@ -429,13 +429,13 @@

    Navigation

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  • Commands from section ‘coordinates’
    • diff --git a/docs/coverage.html b/docs/coverage.html index 2a93c1d..7d3b1f7 100644 --- a/docs/coverage.html +++ b/docs/coverage.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Commands from section ‘coverage’ — gtftk 1.6.1 documentation + Commands from section ‘coverage’ — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

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  • gtftk 1.6.1 documentation »
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  • Commands from section ‘coverage’
    • @@ -165,25 +165,25 @@

    mk_matrix
    $ gtftk mk_matrix -k 8 --bin-around-frac 0.5 -i mini_real_noov_rnd_tx.gtf.gz -t transcript  -d 5000 -u 5000 -w 200 -c hg38  -l  H3K4me3,H3K79me,H3K36me3 -y ENCFF742FDS_H3K4me3_K562_sub.bw ENCFF947DVY_H3K79me2_K562_sub.bw ENCFF431HAA_H3K36me3_K562_sub.bw -o mini_real_tx
- |-- 9:15-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 9:15-WARNING-mk_matrix : ENST00000385018 has length : 82
- |-- 9:15-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 9:15-WARNING-mk_matrix : Filter them out please.
- |-- 9:15-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 9:15-WARNING-mk_matrix : ENST00000583764 has length : 85
- |-- 9:15-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 9:15-WARNING-mk_matrix : Filter them out please.
- |-- 9:15-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 9:15-WARNING-mk_matrix : ENST00000612829 has length : 85
- |-- 9:15-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 9:15-WARNING-mk_matrix : Filter them out please.
- |-- 9:15-WARNING-mk_matrix : Encountered regions shorter than bin number.
- |-- 9:15-WARNING-mk_matrix : ENST00000637495 has length : 68
- |-- 9:15-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
- |-- 9:15-WARNING-mk_matrix : Filter them out please.
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/plugins/mk_matrix.py:503: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only.
+ |-- 10:50-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 10:50-WARNING-mk_matrix : ENST00000385018 has length : 82
+ |-- 10:50-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 10:50-WARNING-mk_matrix : Filter them out please.
+ |-- 10:50-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 10:50-WARNING-mk_matrix : ENST00000583764 has length : 85
+ |-- 10:50-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 10:50-WARNING-mk_matrix : Filter them out please.
+ |-- 10:50-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 10:50-WARNING-mk_matrix : ENST00000612829 has length : 85
+ |-- 10:50-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 10:50-WARNING-mk_matrix : Filter them out please.
+ |-- 10:50-WARNING-mk_matrix : Encountered regions shorter than bin number.
+ |-- 10:50-WARNING-mk_matrix : ENST00000637495 has length : 68
+ |-- 10:50-WARNING-mk_matrix : They will be set to NA or --pseudo-count depending on --zero-to-na.
+ |-- 10:50-WARNING-mk_matrix : Filter them out please.
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/plugins/mk_matrix.py:503: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only.
   df_up = df_up.drop(['start', 'end'], 1)
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/plugins/mk_matrix.py:516: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only.
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/plugins/mk_matrix.py:516: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only.
   df_dws = df_dws.drop(['start', 'end'], 1)
    @@ -236,19 +236,19 @@

    profile
    $ gtftk profile -D -i mini_real_promoter.zip -o profile_prom -pf png -if  example_01.png
- |-- 9:16-WARNING-profile : --group-by not set. Choosing 'bwig'.
+ |-- 10:50-WARNING-profile : --group-by not set. Choosing 'bwig'.
    _images/example_01.png

    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
- |-- 9:16-WARNING-profile : --group-by not set. Choosing 'bwig'.
+ |-- 10:50-WARNING-profile : --group-by not set. Choosing 'bwig'.
    _images/example_01b.png

    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
- |-- 9:16-WARNING-profile : --group-by not set. Choosing 'bwig'.
+ |-- 10:50-WARNING-profile : --group-by not set. Choosing 'bwig'.
    _images/example_02.png @@ -256,113 +256,113 @@

    profile
    $ 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
- |-- 9:16-DEBUG-profile : Using pandas version 1.4.1
- |-- 9:16-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pandas/__init__.py
- |-- 9:16-DEBUG-profile : Using numpy version 1.22.2
- |-- 9:16-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/numpy/__init__.py
- |-- 9:16-DEBUG-profile : Using plotnine version 0.8.0
- |-- 9:16-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/plotnine/__init__.py
- |-- 9:16-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_8pj2pkfc
- |-- 9:16-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_8pj2pkfc
- |-- 9:16-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_8pj2pkfc/mini_real_promoter
- |-- 9:16-INFO-profile : Getting configuration info from input file.
- |-- 9:16-INFO-profile : Reading transcript file.
- |-- 9:16-INFO-profile : Deleting duplicates in transcript-file.
- |-- 9:16-INFO-profile : Checking how many transcripts where found in the transcript list.
- |-- 9:16-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
- |-- 9:16-DEBUG-profile : Color order : ['H3K36me3', 'H3K79me', 'H3K4me3']
- |-- 9:16-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
- |-- 9:16-INFO-profile : Searching coverage columns.
- |-- 9:16-INFO-profile : Melting.
- |-- 9:16-INFO-profile : Ceiling
- |-- 9:16-INFO-profile : Computing column ordering.
- |-- 9:16-INFO-profile : Preparing diagram
- |-- 9:16-INFO-profile : Theming and ordering. Please be patient...
- |-- 9:16-INFO-profile : Preparing x axis
- |-- 9:16-INFO-profile : facet_col 2
- |-- 9:16-INFO-profile : Page width set to 6
- |-- 9:16-INFO-profile : Page height set to 5.0
- |-- 9:16-INFO-profile : Saving diagram to file : example_05.png
- |-- 9:16-INFO-profile : Be patient. This may be long for large datasets.
- |-- 9:16-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_8pj2pkfc
+ |-- 10:50-DEBUG-profile : Using pandas version 1.4.1
+ |-- 10:50-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pandas/__init__.py
+ |-- 10:50-DEBUG-profile : Using numpy version 1.22.2
+ |-- 10:50-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/numpy/__init__.py
+ |-- 10:50-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 10:50-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/plotnine/__init__.py
+ |-- 10:50-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_8t5wfp3l
+ |-- 10:50-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_8t5wfp3l
+ |-- 10:50-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_8t5wfp3l/mini_real_promoter
+ |-- 10:50-INFO-profile : Getting configuration info from input file.
+ |-- 10:50-INFO-profile : Reading transcript file.
+ |-- 10:50-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 10:50-INFO-profile : Checking how many transcripts where found in the transcript list.
+ |-- 10:50-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
+ |-- 10:50-DEBUG-profile : Color order : ['H3K79me', 'H3K36me3', 'H3K4me3']
+ |-- 10:50-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
+ |-- 10:50-INFO-profile : Searching coverage columns.
+ |-- 10:50-INFO-profile : Melting.
+ |-- 10:50-INFO-profile : Ceiling
+ |-- 10:50-INFO-profile : Computing column ordering.
+ |-- 10:50-INFO-profile : Preparing diagram
+ |-- 10:50-INFO-profile : Theming and ordering. Please be patient...
+ |-- 10:50-INFO-profile : Preparing x axis
+ |-- 10:50-INFO-profile : facet_col 2
+ |-- 10:50-INFO-profile : Page width set to 6
+ |-- 10:50-INFO-profile : Page height set to 5.0
+ |-- 10:50-INFO-profile : Saving diagram to file : example_05.png
+ |-- 10:50-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 10:50-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_8t5wfp3l
    _images/example_05.png

    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
- |-- 9:16-DEBUG-profile : Using pandas version 1.4.1
- |-- 9:16-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pandas/__init__.py
- |-- 9:16-DEBUG-profile : Using numpy version 1.22.2
- |-- 9:16-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/numpy/__init__.py
- |-- 9:16-DEBUG-profile : Using plotnine version 0.8.0
- |-- 9:16-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/plotnine/__init__.py
- |-- 9:16-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_doqamm6u
- |-- 9:16-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_doqamm6u
- |-- 9:16-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_doqamm6u/mini_real_promoter
- |-- 9:16-INFO-profile : Getting configuration info from input file.
- |-- 9:16-INFO-profile : Reading transcript file.
- |-- 9:16-INFO-profile : Deleting duplicates in transcript-file.
- |-- 9:16-INFO-profile : Checking how many transcripts where found in the transcript list.
- |-- 9:16-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
- |-- 9:16-DEBUG-profile : Color order : ['protein_coding', 'lincRNA', 'antisense']
- |-- 9:16-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
- |-- 9:16-INFO-profile : Searching coverage columns.
- |-- 9:16-INFO-profile : Melting.
- |-- 9:16-INFO-profile : Ceiling
- |-- 9:16-INFO-profile : Normalizing (ranging)
- |-- 9:16-INFO-profile : Computing column ordering.
- |-- 9:16-INFO-profile : Preparing diagram
- |-- 9:16-INFO-profile : Theming and ordering. Please be patient...
- |-- 9:16-INFO-profile : Preparing x axis
- |-- 9:16-INFO-profile : facet_col 3
- |-- 9:16-INFO-profile : Page width set to 9
- |-- 9:16-INFO-profile : Page height set to 2.0
- |-- 9:16-INFO-profile : Saving diagram to file : example_06.png
- |-- 9:16-INFO-profile : Be patient. This may be long for large datasets.
- |-- 9:16-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_doqamm6u
+ |-- 10:50-DEBUG-profile : Using pandas version 1.4.1
+ |-- 10:50-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pandas/__init__.py
+ |-- 10:50-DEBUG-profile : Using numpy version 1.22.2
+ |-- 10:50-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/numpy/__init__.py
+ |-- 10:50-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 10:50-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/plotnine/__init__.py
+ |-- 10:50-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_ybjjmnt7
+ |-- 10:50-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_ybjjmnt7
+ |-- 10:50-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_ybjjmnt7/mini_real_promoter
+ |-- 10:50-INFO-profile : Getting configuration info from input file.
+ |-- 10:50-INFO-profile : Reading transcript file.
+ |-- 10:50-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 10:50-INFO-profile : Checking how many transcripts where found in the transcript list.
+ |-- 10:50-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
+ |-- 10:50-DEBUG-profile : Color order : ['antisense', 'protein_coding', 'lincRNA']
+ |-- 10:50-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
+ |-- 10:50-INFO-profile : Searching coverage columns.
+ |-- 10:50-INFO-profile : Melting.
+ |-- 10:50-INFO-profile : Ceiling
+ |-- 10:50-INFO-profile : Normalizing (ranging)
+ |-- 10:50-INFO-profile : Computing column ordering.
+ |-- 10:50-INFO-profile : Preparing diagram
+ |-- 10:50-INFO-profile : Theming and ordering. Please be patient...
+ |-- 10:50-INFO-profile : Preparing x axis
+ |-- 10:50-INFO-profile : facet_col 3
+ |-- 10:50-INFO-profile : Page width set to 9
+ |-- 10:50-INFO-profile : Page height set to 2.0
+ |-- 10:50-INFO-profile : Saving diagram to file : example_06.png
+ |-- 10:50-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 10:50-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_ybjjmnt7
    _images/example_06.png 
    $ 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
- |-- 9:16-DEBUG-profile : Using pandas version 1.4.1
- |-- 9:16-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pandas/__init__.py
- |-- 9:16-DEBUG-profile : Using numpy version 1.22.2
- |-- 9:16-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/numpy/__init__.py
- |-- 9:16-DEBUG-profile : Using plotnine version 0.8.0
- |-- 9:16-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/plotnine/__init__.py
- |-- 9:16-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_dxif2ou9
- |-- 9:16-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_dxif2ou9
- |-- 9:16-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_dxif2ou9/mini_real_promoter
- |-- 9:16-INFO-profile : Getting configuration info from input file.
- |-- 9:16-DEBUG-profile : Color order : ['chr18', 'chr20', 'chr21', 'chr8', 'chr13', 'chr16', 'chr12', 'chr14', 'chr7', 'chr15', 'chr2', 'chr11', 'chr19', 'chr5', 'chr6', 'chr4', 'chr22', 'chrX', 'chr1', 'chr3', 'chr10', 'chr9', 'chr17']
- |-- 9:16-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']
- |-- 9:16-INFO-profile : Searching coverage columns.
- |-- 9:16-INFO-profile : Melting.
- |-- 9:16-INFO-profile : Ceiling
- |-- 9:16-INFO-profile : Normalizing (ranging)
- |-- 9:16-INFO-profile : Computing column ordering.
- |-- 9:16-INFO-profile : Preparing diagram
- |-- 9:16-INFO-profile : Theming and ordering. Please be patient...
- |-- 9:16-INFO-profile : Preparing x axis
- |-- 9:16-INFO-profile : facet_col 3
- |-- 9:16-INFO-profile : Page width set to 9
- |-- 9:16-INFO-profile : Page height set to 2.0
- |-- 9:16-INFO-profile : Saving diagram to file : example_06b.png
- |-- 9:16-INFO-profile : Be patient. This may be long for large datasets.
- |-- 9:16-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_dxif2ou9
+ |-- 10:50-DEBUG-profile : Using pandas version 1.4.1
+ |-- 10:50-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pandas/__init__.py
+ |-- 10:50-DEBUG-profile : Using numpy version 1.22.2
+ |-- 10:50-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/numpy/__init__.py
+ |-- 10:50-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 10:50-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/plotnine/__init__.py
+ |-- 10:50-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_sk15z7l6
+ |-- 10:50-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_sk15z7l6
+ |-- 10:50-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_sk15z7l6/mini_real_promoter
+ |-- 10:50-INFO-profile : Getting configuration info from input file.
+ |-- 10:50-DEBUG-profile : Color order : ['chrX', 'chr12', 'chr10', 'chr15', 'chr4', 'chr20', 'chr18', 'chr13', 'chr9', 'chr3', 'chr6', 'chr22', 'chr19', 'chr8', 'chr14', 'chr7', 'chr5', 'chr21', 'chr16', 'chr17', 'chr1', 'chr2', 'chr11']
+ |-- 10:50-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']
+ |-- 10:50-INFO-profile : Searching coverage columns.
+ |-- 10:50-INFO-profile : Melting.
+ |-- 10:50-INFO-profile : Ceiling
+ |-- 10:50-INFO-profile : Normalizing (ranging)
+ |-- 10:51-INFO-profile : Computing column ordering.
+ |-- 10:51-INFO-profile : Preparing diagram
+ |-- 10:51-INFO-profile : Theming and ordering. Please be patient...
+ |-- 10:51-INFO-profile : Preparing x axis
+ |-- 10:51-INFO-profile : facet_col 3
+ |-- 10:51-INFO-profile : Page width set to 9
+ |-- 10:51-INFO-profile : Page height set to 2.0
+ |-- 10:51-INFO-profile : Saving diagram to file : example_06b.png
+ |-- 10:51-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 10:51-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_sk15z7l6
    _images/example_06b.png

    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/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-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.
- |-- 9:16-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-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.
+ |-- 10:51-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
    _images/example_07.png 
    $ 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/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-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.
- |-- 9:17-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-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.
+ |-- 10:51-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
    _images/example_08.png @@ -491,13 +491,13 @@

    Navigation

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    • diff --git a/docs/developers.html b/docs/developers.html index c912769..92262d1 100644 --- a/docs/developers.html +++ b/docs/developers.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Writing your own commands — gtftk 1.6.1 documentation + Writing your own commands — gtftk 1.6.2 documentation @@ -41,7 +41,7 @@

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    • diff --git a/docs/editing.html b/docs/editing.html index 0adeb7f..7a16455 100644 --- a/docs/editing.html +++ b/docs/editing.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Commands from section ‘Editing’ — gtftk 1.6.1 documentation + Commands from section ‘Editing’ — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

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    • @@ -431,7 +431,7 @@

    discretize_key
    $ 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
- |-- 9:17-INFO-discretize_key : Categories: ['A', 'B']
+ |-- 10:51-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
- |-- 9:17-INFO-discretize_key : Categories: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J']
+ |-- 10:51-INFO-discretize_key : Categories: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J']
   96 A
   83 B
   89 C
@@ -573,13 +573,13 @@ 
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index 7706192..0da77f6 100644
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+++ b/docs/genindex.html
@@ -16,7 +16,7 @@
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@@ -36,7 +36,7 @@ 
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    • diff --git a/docs/information.html b/docs/information.html index cac456e..edb1f6f 100644 --- a/docs/information.html +++ b/docs/information.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Commands from section ‘information’ — gtftk 1.6.1 documentation + Commands from section ‘information’ — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

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    • @@ -69,7 +69,7 @@

    apropos
    $ gtftk apropos -k promoter
- |-- 9:17-INFO-apropos : >> Keyword 'promoter' was found in the following command:
+ |-- 10:51-INFO-apropos : >> Keyword 'promoter' was found in the following command:
 	- coverage.
 	- ologram.
 	- divergent.
@@ -730,13 +730,13 @@ 
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    diff --git a/docs/installation.html b/docs/installation.html index d1ee60a..4d9cc7a 100644 --- a/docs/installation.html +++ b/docs/installation.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Installing pygtftk/gtftk — gtftk 1.6.1 documentation + Installing pygtftk/gtftk — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

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    • diff --git a/docs/merge_ologram_stats_01.pdf b/docs/merge_ologram_stats_01.pdf index 2b02ce3..bdeb5fd 100644 Binary files a/docs/merge_ologram_stats_01.pdf and b/docs/merge_ologram_stats_01.pdf differ diff --git a/docs/miscellaneous.html b/docs/miscellaneous.html index 8a8347c..de187b4 100644 --- a/docs/miscellaneous.html +++ b/docs/miscellaneous.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Commands from section ‘miscellaneous’ — gtftk 1.6.1 documentation + Commands from section ‘miscellaneous’ — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

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    • @@ -69,13 +69,13 @@

    control_list
    $ 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
- |-- 9:18-INFO-control_list : 0 duplicate lines have been deleted in reference file.
- |-- 9:18-INFO-control_list : Found 50 genes of the reference in the provided signal file
- |-- 9:18-INFO-control_list : All reference genes were found.
- |-- 9:18-INFO-control_list : Searching for genes with matched signal.
- |-- 9:18-INFO-control_list : Preparing a dataframe for plotting.
- |-- 9:18-INFO-control_list : Saving diagram to file : example_13.png
- |-- 9:18-INFO-control_list : Be patient. This may be long for large datasets.
+ |-- 10:52-INFO-control_list : 0 duplicate lines have been deleted in reference file.
+ |-- 10:52-INFO-control_list : Found 50 genes of the reference in the provided signal file
+ |-- 10:52-INFO-control_list : All reference genes were found.
+ |-- 10:52-INFO-control_list : Searching for genes with matched signal.
+ |-- 10:52-INFO-control_list : Preparing a dataframe for plotting.
+ |-- 10:52-INFO-control_list : Saving diagram to file : example_13.png
+ |-- 10:52-INFO-control_list : Be patient. This may be long for large datasets.
    _images/example_13.png @@ -243,13 +243,13 @@

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    • diff --git a/docs/objects.inv b/docs/objects.inv index 72db0fa..c469d08 100644 Binary files a/docs/objects.inv and b/docs/objects.inv differ diff --git a/docs/ologram.html b/docs/ologram.html index 56efc9d..661e139 100644 --- a/docs/ologram.html +++ b/docs/ologram.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Commands from section ‘ologram’ — gtftk 1.6.1 documentation + Commands from section ‘ologram’ — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

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  • Commands from section ‘ologram’
    • @@ -103,16 +103,16 @@

    ologram
    $ 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
- |-- 9:18-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
- |-- 9:18-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/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+ |-- 10:52-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+ |-- 10:53-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/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt

    @@ -127,7 +127,7 @@

    ologram
    $ 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
- |-- 9:19-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 10:53-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.

    @@ -146,12 +146,12 @@

    ologram
    $ 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
- |-- 9:19-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
- |-- 9:19-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]']
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
-/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.1-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+ |-- 10:54-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 10:54-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]']
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:225: RuntimeWarning: invalid value encountered in sqrt
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.2-py3.9-macosx-10.9-x86_64.egg/pygtftk/stats/beta.py:237: RuntimeWarning: invalid value encountered in sqrt

    @@ -166,8 +166,8 @@

    ologram
    $ 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
- |-- 9:20-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
- |-- 9:20-INFO-discretize_key : Categories: ['[1.0_2.0]', '(2.0_4.0]', '(4.0_6.0]', '(6.0_12.0]', '(12.0_107.0]']
+ |-- 10:55-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 10:55-INFO-discretize_key : Categories: ['[1.0_2.0]', '(2.0_4.0]', '(4.0_6.0]', '(6.0_12.0]', '(12.0_107.0]']

    @@ -201,14 +201,14 @@

    ologram (multiple overlaps)
    $ 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
- |-- 9:21-WARNING : Converting to bed6 format (simple_07_peaks.bed).
- |-- 9:21-WARNING : Converting to bed6 format (simple_07_peaks.1.bed).
- |-- 9:21-WARNING : Converting to bed6 format (simple_07_peaks.2.bed).
- |-- 9:21-WARNING-ologram : Using only 1 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
- |-- 9:21-WARNING-ologram : --more-bed-labels was not set, automatically defaulting to --more-bed file names.
- |-- 9:21-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.
- |-- 9:21-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.
- |-- 9:21-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 + ... ])
+ |-- 10:55-WARNING : Converting to bed6 format (simple_07_peaks.bed).
+ |-- 10:55-WARNING : Converting to bed6 format (simple_07_peaks.1.bed).
+ |-- 10:55-WARNING : Converting to bed6 format (simple_07_peaks.2.bed).
+ |-- 10:55-WARNING-ologram : Using only 1 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 10:55-WARNING-ologram : --more-bed-labels was not set, automatically defaulting to --more-bed file names.
+ |-- 10:55-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.
+ |-- 10:55-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.
+ |-- 10:55-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:

    @@ -816,13 +816,13 @@

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    • diff --git a/docs/py-modindex.html b/docs/py-modindex.html index 1fc665e..ac82a07 100644 --- a/docs/py-modindex.html +++ b/docs/py-modindex.html @@ -16,7 +16,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Python Module Index — gtftk 1.6.1 documentation + Python Module Index — gtftk 1.6.2 documentation @@ -39,7 +39,7 @@

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    • @@ -163,13 +163,13 @@

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    • diff --git a/docs/search.html b/docs/search.html index 44b9d99..b7a2473 100644 --- a/docs/search.html +++ b/docs/search.html @@ -16,7 +16,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Search — gtftk 1.6.1 documentation + Search — gtftk 1.6.2 documentation @@ -42,7 +42,7 @@

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    • @@ -102,13 +102,13 @@

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about supported GTF file formats","Commands from section \u2018annotation\u2019","Help on Python package (pygtftk)","The pygtftk.bwig.bw_coverage module","Commands from section \u2018conversion\u2019","Commands from section \u2018coordinates\u2019","Commands from section \u2018coverage\u2019","Writing your own commands","Commands from section \u2018Editing\u2019","Help on gtftk Unix commands","Welcome to pygtftk documentation page","Commands from section \u2018information\u2019","Installing pygtftk/gtftk","Commands from section \u2018miscellaneous\u2019","Commands from section \u2018ologram\u2019","Commands from section \u2018selection\u2019","Commands from section 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\ No newline at end of file diff --git a/docs/selection.html b/docs/selection.html index 2146c80..04423af 100644 --- a/docs/selection.html +++ b/docs/selection.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Commands from section ‘selection’ — gtftk 1.6.1 documentation + Commands from section ‘selection’ — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

    Navigation

  • previous |
    • -
  • gtftk 1.6.1 documentation »
    • +
  • gtftk 1.6.2 documentation »
  • Commands from section ‘selection’
    • @@ -440,8 +440,8 @@

    random_list
    $ gtftk random_list -n 3 -i simple.gtf | gtftk count
 transcript	3
-exon	7
-CDS	7
+exon	6
+CDS	5

    Arguments:

    @@ -479,15 +479,15 @@

    random_tx
    $ 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	G0004T002
+G0004	G0004T001
 G0005	G0005T001
-G0006	G0006T002
+G0006	G0006T001
 G0007	G0007T002
 G0008	G0008T001
-G0009	G0009T001
+G0009	G0009T002
 G0010	G0010T001
    @@ -811,13 +811,13 @@

    Navigation

  • previous |
    • -
  • gtftk 1.6.1 documentation »
    • +
  • gtftk 1.6.2 documentation »
  • Commands from section ‘selection’
    • diff --git a/docs/sequence.html b/docs/sequence.html index 747f30d..2a5e938 100644 --- a/docs/sequence.html +++ b/docs/sequence.html @@ -17,7 +17,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Commands from section ‘sequence’ — gtftk 1.6.1 documentation + Commands from section ‘sequence’ — gtftk 1.6.2 documentation @@ -45,7 +45,7 @@

    Navigation

  • previous |
    • -
  • gtftk 1.6.1 documentation »
    • +
  • gtftk 1.6.2 documentation »
  • Commands from section ‘sequence’
    • @@ -240,13 +240,13 @@

    Navigation

  • previous |
    • -
  • gtftk 1.6.1 documentation »
    • +
  • gtftk 1.6.2 documentation »
  • Commands from section ‘sequence’
    • diff --git a/docs/source/_static/example_01.png b/docs/source/_static/example_01.png index c3d1644..a60d784 100644 Binary files a/docs/source/_static/example_01.png and b/docs/source/_static/example_01.png differ diff --git a/docs/source/_static/example_02.png b/docs/source/_static/example_02.png index 6100483..3fd60ff 100644 Binary files a/docs/source/_static/example_02.png and b/docs/source/_static/example_02.png differ diff --git a/docs/source/_static/example_05.png b/docs/source/_static/example_05.png index 575c2e8..3d5a7ac 100644 Binary files a/docs/source/_static/example_05.png and b/docs/source/_static/example_05.png differ diff --git a/docs/source/_static/example_06.png b/docs/source/_static/example_06.png index a88e57c..1138dfe 100644 Binary files a/docs/source/_static/example_06.png and b/docs/source/_static/example_06.png differ diff --git a/docs/source/_static/example_06b.png b/docs/source/_static/example_06b.png index ea0ce30..fdffe3a 100644 Binary files a/docs/source/_static/example_06b.png and b/docs/source/_static/example_06b.png differ diff --git a/docs/source/_static/example_08.png b/docs/source/_static/example_08.png index ce6b017..a06bf7d 100644 Binary files a/docs/source/_static/example_08.png and b/docs/source/_static/example_08.png differ diff --git a/docs/source/_static/example_13.png b/docs/source/_static/example_13.png index e6f7e87..96af8d8 100644 Binary files a/docs/source/_static/example_13.png and b/docs/source/_static/example_13.png differ diff --git a/docs/source/_static/example_pa_01.pdf b/docs/source/_static/example_pa_01.pdf index 79bce7c..d038e29 100644 Binary files a/docs/source/_static/example_pa_01.pdf and b/docs/source/_static/example_pa_01.pdf differ diff --git a/docs/source/_static/example_pa_02.pdf b/docs/source/_static/example_pa_02.pdf index b5f56fa..85be607 100644 Binary files a/docs/source/_static/example_pa_02.pdf and b/docs/source/_static/example_pa_02.pdf differ diff --git a/docs/source/_static/example_pa_03.pdf b/docs/source/_static/example_pa_03.pdf index b61c7f8..1407384 100644 Binary files a/docs/source/_static/example_pa_03.pdf and b/docs/source/_static/example_pa_03.pdf differ diff --git a/docs/source/_static/example_pa_04.pdf b/docs/source/_static/example_pa_04.pdf index 59a43b7..64cd44e 100644 Binary files a/docs/source/_static/example_pa_04.pdf and b/docs/source/_static/example_pa_04.pdf differ diff --git a/docs/source/_static/merge_ologram_stats_01.pdf b/docs/source/_static/merge_ologram_stats_01.pdf index bdeb5fd..5800729 100644 Binary files a/docs/source/_static/merge_ologram_stats_01.pdf and b/docs/source/_static/merge_ologram_stats_01.pdf differ diff --git a/docs/source/_static/treeified.pdf b/docs/source/_static/treeified.pdf index e944be6..4f781c1 100644 Binary files a/docs/source/_static/treeified.pdf and b/docs/source/_static/treeified.pdf differ diff --git a/docs/source/conf.py b/docs/source/conf.py index 0262e59..489d150 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -58,10 +58,10 @@ # built documents. # # The short X.Y version. -version = u'1.6.1' +version = u'1.6.2' # The full version, including alpha/beta/rc tags. -release = u'1.6.1' +release = u'1.6.2' # The language for content autogenerated by Sphinx. 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Puthier, F. Lopez and Q. Ferre author-email = denis.puthier@univ-amu.fr