diff --git a/.gitignore b/.gitignore index 0dbc783..63f1d05 100644 --- a/.gitignore +++ b/.gitignore @@ -84,6 +84,9 @@ target/ # VSCode .vscode +# PyCharm +.idea + # pyenv .python-version diff --git a/Makefile b/Makefile index 3ba3b1a..35d91db 100644 --- a/Makefile +++ b/Makefile @@ -237,10 +237,10 @@ release_pip_osx: @ echo "# Creating osx compliant package (pip) #" @ echo "#-----------------------------------------------#" @ mkdir -p wheels - @ conda create -n python_dev_38 python=3.8 -y; \ - conda activate python_dev_38 ; \ + @ conda create -n python_dev_39 python=3.9 -y; \ + conda activate python_dev_39 ; \ pip install -r requirements.txt ; \ - rm -rf dist build; python3.8 setup.py bdist_wheel ; \ + rm -rf dist build; python3.9 setup.py bdist_wheel ; \ cp dist/*whl wheels ; \ rm -rf dist build diff --git a/docs/_images/example_02.png b/docs/_images/example_02.png index bd5e012..0631793 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 7f11837..472bc48 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 59d173c..3029105 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 e9b98e0..d3828de 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 7a41f5b..a3af2de 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 ca569cc..e117925 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 a0c48af..6ab41f5 100644 Binary files a/docs/_images/example_13.png and b/docs/_images/example_13.png differ diff --git a/docs/_static/basic.css b/docs/_static/basic.css index aa9df31..bf18350 100644 --- a/docs/_static/basic.css +++ b/docs/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -731,8 +731,9 @@ dl.glossary dt { .classifier:before { font-style: normal; - margin: 0.5em; + margin: 0 0.5em; content: ":"; + display: inline-block; } abbr, acronym { @@ -756,6 +757,7 @@ span.pre { -ms-hyphens: none; -webkit-hyphens: none; hyphens: none; + white-space: nowrap; } div[class*="highlight-"] { @@ -819,7 +821,7 @@ div.code-block-caption code { table.highlighttable td.linenos, span.linenos, -div.doctest > div.highlight span.gp { /* gp: Generic.Prompt */ +div.highlight span.gp { /* gp: Generic.Prompt */ user-select: none; -webkit-user-select: text; /* Safari fallback only */ -webkit-user-select: none; /* Chrome/Safari */ diff --git a/docs/_static/doctools.js b/docs/_static/doctools.js index 61ac9d2..e509e48 100644 --- a/docs/_static/doctools.js +++ b/docs/_static/doctools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for all documentation. * - * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -264,6 +264,9 @@ var Documentation = { hideSearchWords : function() { $('#searchbox .highlight-link').fadeOut(300); $('span.highlighted').removeClass('highlighted'); + var url = new URL(window.location); + url.searchParams.delete('highlight'); + window.history.replaceState({}, '', url); }, /** @@ -301,12 +304,14 @@ var Documentation = { window.location.href = prevHref; return false; } + break; case 39: // right var nextHref = $('link[rel="next"]').prop('href'); if (nextHref) { window.location.href = nextHref; return false; } + break; } } }); diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index b859b47..65f6a1c 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: '1.5.3', + VERSION: '1.6.0', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/_static/example_01.png b/docs/_static/example_01.png index 1b4d486..963135a 100644 Binary files a/docs/_static/example_01.png and b/docs/_static/example_01.png differ diff --git a/docs/_static/example_01b.png b/docs/_static/example_01b.png index 9eeb98a..7423ae0 100644 Binary files a/docs/_static/example_01b.png and b/docs/_static/example_01b.png differ diff --git a/docs/_static/example_02.png b/docs/_static/example_02.png index 0631793..5894045 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 472bc48..575c2e8 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 3029105..1b5b76f 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 d3828de..b5598fe 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 a3af2de..818934e 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 e117925..0c2fe31 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 6ab41f5..9b95a65 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 0b2f1ff..7ffe21e 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 30982b3..72f3df3 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 9dcac00..4e7fb52 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 3e6fed2..49c057e 100644 Binary files a/docs/_static/example_pa_04.pdf and b/docs/_static/example_pa_04.pdf differ diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js index 863704b..ebe2f03 100644 --- a/docs/_static/language_data.js +++ b/docs/_static/language_data.js @@ -5,7 +5,7 @@ * This script contains the language-specific data used by searchtools.js, * namely the list of stopwords, stemmer, scorer and splitter. * - * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/docs/_static/merge_ologram_stats_01.pdf b/docs/_static/merge_ologram_stats_01.pdf index 6fb2ee4..b13fcfc 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/nature.css b/docs/_static/nature.css index c4768af..beb3a60 100644 --- a/docs/_static/nature.css +++ b/docs/_static/nature.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- nature theme. * - * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js index e09f926..2d77859 100644 --- a/docs/_static/searchtools.js +++ b/docs/_static/searchtools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for the full-text search. * - * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -282,7 +282,10 @@ var Search = { complete: function(jqxhr, textstatus) { var data = jqxhr.responseText; if (data !== '' && data !== undefined) { - listItem.append(Search.makeSearchSummary(data, searchterms, hlterms)); + var summary = Search.makeSearchSummary(data, searchterms, hlterms); + if (summary) { + listItem.append(summary); + } } Search.output.append(listItem); setTimeout(function() { @@ -325,7 +328,9 @@ var Search = { var results = []; for (var prefix in objects) { - for (var name in objects[prefix]) { + for (var iMatch = 0; iMatch != objects[prefix].length; ++iMatch) { + var match = objects[prefix][iMatch]; + var name = match[4]; var fullname = (prefix ? prefix + '.' : '') + name; var fullnameLower = fullname.toLowerCase() if (fullnameLower.indexOf(object) > -1) { @@ -339,7 +344,6 @@ var Search = { } else if (parts[parts.length - 1].indexOf(object) > -1) { score += Scorer.objPartialMatch; } - var match = objects[prefix][name]; var objname = objnames[match[1]][2]; var title = titles[match[0]]; // If more than one term searched for, we require other words to be @@ -498,6 +502,9 @@ var Search = { */ makeSearchSummary : function(htmlText, keywords, hlwords) { var text = Search.htmlToText(htmlText); + if (text == "") { + return null; + } var textLower = text.toLowerCase(); var start = 0; $.each(keywords, function() { diff --git a/docs/_static/treeified.pdf b/docs/_static/treeified.pdf index f5f6263..c781d5e 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 3cbff43..febd99a 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 1.5.3 documentation + Warning about supported GTF file formats — gtftk 1.6.0 documentation @@ -45,7 +45,7 @@

Navigation

  • previous |
    • -
  • gtftk 1.5.3 documentation »
    • +
  • gtftk 1.6.0 documentation »
  • Warning about supported GTF file formats
    • @@ -151,20 +151,26 @@

    Naming conventions
    -

    Table of Contents

    -
    @@ -420,8 +420,9 @@

    intron_sizes
    -

    Table of Contents

    -
    @@ -70,7 +70,7 @@

    Help on Python package (pygtftk)
    -class pygtftk.gtf_interface.GTF(input_obj=None, check_ensembl_format=True, new_data=None)
    +class pygtftk.gtf_interface.GTF(input_obj=None, check_ensembl_format=True, new_data=None)

    An interface to a GTF file. This object returns a GTF, TAB or FASTA object.

    @@ -1535,7 +1535,7 @@

    Help on Python package (pygtftk)
    -class pygtftk.fasta_interface.FASTA(fn, ptr, intron, rev_comp)
    +class pygtftk.fasta_interface.FASTA(fn, ptr, intron, rev_comp)

    A class representation of a fasta file connection. A end product from a GTF object.

    @@ -1595,7 +1595,7 @@

    Help on Python package (pygtftk)
    -class pygtftk.tab_interface.TAB(fn, ptr, dll=None)
    +class pygtftk.tab_interface.TAB(fn, ptr, dll=None)

    A class representation of a tabulated matrix. An end product from a GTF object.

    @@ -1715,7 +1715,7 @@

    Help on Python package (pygtftk)
    -class pygtftk.Line.FastaSequence(ptr=None, alist=None, feat='transcript', rev_comp=False)
    +class pygtftk.Line.FastaSequence(ptr=None, alist=None, feat='transcript', rev_comp=False)

    A class representating a fasta file line.

    @@ -1757,7 +1757,7 @@

    Help on Python package (pygtftk)
    -class pygtftk.Line.Feature(ptr=None, alist=None)
    +class pygtftk.Line.Feature(ptr=None, alist=None)

    Class representation of a genomic feature. Corresponds to a GTF line.

    @@ -1838,7 +1838,7 @@

    Help on Python package (pygtftk)
    -classmethod from_list(a_list)
    +classmethod from_list(a_list)

    Create a Feature object from a list.

    Params alist
    @@ -2142,7 +2142,7 @@

    Help on Python package (pygtftk)
    -class pygtftk.Line.FieldSet(ptr=None, size=None, alist=None, ft_type=None)
    +class pygtftk.Line.FieldSet(ptr=None, size=None, alist=None, ft_type=None)

    A class representating a set of Fields obtained from a splitted line.

    @@ -2203,7 +2203,7 @@

    Help on Python package (pygtftk)quentin.q.ferre@gmail.com>

    -class pygtftk.stats.intersect.overlap_stats_shuffling.ComputingIntersectionPartial(Lr1, Li1, Lrs, Lis, all_chrom1, all_chrom2, use_markov_shuffling, keep_intact_in_shuffling, nb_threads)
    +class pygtftk.stats.intersect.overlap_stats_shuffling.ComputingIntersectionPartial(Lr1, Li1, Lrs, Lis, all_chrom1, all_chrom2, use_markov_shuffling, keep_intact_in_shuffling, nb_threads)

    This is a replacer for a wrapper for compute_all_intersections_minibatch, needed for multiprocessing below This was needed because the argument that changes in multiproessing in minibatch_len, and it’s not the leftmost argument, so functools.partial cannot be used

    @@ -2280,7 +2280,7 @@

    Help on Python package (pygtftk)quentin.q.ferre@gmail.com>

    -class pygtftk.stats.intersect.overlap_stats_compute.CombinationExactMapping(all_combis, mapping)
    +class pygtftk.stats.intersect.overlap_stats_compute.CombinationExactMapping(all_combis, mapping)

    A wrapper containing a list of all combinations and a vector giving, for each combination, the ID of all other combinations that are a match for it.

    For example, if working with inexact combinations, [1,1,1] is a match when querying [1,1,0]

    @@ -2297,13 +2297,13 @@

    Help on Python package (pygtftk)
    -class pygtftk.stats.intersect.overlap_stats_compute.Counter(initval=0)
    +class pygtftk.stats.intersect.overlap_stats_compute.Counter(initval=0)

    Multiprocessing-compatible counter that can be incremented.

    -class pygtftk.stats.intersect.overlap_stats_compute.DictionaryWithIndex(data, index, data_default_factory=<function DictionaryWithIndex.<lambda>>, will_store_an_all_overlaps_object=False)
    +class pygtftk.stats.intersect.overlap_stats_compute.DictionaryWithIndex(data, index, data_default_factory=<function DictionaryWithIndex.<lambda>>, will_store_an_all_overlaps_object=False)

    A wrapper allowing to query a dictionary so that an item can also return values from several other items. The dictionary will return concatenated values from several keys when asked for.

    It will return values from itself PLUS everything in the index

    @@ -2331,7 +2331,7 @@

    Help on Python package (pygtftk)
    -class pygtftk.stats.intersect.overlap_stats_compute.HashableArray(input_array)
    +class pygtftk.stats.intersect.overlap_stats_compute.HashableArray(input_array)

    A subclass of NumPy’s ndarray that can be used as dictionary key. A dictionary of such arrays will consume less RAM than a tuple, especially when pickled.

    This is however immutable, and should not be used on arrays that you intend to modify.

    @@ -2341,7 +2341,7 @@

    Help on Python package (pygtftk)
    -class pygtftk.stats.intersect.overlap_stats_compute.SparseListOfLists(starting_index=0)
    +class pygtftk.stats.intersect.overlap_stats_compute.SparseListOfLists(starting_index=0)
    Container for a list of this type :
    [

    [elements], [], [], [], [other_elements], [], [], …

    @@ -2593,7 +2593,7 @@

    Help on Python package (pygtftk)

    The pygtftk.stats.beta module

    -class pygtftk.stats.beta.BetaCalculator(precision=320, use_log=True, itermax=50000, ft_type='Unknown')
    +class pygtftk.stats.beta.BetaCalculator(precision=320, use_log=True, itermax=50000, ft_type='Unknown')

    Computing the beta distribution in Python using mpmath.

    Using routines from the GNU Scientific Library (beta_inc.c): <Copyright (C) 2007 Brian Gough and Copyright (C) 1996, 1997, 1998, 1999, 2000 Gerard Jungman>

    @@ -2717,7 +2717,7 @@

    Help on Python package (pygtftk)quentin.q.ferre@gmail.com>

    -class pygtftk.stats.intersect.modl.tree.Library
    +class pygtftk.stats.intersect.modl.tree.Library

    A tree (or more accurately, graph) based representation of combinations of elements.

    Combinations are represented as tuples. For example, if the possible elements are {A,B,C,D}, the combination A+C is represented as (1,0,1,0).

    Nodes will be assigned under the following principle : each node X that contains all flags of a node Y. @@ -2750,14 +2750,14 @@

    Help on Python package (pygtftk)
    -class pygtftk.stats.intersect.modl.tree.Node(word)
    +class pygtftk.stats.intersect.modl.tree.Node(word)

    Represents a node of the tree. Each node is a word. A word must be a tuple such as (1,1,0,0) meaning A+B if the possibilities are {A,B,C,D}

    -pygtftk.stats.intersect.modl.tree.apply_recursively_to_all_nodes(node, function, global_results, no_duplicates=True, stop_condition=<function <lambda>>)
    +pygtftk.stats.intersect.modl.tree.apply_recursively_to_all_nodes(node, function, global_results, no_duplicates=True, stop_condition=<function <lambda>>)

    General utility function to recursively apply a function to all nodes of a tree. Also pass a global_results dict to be added to.

    Since nodes can have several parents, by default this will remember which nodes @@ -2823,7 +2823,7 @@

    Help on Python package (pygtftk)
    -class pygtftk.stats.intersect.modl.dict_learning.Modl(flags_matrix, multiple_overlap_target_combi_size=- 1, multiple_overlap_max_number_of_combinations=5, nb_threads=1, step_1_factor_allowance=2, error_function=None, smother=True, normalize_words=True, step_2_alpha=None, discretization_threshold=0, step_1_alphas=None)
    +class pygtftk.stats.intersect.modl.dict_learning.Modl(flags_matrix, multiple_overlap_target_combi_size=- 1, multiple_overlap_max_number_of_combinations=5, nb_threads=1, step_1_factor_allowance=2, error_function=None, smother=True, normalize_words=True, step_2_alpha=None, discretization_threshold=0, step_1_alphas=None)

    This class encapsulates the MODL approach :

    Takes as input a matrix of flags, with one flag per intersection, and returns the list of interesting combis.

    @@ -2986,12 +2986,12 @@

    Help on Python package (pygtftk)
    -exception pygtftk.utils.GTFtkError(value)
    +exception pygtftk.utils.GTFtkError(value)

    -exception pygtftk.utils.GTFtkInteractiveError
    +exception pygtftk.utils.GTFtkInteractiveError
    @@ -3676,8 +3676,9 @@

    Help on Python package (pygtftk)
    -

    Table of Contents

    -
    @@ -136,12 +136,16 @@

    Navigation

    $ gtftk mk_matrix -h
@@ -216,19 +236,19 @@ 
    profile
    $ gtftk profile -D -i mini_real_promoter.zip -o profile_prom -pf png -if  example_01.png
- |-- 15:51-WARNING-profile : --group-by not set. Choosing 'bwig'.
+ |-- 0:18-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
- |-- 15:51-WARNING-profile : --group-by not set. Choosing 'bwig'.
+ |-- 0:18-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
- |-- 15:51-WARNING-profile : --group-by not set. Choosing 'bwig'.
+ |-- 0:18-WARNING-profile : --group-by not set. Choosing 'bwig'.
    _images/example_02.png @@ -236,113 +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
- |-- 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
+ |-- 0:18-DEBUG-profile : Using pandas version 1.4.1
+ |-- 0:18-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pandas/__init__.py
+ |-- 0:18-DEBUG-profile : Using numpy version 1.22.2
+ |-- 0:18-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/numpy/__init__.py
+ |-- 0:18-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 0:18-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/plotnine/__init__.py
+ |-- 0:18-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_j7mimur1
+ |-- 0:18-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_j7mimur1
+ |-- 0:18-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_j7mimur1/mini_real_promoter
+ |-- 0:18-INFO-profile : Getting configuration info from input file.
+ |-- 0:18-INFO-profile : Reading transcript file.
+ |-- 0:18-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 0:18-INFO-profile : Checking how many transcripts where found in the transcript list.
+ |-- 0:18-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
+ |-- 0:18-DEBUG-profile : Color order : ['H3K36me3', 'H3K79me', 'H3K4me3']
+ |-- 0:18-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
+ |-- 0:18-INFO-profile : Searching coverage columns.
+ |-- 0:18-INFO-profile : Melting.
+ |-- 0:18-INFO-profile : Ceiling
+ |-- 0:18-INFO-profile : Computing column ordering.
+ |-- 0:18-INFO-profile : Preparing diagram
+ |-- 0:18-INFO-profile : Theming and ordering. Please be patient...
+ |-- 0:18-INFO-profile : Preparing x axis
+ |-- 0:18-INFO-profile : facet_col 2
+ |-- 0:18-INFO-profile : Page width set to 6
+ |-- 0:18-INFO-profile : Page height set to 5.0
+ |-- 0:18-INFO-profile : Saving diagram to file : example_05.png
+ |-- 0:18-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 0:18-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_j7mimur1

    _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
- |-- 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
+ |-- 0:18-DEBUG-profile : Using pandas version 1.4.1
+ |-- 0:18-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pandas/__init__.py
+ |-- 0:18-DEBUG-profile : Using numpy version 1.22.2
+ |-- 0:18-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/numpy/__init__.py
+ |-- 0:18-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 0:18-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/plotnine/__init__.py
+ |-- 0:18-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_5exvj2_e
+ |-- 0:18-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_5exvj2_e
+ |-- 0:18-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_5exvj2_e/mini_real_promoter
+ |-- 0:18-INFO-profile : Getting configuration info from input file.
+ |-- 0:18-INFO-profile : Reading transcript file.
+ |-- 0:18-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 0:18-INFO-profile : Checking how many transcripts where found in the transcript list.
+ |-- 0:18-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
+ |-- 0:18-DEBUG-profile : Color order : ['antisense', 'lincRNA', 'protein_coding']
+ |-- 0:18-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
+ |-- 0:18-INFO-profile : Searching coverage columns.
+ |-- 0:18-INFO-profile : Melting.
+ |-- 0:18-INFO-profile : Ceiling
+ |-- 0:18-INFO-profile : Normalizing (ranging)
+ |-- 0:18-INFO-profile : Computing column ordering.
+ |-- 0:18-INFO-profile : Preparing diagram
+ |-- 0:18-INFO-profile : Theming and ordering. Please be patient...
+ |-- 0:18-INFO-profile : Preparing x axis
+ |-- 0:18-INFO-profile : facet_col 3
+ |-- 0:18-INFO-profile : Page width set to 9
+ |-- 0:18-INFO-profile : Page height set to 2.0
+ |-- 0:18-INFO-profile : Saving diagram to file : example_06.png
+ |-- 0:18-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 0:18-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_5exvj2_e
    _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
- |-- 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
+ |-- 0:18-DEBUG-profile : Using pandas version 1.4.1
+ |-- 0:18-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pandas/__init__.py
+ |-- 0:18-DEBUG-profile : Using numpy version 1.22.2
+ |-- 0:18-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/numpy/__init__.py
+ |-- 0:18-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 0:18-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/plotnine/__init__.py
+ |-- 0:18-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_c1qkptou
+ |-- 0:18-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_c1qkptou
+ |-- 0:18-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_c1qkptou/mini_real_promoter
+ |-- 0:18-INFO-profile : Getting configuration info from input file.
+ |-- 0:18-DEBUG-profile : Color order : ['chr10', 'chr1', 'chr8', 'chr13', 'chr18', 'chr21', 'chr3', 'chrX', 'chr11', 'chr12', 'chr22', 'chr19', 'chr15', 'chr6', 'chr7', 'chr20', 'chr14', 'chr16', 'chr2', 'chr4', 'chr5', 'chr9', 'chr17']
+ |-- 0:18-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']
+ |-- 0:18-INFO-profile : Searching coverage columns.
+ |-- 0:18-INFO-profile : Melting.
+ |-- 0:18-INFO-profile : Ceiling
+ |-- 0:18-INFO-profile : Normalizing (ranging)
+ |-- 0:18-INFO-profile : Computing column ordering.
+ |-- 0:18-INFO-profile : Preparing diagram
+ |-- 0:18-INFO-profile : Theming and ordering. Please be patient...
+ |-- 0:18-INFO-profile : Preparing x axis
+ |-- 0:18-INFO-profile : facet_col 3
+ |-- 0:18-INFO-profile : Page width set to 9
+ |-- 0:18-INFO-profile : Page height set to 2.0
+ |-- 0:18-INFO-profile : Saving diagram to file : example_06b.png
+ |-- 0:18-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 0:18-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_c1qkptou
    _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/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.
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.0-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.
+ |-- 0:18-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/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.
+/Users/puthier/anaconda3/envs/pygtftk_py3.9_dev/lib/python3.9/site-packages/pygtftk-1.6.0-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.
+ |-- 0:19-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
    _images/example_08.png @@ -413,8 +433,9 @@

    profile
    -

    Table of Contents

    -
    @@ -196,9 +196,11 @@

    Writing your own commands
    -

    Previous topic

    -

    The pygtftk.bwig.bw_coverage module

    +

    This Page

    \ No newline at end of file diff --git a/docs/editing.html b/docs/editing.html index 0e19692..aa745e4 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 1.5.3 documentation + Commands from section ‘Editing’ — gtftk 1.6.0 documentation @@ -45,7 +45,7 @@

    Navigation

  • previous |
    • -
  • gtftk 1.5.3 documentation »
    • +
  • gtftk 1.6.0 documentation »
  • Commands from section ‘Editing’
    • @@ -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
- |-- 15:52-INFO-discretize_key : Categories: ['A', 'B']
+ |-- 0:19-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
- |-- 15:52-INFO-discretize_key : Categories: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J']
+ |-- 0:19-INFO-discretize_key : Categories: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J']
   96 A
   83 B
   89 C
@@ -512,8 +512,9 @@ 
    discretize_key
         
    
-  
    Table of Contents
    
-  
      
+  
+  
+  
   
      
     
      This Page
      
     
     
      
     
   
 
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index 641d4c5..0b2f1ff 100644
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index 7a1146e..30982b3 100644
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diff --git a/docs/genindex.html b/docs/genindex.html
index 8b8c3f2..ec85324 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 1.5.3 documentation
+    Index — gtftk 1.6.0 documentation
     
     
     
@@ -36,7 +36,7 @@ 
      Navigation
      
         
    • 
           modules |
      • 
-        
    • gtftk 1.5.3 documentation »
      • 
+        
    • gtftk 1.6.0 documentation »
      • 
         
    • Index
      •  
       
    
     
      
@@ -714,7 +714,7 @@ 
    W
    
   
    Quick search
    
     
    
     
    
-      
+      
       
     
    
     
    
@@ -733,14 +733,14 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • gtftk 1.5.3 documentation »
    • 
+        
  • gtftk 1.6.0 documentation »
    • 
         
  • Index
    •  
       
     
    
     
   
 
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+++ b/docs/gtftk_args.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     
-    Help on gtftk Unix commands — gtftk 1.5.3 documentation
+    Help on gtftk Unix commands — gtftk 1.6.0 documentation
     
     
     
@@ -45,7 +45,7 @@ 
    Navigation
    
         
  • 
           previous |
    • 
-        
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    • 
+        
  • gtftk 1.6.0 documentation »
    • 
         
  • Help on gtftk Unix commands
    •
    @@ -242,8 +242,9 @@

    Command-wide arguments
    @@ -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
- |-- 15:54-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 0:21-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
- |-- 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
+ |-- 0:22-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 0:22-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-1.6.0-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-1.6.0-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-1.6.0-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-1.6.0-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
- |-- 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.
+ |-- 0:23-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 0:23-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
- |-- 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 + ... ])
+ |-- 0:23-WARNING : Converting to bed6 format (simple_07_peaks.bed).
+ |-- 0:23-WARNING : Converting to bed6 format (simple_07_peaks.1.bed).
+ |-- 0:23-WARNING : Converting to bed6 format (simple_07_peaks.2.bed).
+ |-- 0:23-WARNING-ologram : Using only 1 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 0:23-WARNING-ologram : --more-bed-labels was not set, automatically defaulting to --more-bed file names.
+ |-- 0:23-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.
+ |-- 0:23-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.
+ |-- 0:23-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:

    @@ -282,7 +282,7 @@

    Itemset mining detailsFor more details about usage and implementation, please read the notes below.

    Arguments:

    $ gtftk ologram -h
-  Usage: gtftk ologram [-i GTF] [-c TXT] -p BED [-b [more_bed [more_bed ...]]] [-l more_bed_labels] [-kis keep_intact_in_shuffling] [-e BED] [-bi BED] [-u upstream] [-d downstream] [-m more_keys] [-n] [-mo] [-mocs multiple_overlap_target_combi_size] [-monc multiple_overlap_max_number_of_combinations] [-moc multiple_overlap_custom_combis] [-ex] [-k nb_threads] [-s seed] [-mn minibatch_nb] [-ms minibatch_size] [-ma] [-o DIR] [-pw pdf_width] [-ph pdf_height] [-pf pdf_file_alt] [-x] [-y] [-tp tsv_file_path] [-r] [-j {None,nb_intersections_expectation_shuffled,nb_intersections_variance_shuffled,nb_intersections_negbinom_fit_quality,nb_intersections_log2_fold_change,nb_intersections_true,nb_intersections_pvalue,summed_bp_overlaps_expectation_shuffled,summed_bp_overlaps_variance_shuffled,summed_bp_overlaps_negbinom_fit_quality,summed_bp_overlaps_log2_fold_change,summed_bp_overlaps_true,summed_bp_overlaps_pvalue}]
+  Usage: gtftk ologram [-i GTF] [-c TXT] -p BED [-b [more_bed ...]] [-l more_bed_labels] [-kis keep_intact_in_shuffling] [-e BED] [-bi BED] [-u upstream] [-d downstream] [-m more_keys] [-n] [-mo] [-mocs multiple_overlap_target_combi_size] [-monc multiple_overlap_max_number_of_combinations] [-moc multiple_overlap_custom_combis] [-ex] [-k nb_threads] [-s seed] [-mn minibatch_nb] [-ms minibatch_size] [-ma] [-o DIR] [-pw pdf_width] [-ph pdf_height] [-pf pdf_file_alt] [-x] [-y] [-tp tsv_file_path] [-r] [-j {None,nb_intersections_expectation_shuffled,nb_intersections_variance_shuffled,nb_intersections_negbinom_fit_quality,nb_intersections_log2_fold_change,nb_intersections_true,nb_intersections_pvalue,summed_bp_overlaps_expectation_shuffled,summed_bp_overlaps_variance_shuffled,summed_bp_overlaps_negbinom_fit_quality,summed_bp_overlaps_log2_fold_change,summed_bp_overlaps_true,summed_bp_overlaps_pvalue}]
                         [-a {None,nb_intersections_expectation_shuffled,nb_intersections_variance_shuffled,nb_intersections_negbinom_fit_quality,nb_intersections_log2_fold_change,nb_intersections_true,nb_intersections_pvalue,summed_bp_overlaps_expectation_shuffled,summed_bp_overlaps_variance_shuffled,summed_bp_overlaps_negbinom_fit_quality,summed_bp_overlaps_log2_fold_change,summed_bp_overlaps_true,summed_bp_overlaps_pvalue}] [-g pval_threshold] [-z] [-f] [-w] [-q] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -751,8 +751,9 @@ 
    OLOGRAM file structure
       
     
   
 
\ No newline at end of file
diff --git a/docs/search.html b/docs/search.html
index def28f8..8a21367 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 1.5.3 documentation
+    Search — gtftk 1.6.0 documentation
     
     
     
@@ -42,7 +42,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • gtftk 1.5.3 documentation »
    • 
+        
  • gtftk 1.6.0 documentation »
    • 
         
  • Search
    •
    @@ -54,13 +54,14 @@

    Navigation

    Search

    -
    - +

    @@ -70,7 +71,7 @@

    Search

    - +
    @@ -101,14 +102,14 @@

    Navigation

  • modules |
    • -
  • gtftk 1.5.3 documentation »
    • +
  • gtftk 1.6.0 documentation »
  • Search
    • \ No newline at end of file diff --git a/docs/searchindex.js b/docs/searchindex.js index b95ebe3..4872936 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ 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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 \u2018sequence\u2019"],titleterms:{"class":2,The:[2,3],about:0,activ:9,add_exon_nb:11,add_prefix:8,annot:1,apropo:11,argument:9,bash:9,bed_to_gtf:4,beta:2,bw_coverag:3,bwig:3,closest_gen:1,col_from_tab:13,command:[1,4,5,6,7,8,9,11,13,14,15,16],complet:9,content:10,control_list:13,convent:0,converg:1,convers:4,convert:4,convert_ensembl:4,coordin:5,count:11,count_key_valu:11,coverag:6,del_attr:8,detail:14,dict_learn:2,discretize_kei:8,diverg:1,document:10,edit:8,exon_s:1,fasta:2,feature_s:11,file:[0,14],format:0,from:[1,4,5,6,8,11,13,14,15,16],funtion:9,get:9,get_5p_3p_coord:5,get_attr_list:11,get_attr_value_list:11,get_exampl:11,get_feat_seq:16,get_feature_list:11,get_tx_seq:16,gtf:[0,2],gtftk:[2,9,12],h:9,help:[2,9],inform:11,instal:12,intergen:5,intersect:2,intron:5,intron_s:1,itemset:14,join_attr:8,join_multi_fil:8,line:2,list:9,main:9,merge_attr:8,midpoint:5,mine:14,miscellan:13,mk_matrix:6,modl:[2,14],modul:[2,3],multipl:14,name:0,nb_exon:11,nb_transcript:11,negbin_fit:2,note:14,ologram:14,ologram_merge_run:14,ologram_merge_stat:14,ologram_modl_treeifi:14,overlap:[1,14],overlap_stats_comput:2,overlap_stats_shuffl:2,own:7,packag:2,page:10,parser:9,profil:6,pygtftk:[2,3,10,12],python:2,random_list:15,random_tx:15,retriev:11,rm_dup_tss:15,section:[1,4,5,6,8,11,13,14,15,16],select:15,select_by_go:15,select_by_intron_s:15,select_by_kei:15,select_by_loc:15,select_by_max_exon_nb:15,select_by_nb_exon:15,select_by_numeric_valu:15,select_by_regexp:15,select_by_tx_s:15,select_most_5p_tx:15,seqid_list:11,sequenc:16,shift:5,short_long:15,splicing_sit:5,stat:2,structur:14,subroutin:2,support:0,tab:2,tabl:10,tabul:4,test:9,tree:2,tss_dist:11,unix:9,util:2,warn:0,welcom:10,wide:9,write:7,your:7}}) \ No newline at end of file diff --git a/docs/selection.html b/docs/selection.html index 1128d12..1659247 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 1.5.3 documentation + Commands from section ‘selection’ — gtftk 1.6.0 documentation @@ -45,7 +45,7 @@

    Navigation

  • previous |
    • -
  • gtftk 1.5.3 documentation »
    • +
  • gtftk 1.6.0 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	5
+exon	4
+CDS	3

    Arguments:

    @@ -479,10 +479,10 @@

    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	G0001T001
+G0001	G0001T002
 G0002	G0002T001
 G0003	G0003T001
-G0004	G0004T002
+G0004	G0004T001
 G0005	G0005T001
 G0006	G0006T001
 G0007	G0007T001
@@ -742,8 +742,9 @@ 
    short_long
         
    
-  
    Table of Contents
    
-  
     
      
@@ -183,8 +183,9 @@ 
    get_feat_seq
         
    
-  
    Table of Contents
    
-  
      
+  
+  
+  
   
      
     
      This Page
      
     
     
      
     
   
 
\ No newline at end of file
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index b13fcfc..2b02ce3 100644
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index c781d5e..15d9557 100644
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diff --git a/docs/source/conf.py b/docs/source/conf.py
index f68271f..175e523 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -58,10 +58,10 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.5.3'
+version = u'1.6.0'
 
 # The full version, including alpha/beta/rc tags.
-release = u'1.5.3'
+release = u'1.6.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
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index b13fcfc..2b02ce3 100644
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diff --git a/docs/source/treeified.pdf b/docs/source/treeified.pdf
index c781d5e..15d9557 100644
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diff --git a/pygtftk/stats/intersect/overlap_stats_compute.py b/pygtftk/stats/intersect/overlap_stats_compute.py
index 16a5709..6078f07 100644
--- a/pygtftk/stats/intersect/overlap_stats_compute.py
+++ b/pygtftk/stats/intersect/overlap_stats_compute.py
@@ -59,6 +59,12 @@ def pybedtool_to_pythonlist(bed): return bed.to_dataframe().iloc[:, :3].values.t
     beds = tuple([bedA] + bedsB)  # Process all beds at once
     all_chrom = set([line[0] for line in bedA])  # Work only on all chromosomes of bedA
 
+
+    # Sanity check: if all_chrom is an empty list, throw an error
+    if not all_chrom:
+        msg = "Trying to call `find_intersection` with an empty `all_chrom`. This likely means there are no common chromosomes between your query and reference sets, or that one of the query or references is empty."
+        message(msg, type="ERROR")
+
     true_intersection = oc.find_intersection(beds, all_chrom, return_flags=True)
 
     return true_intersection
@@ -1210,7 +1216,11 @@ def stats_multiple_overlap(all_overlaps, bedA, bedsB, all_feature_labels, nb_thr
     ## Transpose the results into `mappings`
     mappings = list()
     for future in futures:
-        mappings.append(future.result())
+
+        try:
+            mappings.append(future.result())
+        except cf.process.BrokenProcessPool:
+            message('A process in the process pool was terminated abruptly while the future was running or pending. This likely means you ran out of RAM. Try restarting the command with fewer threads or smaller minibatches', type="ERROR")
  
     # Unlist mappings
     mappings = [mapping for sublist in mappings for mapping in sublist]
diff --git a/pygtftk/stats/intersect/overlap_stats_shuffling.py b/pygtftk/stats/intersect/overlap_stats_shuffling.py
index 1d1bdc8..641c800 100644
--- a/pygtftk/stats/intersect/overlap_stats_shuffling.py
+++ b/pygtftk/stats/intersect/overlap_stats_shuffling.py
@@ -13,6 +13,7 @@
 import multiprocessing
 import time
 from collections import OrderedDict
+import concurrent.futures as cf
 from concurrent.futures import ProcessPoolExecutor
 
 import numpy as np
@@ -448,10 +449,13 @@ def compute_overlap_stats(bedA, bedsB,
     pool.shutdown() # Release the resources as soon as you are done with those, we won't submit any more jobs to you
 
 
+
     # Transpose the results into all_intersections
     for future in futures:
-        all_intersections += future.result()
-
+        try:
+            all_intersections += future.result()
+        except cf.process.BrokenProcessPool:
+            message('A process in the process pool was terminated abruptly while the future was running or pending. This likely means you ran out of RAM. Try restarting the command with fewer threads or smaller minibatches', type="ERROR")
 
 
 
diff --git a/pygtftk/version.py b/pygtftk/version.py
index 65f7fb7..30dc3d4 100644
--- a/pygtftk/version.py
+++ b/pygtftk/version.py
@@ -1,2 +1,2 @@
-__base_version__='1.5.3'
-__version__='1.5.3'
+__base_version__='1.6.0'
+__version__='1.6.0'
diff --git a/setup.cfg b/setup.cfg
index 8952ab9..e5ee2eb 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,11 +1,11 @@
 [metadata]
 name = pygtftk
-version = 1.5.3
+version = 1.6.0
 author = D. Puthier, F. Lopez and Q. Ferre
 author-email = denis.puthier@univ-amu.fr
 
 [options]
-python_requires = >=3.8,<3.9
+python_requires = >=3.9,<3.10
 
 [egg_info]
 tag_build =
diff --git a/setup.py b/setup.py
index 1b7ad8c..b11f67b 100644
--- a/setup.py
+++ b/setup.py
@@ -54,13 +54,13 @@
 __url_source__ = 'https://github.com/dputhier/pygtftk'
 __url_tracker__ = 'https://github.com/dputhier/pygtftk'
 __keywords__ = 'genomics bioinformatics GTF BED'
-__python_requires__ = '>=3.8,<3.9'
+__python_requires__ = '>=3.9,<3.10'
 __classifiers__ = ("License :: OSI Approved :: MIT License",
                    "Operating System :: MacOS",
                    "Operating System :: POSIX :: Linux",
                    "Development Status :: 4 - Beta",
                    "Environment :: Console",
-                   "Programming Language :: Python :: 3.8",
+                   "Programming Language :: Python :: 3.9",
                    "Intended Audience :: Science/Research",
                    "Natural Language :: English",
                    "Topic :: Scientific/Engineering :: Bio-Informatics",