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Commit d46870ae authored by Fabrice ALLAIN's avatar Fabrice ALLAIN
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*: update tutorial doc & fix logger issue during cache data due to the previous rolleback

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docs/configuration.rst
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Configuration
Configuration
=============
The following tables list the available parameters with the corresponding
......
docs/contents.rst
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......@@ -6,20 +6,8 @@
installation
configuration
usage
contributing
.. toctree::
:maxdepth: 2
:caption: Tutorial
tutorial
.. toctree::
:maxdepth: 2
:caption: Examples
examples/bpt1/bpt1
examples/malecoli/malecoli
contributing
.. toctree::
:maxdepth: 4
......
docs/examples/bpt1/bpt1.rst deleted 100644 → 0
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BPT1_BOVIN structure prediction with EC map
===========================================
Contact map analysis
--------------------
**Input**
.. code-block:: console
(venv) [user@host examples] > ariaec maplot bpt1/data/BPT1_BOVIN.fa bpt1/data/BPT1_BOVIN.indextableplus bpt1/data/BPT1_BOVIN.native.aligned.pdb bpt1/data/BPT1_BOVIN_contacts.gremlin.out -o bpt1/out -t pdb gremlin
**Output**
.. code-block:: console
================================================================================
ARIA Evolutive Contact toolbox
================================================================================
INFO Initialize settings
INFO Making output directories
INFO Reading fasta file /c7/home/fallain/tmp/bpt1/data/bpt1_bovin.fa
INFO Amino acid sequence: FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
INFO Checking if file /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format
INFO Format type correct (indextableplus)
INFO Reading secondary structure file /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN.indextableplus [indextableplus]
INFO Loading ss dist file
INFO Reading distance file /c7/home/fallain/.conda/envs/aria/lib/python2.7/site-packages/aria/conbox/data/ss_dist.txt
INFO Align secondary structure sequence with protein sequence
INFO Reading /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN.native.aligned.pdb file
INFO Updating distance map with pdb file
INFO Generate contact map using contact definition defaultdict(None, {'default_cutoff': 8.0})
INFO Using default cutoff
INFO Reading /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN_contacts.gremlin.out file
INFO Pdb map set as reference
INFO Generate contact map plot (/c7/home/fallain/tmp/bpt1/out/BPT1_BOVIN.maplot.pdf)
INFO Generate map report file (/c7/home/fallain/tmp/bpt1/out/mapreport)
INFO Generate roc file (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.roc.csv)
INFO Generate roc plot (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.roc.pdf)
INFO Generate precall file (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.roc.csv)
INFO Generate precall plot (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.precall.pdf)
INFO Generate contact file (/c7/home/fallain/tmp/bpt1/out/BPT1_BOVIN_contacts_gremlin.contact.txt)
INFO Generate stat file (/c7/home/fallain/tmp/bpt1/out/maplot.contactcmp.csv)
INFO Contact list: [(1, 39), (1, 42), (1, 51), (3, 22), (3, 25), (3, 45), (3, 47), (3, 51), (4, 23), (4, 38), (4, 39), (4, 42), (4, 49), (5, 23), (6, 19), (7, 37), (8, 12), (8, 31), (8, 33), (9, 19), (9, 34), (9, 37), (9, 41), (10, 33), (10, 36), (11, 33), (11, 35), (12, 8), (12, 20), (12, 31), (12, 33), (13, 33), (13, 34), (14, 31), (14, 33), (14, 36), (15, 31), (16, 29), (16, 31), (17, 41), (17, 43), (18, 28), (18, 29), (18, 45), (19, 6), (19, 9), (19, 28), (19, 29), (20, 12), (20, 25), (20, 27), (21, 28), (22, 3), (22, 25), (22, 28), (23, 4), (23, 5), (23, 26), (23, 29), (23, 43), (24, 28), (25, 3), (25, 20), (25, 22), (25, 28), (25, 46), (25, 53), (26, 23), (27, 20), (27, 48), (27, 52), (28, 18), (28, 19), (28, 21), (28, 22), (28, 24), (28, 25), (29, 16), (29, 18), (29, 19), (29, 23), (30, 33), (30, 37), (30, 38), (31, 8), (31, 12), (31, 14), (31, 15), (31, 16), (32, 37), (32, 38), (32, 40), (32, 41), (33, 8), (33, 10), (33, 11), (33, 12), (33, 13), (33, 14), (33, 30), (34, 9), (34, 13), (34, 37), (35, 11), (36, 10), (36, 14), (36, 39), (36, 50), (37, 7), (37, 9), (37, 30), (37, 32), (37, 34), (37, 41), (38, 4), (38, 30), (38, 32), (38, 41), (39, 1), (39, 4), (39, 36), (40, 32), (41, 9), (41, 17), (41, 32), (41, 37), (41, 38), (42, 1), (42, 4), (43, 17), (43, 23), (43, 47), (44, 47), (45, 3), (45, 18), (45, 49), (46, 25), (46, 49), (46, 50), (47, 3), (47, 43), (47, 44), (47, 51), (48, 27), (48, 52), (49, 4), (49, 45), (49, 46), (49, 53), (50, 36), (50, 46), (50, 53), (51, 1), (51, 3), (51, 47), (52, 27), (52, 48), (53, 25), (53, 49), (53, 50)]
INFO Generate contact map plot (/c7/home/fallain/tmp/bpt1/out/.maplot.pdf)
INFO Generate contact file (/c7/home/fallain/tmp/bpt1/out/BPT1_BOVIN_native_aligned.contact.txt)
Setup
-----
.. code-block:: console
> ariaec -o examples/bpt1/out -c examples/bpt1/data/config.ini setup examples/bpt1/data/BPT1_BOVIN.fa examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out -t gremlin -s examples/bpt1/data/BPT1_BOVIN.indextableplus
**Output**
.. code-block:: console
================================================================================
ARIA Evolutive Contact toolbox
================================================================================
INFO Initialize settings
INFO Updating settings according to config file
INFO Making output directories
reading FASTA file examples/bpt1/data/BPT1_BOVIN.fa
INFO Amino acid sequence: FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
INFO Checking if file examples/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format
INFO Format type correct (indextableplus)
INFO Reading secondary structure file examples/bpt1/data/BPT1_BOVIN.indextableplus [indextableplus]
INFO Loading ss dist file
INFO Reading distance file aria/conbox/data/ss_dist.txt
INFO Align secondary structure sequence with protein sequence
INFO Reader focused on file(s) ['examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out'] ['gremlin']
INFO Reading examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out file
INFO Filtering gremlin contact map
INFO ...Position filter
INFO Removed 21 contacts.
INFO ...Conservation filter
INFO Conservation filter only works with indextableplus files !
INFO ...Secondary structure clash filter
INFO Removed 1 contacts.
INFO ...Disulfure bridge unicity filter
INFO Removed 11 contacts.
INFO Setting contact number with treshold 1.0
INFO Update gremlin maplot
INFO Update gremlin scoremap
INFO Select top 53 contacts according to scoremap
writing to the file: examples/bpt1/out/etc/BPT1_BOVIN.seq
INFO Load molecule file and convert it into xml format
MESSAGE [SequenceList]: reading sequence examples/bpt1/out/etc/BPT1_BOVIN.seq
reading examples/bpt1/out/etc/BPT1_BOVIN.seq
INFO Writing tbl files ...
INFO Dihedral restraints for secondary structures (examples/bpt1/out/tbl/BPT1_BOVIN_dihed.tbl)
INFO Secondary structure restraints (examples/bpt1/out/tbl/BPT1_BOVIN_ssdist.tbl)
INFO Helix bond restraints (examples/bpt1/out/tbl/BPT1_BOVIN_hbond.tbl)
INFO Writing gremlin ARIA XML distance restraints
INFO Using contact scores as selection criteria
INFO Selecting 53 contacts
INFO 0%| | 0/53 [00:00<?, ?it/s]
INFO 100%|##########| 53/53 [00:00<00:00, 1485.97it/s]
INFO Write 53 xml distance restraints in examples/bpt1/out/xml/BPT1_BOVIN_gremlin.xml
INFO Loading aria template file aria_project_v2.3.4.xml
INFO Directory /tmp/BPT1_BOVIN/gremlin doesn't exist.
INFO Create new directory /tmp/BPT1_BOVIN/gremlin
INFO Writing ARIA project file (examples/bpt1/out/ariaproject.xml)
INFO Generate contact file (examples/bpt1/out/etc/BPT1_BOVIN_gremlin_filtered.contact.txt)
ARIA Setup
----------
.. code-block:: console
> aria2 -s examples/bpt1/out/ariaproject.xml
**Output**
.. code-block:: console
ARIA Version 2.3.2. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping, and Michael Nilges.
If you use this software, please quote the following reference(s):
Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR
structure calculation. Bioinformatics 23:381-382
Loading project "ariaproject.xml"...
Setting-up examples/bpt1/out/ariaproject.xml (run: 1)
MESSAGE [Project]: Protocols copied.
MESSAGE [Project]: Directory tree created.
MESSAGE [Project]: Copying data files into local data-directory...
Done.
For running ARIA: aria2 examples/bpt1/out/ariaproject.xml
ARIA Run
--------
.. code-block:: console
> aria2 examples/bpt1/out/ariaproject.xml
**Output**
.. code-block:: console
ARIA Version 2.3.2. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping, and Michael Nilges.
If you use this software, please quote the following reference(s):
Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR
structure calculation. Bioinformatics 23:381-382
Loading project "ariaproject.xml"...
MESSAGE [Project]: Temporary directory has been set to /tmp/BPT1_BOVIN/gremlin/
aria_temp.tmpw0BTnZ1524489605
MESSAGE [Project]: Host list check has been disabled.
MESSAGE [Project]: -------------------- Reading data --------------------
MESSAGE [Project]: Cache is enabled.
MESSAGE [Project]: Cache file does not exist. Creating new file.
MESSAGE [Project]: Reading molecule definition examples/bpt1/out/run1/data/
sequence/BPT1_BOVIN.xml.
MESSAGE [Project]: Data files read.
MESSAGE [Project]: Data files cached.
MESSAGE [Project]: ------------------- Filtering input data -------------------
MESSAGE [NOESYSpectrumFilter.TP]: Spectrum filter report written to file "
examples/bpt1/out/run1/data/spectra/
peak_list.filtered"
MESSAGE [Project]: ---------------- Preparing structure engine ----------------
MESSAGE [CNS]: Sequence PDB-file written.
MESSAGE [CNS]: PSF-file has been created.
MESSAGE [CNS]: Template PDB-file has been created.
MESSAGE [Project]: Starting ARIA main protocol on Mon Apr 23 15:20:31 2018
MESSAGE [Project]: -------------------- Assigning spectra --------------------
MESSAGE [Protocol]: ---------------------- Iteration 0 -----------------------
MESSAGE [Protocol]: Calibrating spectrum "gremlin"...
MESSAGE [Job]: Submitted batch job 18432586 (run_cns_99)
MESSAGE [Job]: Submitted batch job 18432587 (run_cns_96)
...
MESSAGE [CNS]: Starting analyses...
MESSAGE [CNS]: Analyses done. Results are in examples/bpt1/out/run1/structures/
it8/analysis
MESSAGE [Project]: Temporary directory "tmp/BPT1_BOVIN/gremlin/aria_temp.tmpRNyO3Q1524493463" removed.
MESSAGE [Project]: ARIA run completed at Mon Apr 23 17:25:08 2018
Violation analysis
------------------
Violation analysis for the last iteration
.. code-block:: console
> ariaec -c examples/bpt1/data/config.ini -o examples/bpt1/out/run1/structures/it8 analysis -r examples/bpt1/data/BPT1_BOVIN.native.aligned.pdb examples/bpt1/out/ariaproject.xml examples/bpt1/out/run1/structures/it8 gremlin
**Output**
.. code-block:: console
================================================================================
ARIA Evolutive Contact toolbox
================================================================================
INFO Initialize settings
INFO Updating settings according to config file
INFO Reading distance restraints file(s)
INFO Wrote 143 xml distance restraints in examples/bpt1/out/run1/structures/it0/unambig_restraints.xml
INFO Reading native structure
MESSAGE [StructureEnsemble]: Reading PDB files ...
MESSAGE [StructureEnsemble]: PDB files read.
INFO Reading structure ensemble(s)
INFO Clusters found in this iteration, compute analysis foreach generated cluster ensemble
INFO Violation analysis
INFO Writing violation analysis of clust 0 examples/bpt1/out/run1/structures/it0/violations.csv file
INFO Writing violation analysis of clust 1 examples/bpt1/out/run1/structures/it0/violations.csv file
MESSAGE [StructureEnsemble]: Reading PDB files ...
MESSAGE [StructureEnsemble]: PDB files read.
.. _CNS: http://cns-online.org/v1.3/
.. _ARIA: http://aria.pasteur.fr
.. _GREMLIN: http://gremlin.bakerlab.org/gremlin_faq.php
.. raw:: html
<style>
.panel {
padding: 0 18px;
background-color: white;
max-height: 0;
overflow: hidden;
transition: max-height 0.2s ease-out;
}
</style>
<script>
var acc = document.getElementsByClassName("accordion");
var i;
for (i = 0; i < acc.length; i++) {
acc[i].addEventListener("click", function() {
this.classList.toggle("active");
var panel = this.nextElementSibling;
if (panel.style.maxHeight){
panel.style.maxHeight = null;
} else {
panel.style.maxHeight = panel.scrollHeight + "px";
}
});
}
</script>
\ No newline at end of file
docs/examples/malecoli/malecoli.rst deleted 100644 → 0
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MALE_ECOLI folding with EC and NMR restraints
=============================================
We show an example of structure calculation combining sparse NMR data and
evolutionary restraints from EVFold_ server. The files related to this example
can be found in the ``docs`` folder or :download:`here <../../examples.tar.gz>`
Setup
-----
.. warning::
We actually need an ARIA project file in the setup step if we want to mix
evolutionary with experimental restraints. Only the data section is
conserved actually. You still needs to give a configuration file for the
other project parameters.
.. code-block:: console
> ariaec setup examples/malecoli/data/MALE_ECOLI.fa examples/malecoli/data/MALE_ECOLI_contacts.evfold.out -t plmev -o examples/malecoli/out -c examples/malecoli/data/config.ini -p examples/malecoli/data/ariaproject_nmr.xml
**Output**
.. code-block:: console
================================================================================
ARIA Evolutive Contact toolbox
================================================================================
INFO Initialize settings
INFO Updating settings according to config file
INFO Making output directories
reading FASTA file examples/malecoli/data/MALE_ECOLI.fa
INFO Amino acid sequence: KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK
INFO Reader focused on file(s) ['examples/malecoli/data/MALE_ECOLI_contacts.evfold.out'] ['evcoupling']
INFO Conkit doesn't support evcoupling
INFO Checking if file examples/malecoli/data/MALE_ECOLI_contacts.evfold.out correspond to evcoupling format
INFO Format type correct
INFO Reading examples/malecoli/data/MALE_ECOLI_contacts.evfold.out file
INFO Loading contact file
INFO Filtering evcoupling contact map
INFO ...Position filter
INFO ...Conservation filter
WARNING No conservation information. Can't use related filter
INFO ...Secondary structure clash filter
WARNING No secondary structure information. Can't use secondary structure filter
INFO ...Disulfure bridge unicity filter
INFO Setting contact number with treshold 1.0
INFO Update evcoupling maplot
INFO Update evcoupling scoremap
INFO Select top 370 contacts according to scoremap
writing to the file: examples/malecoli/out/etc/MALE_ECOLI.seq
INFO Load molecule file and convert it into xml format
MESSAGE [SequenceList]: reading sequence examples/malecoli/out/etc/
MALE_ECOLI.seq
reading examples/malecoli/out/etc/MALE_ECOLI.seq
INFO Writing tbl files ...
INFO Writing evcoupling ARIA XML distance restraints
INFO Using contact scores as selection criteria
INFO Selecting 370 contacts
INFO 0%| | 0/370 [00:00<?, ?it/s]
INFO 100%|##########| 370/370 [00:00<00:00, 855.92it/s]
INFO Write 370 xml distance restraints in examples/malecoli/out/xml/MALE_ECOLI_evcoupling.xml
INFO Loading aria template file aria/conbox/templates/aria_project_v2.3.4.xml
INFO Directory /tmp/MALE_ECOLI/evcoupling doesn't exist.
INFO Create new directory /tmp/MALE_ECOLI/evcoupling
WARNING No output file defined in host_command. You should add the output option (-o) to your command.
INFO Writing ARIA project file (examples/malecoli/out/ariaproject.xml)
INFO Reading ARIA project file
INFO Update spectrum data in project
INFO Update sequence data in project
INFO Update dihedrals data in project
INFO Update rdcs data in project
INFO Update rdcs annealing parameters
INFO Writing new ARIA xml file (examples/malecoli/out/ariaproject.xml)
INFO Generate contact file (examples/malecoli/out/etc/MALE_ECOLI_evcoupling_filtered.contact.txt)
.. _EVFold: http://evfold.org/evfold-web/evfold.do
\ No newline at end of file
docs/tutorial.rst
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========
Tutorial
========
.. note::
Even if data for this tutorial are already in the ``docs/examples`` folder. You
......@@ -113,15 +117,145 @@ infrastructure of the project.
Running ARIA
------------
We use `aria2` command without the ``-s`` flag to launch structure calculations
.. code-block:: console
(venv) [user@host tmp] > aria2 --no-test bpt1/out/ariaproject.xml
.. .......................................................................... ..
.. ARIA -- Ambiguous Restraints for Iterative Assignment ..
.. ..
.. A software for automated NOE assignment ..
.. ..
.. Version 2.3 ..
.. ..
.. ..
.. Copyright (C) Benjamin Bardiaux, Michael Habeck, Therese Malliavin, ..
.. Wolfgang Rieping, and Michael Nilges ..
.. ..
.. All rights reserved. ..
.. ..
.. NO WARRANTY. This software package is provided 'as is' without warranty of ..
.. any kind, expressed or implied, including, but not limited to the implied ..
.. warranties of merchantability and fitness for a particular purpose or ..
.. a warranty of non-infringement. ..
.. ..
.. Distribution of substantively modified versions of this module is ..
.. prohibited without the explicit permission of the copyright holders. ..
.. ..
.. .......................................................................... ..
Loading project "ariaproject.xml"...
INFO [Project]: Temporary directory has been set to /tmp/BPT1_BOVIN/gremlin/
aria_temp.tmpAVTAwy1562832135
INFO [Project]: Host list check has been disabled.
INFO [Project]: -------------------- Reading data --------------------
INFO [Project]: Cache is enabled.
INFO [Project]: Cache file does not exist. Creating new file.
INFO [Project]: Reading molecule definition /tmp/bpt1/out/
run1/data/sequence/BPT1_BOVIN.xml.
INFO [Project]: Data files read.
INFO [Project]: Data files cached.
INFO [Project]: ------------------- Filtering input data -------------------
INFO [NOESYSpectrumFilter.TP]: Spectrum filter report written to file "/tmp
/bpt1/out/run1/data/spectra/peak_list.filtered"
INFO [Project]: ---------------- Preparing structure engine ----------------
INFO [CNS]: Sequence PDB-file written.
INFO [CNS]: PSF-file has been created.
INFO [CNS]: Template PDB-file has been created.
INFO [Project]: Starting ARIA main protocol on ...
INFO [Project]: -------------------- Assigning spectra --------------------
INFO [Protocol]: ---------------------- Iteration 0 -----------------------
INFO [Protocol]: Calibrating spectrum "gremlin"...
INFO [Protocol]: Waiting for completion of structure calculation...
...
INFO [Project]: ARIA run completed at ...
.. warning::
Most of the time the ``--no-test`` flags needs to be activated
Most of the time the ``--no-test`` flags needs to be activated in order to
disables the initial dry run of the commands (specified in the host
list) used to launch a structure calculation. Those dry run are not
compatible with several hosts.
Structure calculation with EC & NMR restraints
==============================================
Another possibility is to use an already existing ARIA project with NMR
restraints and use ``ariaec setup`` with the ``-p`` flag to update it with EC
restraints.
.. code-block:: console
(venv) [user@host tmp] > ariaec setup malecoli/data/MALE_ECOLI.fa malecoli/data/MALE_ECOLI_contacts.evfold.out -t evcoupling -o malecoli/out -c malecoli/data/config.ini -p malecoli/data/ariaproject_nmr.xml
================================================================================
ARIA Evolutive Contact toolbox
================================================================================
INFO Initialize settings
INFO Updating settings according to config file
INFO Making output directories
INFO Reading fasta file /c7/home/fallain/tmp/malecoli/data/male_ecoli.fa
INFO Amino acid sequence: KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK
INFO The file format evcoupling is not supported by the conkit plugin. Switching to homemade parsers.
INFO Checking if file /c7/home/fallain/tmp/malecoli/data/MALE_ECOLI_contacts.evfold.out correspond to our definition of evcoupling format
INFO Reading /c7/home/fallain/tmp/malecoli/data/MALE_ECOLI_contacts.evfold.out file
INFO Loading contact file
INFO Alignment of sequence in contact file (evcoupling) with reference (MALE_ECOLI.fa)
****TGARILALSALTTMMFSASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKY***DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLE*YLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRI--
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||.||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
--------------------------KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK
Score=364
WARNING Found a shift of 26 residues in positions given within contact list
INFO Update index in contact list and remove unassigned contacts
INFO Remove contacts outside sequence bonds
INFO Filtering evcoupling contact map
INFO ...Position filter
INFO ...Conservation filter
WARNING No conservation information. Can't use related filter
INFO ...Secondary structure clash filter
WARNING No secondary structure information. Can't use secondary structure filter
INFO ...Disulfure bridge unicity filter
INFO Setting contact number with treshold 1.0
INFO Update evcoupling maplot
INFO Update evcoupling scoremap
INFO Select top 370 contacts according to scoremap
writing to the file: /c7/home/fallain/tmp/malecoli/out/etc/MALE_ECOLI.seq
INFO Load molecule file and convert it into xml format
INFO [SequenceList]: reading sequence /c7/home/fallain/tmp/malecoli/out/etc/
MALE_ECOLI.seq
reading /c7/home/fallain/tmp/malecoli/out/etc/
MALE_ECOLI.seq
INFO Writing tbl files ...
INFO Writing evcoupling ARIA XML distance restraints
INFO Using contact scores as selection criteria
INFO Selecting 370 contacts
INFO 0%| | 0/370 [00:00<?, ?it/s]
INFO 100%|##########| 370/370 [00:00<00:00, 1245.07it/s]
INFO Write 370 xml distance restraints in /c7/home/fallain/tmp/malecoli/out/xml/MALE_ECOLI_evcoupling.xml
INFO Loading aria template file /c7/home/fallain/Projects/ariaec/src/ariaec/src/aria/conbox/templates/aria_project_v2.3.4.xml
INFO Directory /baycells/scratch/fallain/tmp/MALE_ECOLI/evcoupling doesn't exist.
INFO Create new directory /baycells/scratch/fallain/tmp/MALE_ECOLI/evcoupling
INFO Writing ARIA project file (/c7/home/fallain/tmp/malecoli/out/ariaproject.xml)
INFO Reading ARIA project file
INFO Update spectrum data in project
INFO Update sequence data in project
INFO Update dihedrals data in project
INFO Update rdcs data in project
INFO Update rdcs annealing parameters
INFO Writing new ARIA xml file (/c7/home/fallain/tmp/malecoli/out/ariaproject.xml)
INFO Generate contact file (/c7/home/fallain/tmp/malecoli/out/etc/MALE_ECOLI_evcoupling_filtered.contact.txt)
.. warning::
The ARIA project file is mandatory during the setup step if we want to mix
evolutionary with experimental restraints. Only the data section is
conserved actually. You still needs to give a configuration file for the
other project parameters.
Analysis
========
......@@ -226,3 +360,34 @@ file with the path to the executable of the quality tool.
Violation analysis
------------------
Additionally, we can use the ``ariaec analysis`` command to generate
supplementary analysis file for a given ARIA iteration.
.. code-block:: console
(venv) [user@host tmp] > ariaec analysis bpt1/out/ariaproject.xml bpt1/out/run1/structures/it8 gremlin -r bpt1/data/BPT1_BOVIN.native.aligned.pdb -c bpt1/data/config.ini -o bpt1/out/run1/structures/it8
================================================================================
ARIA Evolutive Contact toolbox
================================================================================
INFO Initialize settings
INFO Updating settings according to config file
INFO Ensemble analysis will be done on restraints and ensemble from it7 with violation criteria of it8
INFO Reading distance restraints file(s)
INFO Reading native structure
INFO [StructureEnsemble]: Reading PDB files ...
INFO [StructureEnsemble]: PDB files read.
INFO Reading structure ensemble(s)
INFO Clusters found in this iteration, compute analysis foreach generated cluster ensemble
INFO [StructureEnsemble]: Reading PDB files ...
INFO [StructureEnsemble]: PDB files read.
INFO [StructureEnsemble]: Reading PDB files ...
INFO [StructureEnsemble]: PDB files read.
INFO Violation analysis
INFO Writing violation analysis of clust 0 /tmp/bpt1/out/run1/structures/it8/violations.csv file
INFO Writing violation analysis of clust 1 /tmp/bpt1/out/run1/structures/it8/violations.csv file
INFO [StructureEnsemble]: Reading PDB files ...
INFO [StructureEnsemble]: PDB files read.
src/aria/core/ariabase.py
View file @ d46870ae
......@@ -258,8 +258,8 @@ class AriaBaseClass:
d['logger'] = logging.getLogger(self.__module__)
self.__dict__.update(d)
if self.__class__.display_debug:
logging.getLogger().setLevel(logging.DEBUG)
# if self.__class__.display_debug:
# logging.getLogger().setLevel(logging.DEBUG)
def __getstate__(self):
"""
......
src/aria/core/tools.py
View file @ d46870ae
......@@ -84,10 +84,13 @@ def Dump(this, filename, mode='w', as_string=0, gzip=0):
# Issues if we try to dump the logger since it contains the log file instance
# TODO: do better testing
def remove_logger(this):
if hasattr(elt, "items"):
for foo in elt.items():
if hasattr(this, "items"):
for foo in this.items():
if hasattr(foo, "logger"):
delattr(foo, "logger")
else:
if hasattr(this, "logger"):
delattr(this, "logger")
if type(this) == list:
for elt in this:
......
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