Louis BECQUEY / RNANet

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Louis BECQUEY
4b10a3b2 1 parent 33fafe91

NR class representatives only for rRNA distance matrices

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Showing 5 changed files with 6 additions and 1 deletions
...@@ -23,3 +23,5 @@ scripts/*.sh ...@@ -23,3 +23,5 @@ scripts/*.sh
23 scripts/*.tar 23 scripts/*.tar
24 scripts/measure.py 24 scripts/measure.py
25 scripts/recompute_some_chains.py 25 scripts/recompute_some_chains.py
26 +scripts/convert_rna_jsons.py
27 +scripts/recompute_family.py
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...@@ -8,6 +8,9 @@ FEATURE CHANGES ...@@ -8,6 +8,9 @@ FEATURE CHANGES
8 The LSU and SSU are now aligned with Infernal options '--cpu 10 --mxsize 8192 --mxtau 0.1', which is slow, 8 The LSU and SSU are now aligned with Infernal options '--cpu 10 --mxsize 8192 --mxtau 0.1', which is slow,
9 requires up to 100 GB of RAM, and yields a suboptimal alignment (tau=0.1 is quite bad), but is homogenous with the other families. 9 requires up to 100 GB of RAM, and yields a suboptimal alignment (tau=0.1 is quite bad), but is homogenous with the other families.
10 - The LSU and SSU therefore have defined cm_coords fields, and therefore distance matrices can be computed. 10 - The LSU and SSU therefore have defined cm_coords fields, and therefore distance matrices can be computed.
11 + - Distances matrices are computed on all availables molecules of the family by default, but you can use statistics.py --non-redundant to only
12 + select the equivalence class representatives at a given resolution into account (new option). For storage reasons, rRNAs are always run in
13 + this mode (but this might change in the future : space required is 'only' ~300 GB).
11 - We now provide for download the renumbered (standardised) 3D MMCIF files, the nucleotides being numbered by their "index_chain" in the database. 14 - We now provide for download the renumbered (standardised) 3D MMCIF files, the nucleotides being numbered by their "index_chain" in the database.
12 - We now provide for download the sequences of the 3D chains aligned by Rfam family (without Rfam sequences, which have been removed). 15 - We now provide for download the sequences of the 3D chains aligned by Rfam family (without Rfam sequences, which have been removed).
13 - statistics.py now computes histograms and a density estimation with Gaussian mixture models for a large set of geometric parameters, 16 - statistics.py now computes histograms and a density estimation with Gaussian mixture models for a large set of geometric parameters,
...@@ -23,7 +26,7 @@ FEATURE CHANGES ...@@ -23,7 +26,7 @@ FEATURE CHANGES
23 BUG CORRECTIONS 26 BUG CORRECTIONS
24 - New code file geometric_stats.py 27 - New code file geometric_stats.py
25 - New automation script that starts from scratch 28 - New automation script that starts from scratch
26 - - Many small fixes 29 + - Many small fixes, leading to the support of many previously "known issues"
27 - Performance tweaks 30 - Performance tweaks
28 31
29 TECHNICAL CHANGES 32 TECHNICAL CHANGES
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