R

RNANet

Building a dataset following the ProteinNet philosophy, but for RNA

1f847a30 More command line options · by Louis BECQUEY

RNANet

Building a dataset following the ProteinNet philosophy, but for RNA.

We use the Rfam mappings between 3D structures and known Rfam families, using the sequences that are known to belong to an Rfam family (hits provided in RF0XXXX.fasta files from Rfam). Future versions might compute a real MSA-based clusering directly with Rfamseq ncRNA sequences, like ProteinNet does with protein sequences, but this requires a tool similar to jackHMMER in the Infernal software suite, which is not available yet.

This script prepares the dataset from available public data in PDB and Rfam.

Please cite: Coming soon, expect it in 2021

What it does

The script follows these steps:

  • Gets a list of 3D structures containing RNA from BGSU's non-redundant list (but keeps the redundant structures /!\),
  • Asks Rfam for mappings of these structures onto Rfam families (~ a half of structures have a direct mapping, some more are inferred using the redundancy list)
  • Downloads the corresponding 3D structures (mmCIFs)
  • If desired, extracts the right chain portions that map onto an Rfam family

Now, compute the features:

  • Extract the sequence for every 3D chain
  • Downloads Rfamseq ncRNA sequence hits for the concerned Rfam families
  • Realigns Rfamseq hits and sequences from the 3D structures together to obtain a multiple sequence alignment for each Rfam family (using cmalign, except for ribosomal LSU and SSU, where SINA is used)
  • Computes nucleotide frequencies at every position for each alignment
  • For each aligned 3D chain, get the nucleotide frequencies in the corresponding RNA family for each residue

Then, compute the labels:

  • Run DSSR on every RNA structure to get a variety of descriptors per position, describing secondary and tertiary structure. Basepair types annotations include intra-chain and inter-chain interactions.

Finally, export this data from the SQLite database into flat CSV files.

Output files

  • results/RNANet.db is a SQLite database file containing several tables with all the information, which you can query yourself with your custom requests,
  • 3D-folder-you-passed-in-option/datapoints/* are flat text CSV files, one for one RNA chain mapped to one RNA family, gathering the per-position nucleotide descriptors,
  • results/RNANET_datapoints_latest.tar.gz is a compressed archive of the above CSV files (only if you passed the --archive option)
  • path-to-3D-folder-you-passed-in-option/rna_mapped_to_Rfam If you used the --extract option, this folder contains one mmCIF file per RNA chain mapped to one RNA family, without other chains, proteins (nor ions and ligands by default)
  • results/summary_latest.csv summarizes information about the RNA chains
  • results/families_latest.csv summarizes information about the RNA families

If you launch successive executions of RNANet, the previous tar.gz archive and the two summary CSV files are stored in the results/archive/ folder.

Other folders are created and not deleted, which you might want to conserve to avoid re-computations in later runs:

  • path-to-sequence-folder-you-passed-in-option/rfam_sequences/fasta/ contains compressed FASTA files of the homologous sequences used, by Rfam family.
  • path-to-sequence-folder-you-passed-in-option/realigned/ contains families covariance models (*.cm), unaligned list of sequences (*.fa), and multiple sequence alignments in both formats Stockholm and Aligned-FASTA (*.stk and *.afa). Also contains SINA homolgous sequences databases LSU.arb and SSU.arb, and their index files (*.sidx).
  • path-to-3D-folder-you-passed-in-option/RNAcifs/ contains mmCIF structures directly downloaded from the PDB, which contain RNA chains,
  • path-to-3D-folder-you-passed-in-option/annotations/ contains the raw JSON annotation files of the previous mmCIF structures. You may find additional information into them which is not properly supported by RNANet yet.

How to run

Required computational resources

  • CPU: no requirements. The program is optimized for multi-core CPUs, you might want to use Intel Xeons, AMD Ryzens, etc.
  • GPU: not required
  • RAM: 16 GB with a large swap partition is okay. 32 GB is recommended (usage peaks at ~27 GB)
  • Storage: to date, it takes 60 GB for the 3D data (36 GB if you don't use the --extract option), 11 GB for the sequence data, and 7GB for the outputs (5.6 GB database, 1 GB archive of CSV files). You need to add a few more for the dependencies. Pick a 100GB partition and you are good to go. The computation speed is way better if you use a fast storage device (e.g. SSD instead of hard drive, or even better, a NVMe SSD) because of constant I/O with the SQlite database.
  • Network : We query the Rfam public MySQL server on port 4497. Make sure your network enables communication (there should not be any issue on private networks, but maybe you company/university closes ports by default). You will get an error message if the port is not open. Around 30 GB of data is downloaded.

To give you an estimation, our last full run took exactly 12h, excluding the time to download the MMCIF files containing RNA (around 25GB to download) and the time to compute statistics. Measured the 23rd of June 2020 on a 16-core AMD Ryzen 7 3700X CPU @3.60GHz, plus 32 Go RAM, and a 7200rpm Hard drive. Total CPU time spent: 135 hours (user+kernel modes), corresponding to 12h (actual time spent with the 16-core CPU).

Update runs are much quicker, around 3 hours. It depends mostly on what RNA families are concerned by the update.

Dependencies

You need to install:

  • DSSR, you need to register to the X3DNA forum here and then download the DSSR binary on that page.
  • Infernal, to download at Eddylab, several options are available depending on your preferences. Make sure to have the cmalign, esl-alimanip and esl-reformat binaries in your $PATH variable, so that RNANet.py can find them.You don't need the whole X3DNA suite of tools, just DSSR is fine. Make sure to have the x3dna-dssr binary in your $PATH variable so that RNANet.py finds it.
  • SINA, follow these instructions for example. Make sure to have the sina binary in your $PATH.
  • Python >= 3.8, (Unfortunately, python3.6 is no longer supported, because of changes in the multiprocessing and Threading packages. Untested with Python 3.7.*)
  • The following Python packages: python3.8 -m pip install numpy matplotlib pandas biopython psutil pymysql requests sqlalchemy sqlite3 tqdm

Command line

Run ./RNANet.py --3d-folder path/to/3D/data/folder --seq-folder path/to/sequence/data/folder [ - other options ]. It requires solid hardware to run. It takes around around 12 to 15 hours the first time, and 1 to 3h then, tested on a server with 32 cores and 48GB of RAM. The detailed list of options is below:

-h [ --help ]                   Print this help message
--version                       Print the program version

-r 4.0 [ --resolution=4.0 ]     Maximum 3D structure resolution to consider a RNA chain.
-s                              Run statistics computations after completion
--extract                       Extract the portions of 3D RNA chains to individual mmCIF files.
--keep-hetatm=False             (True | False) Keep ions, waters and ligands in produced mmCIF files. 
                                Does not affect the descriptors.
--fill-gaps=True                (True | False) Replace gaps in nt_align_code field due to unresolved residues
                                by the most common nucleotide at this position in the alignment.
--3d-folder=…                   Path to a folder to store the 3D data files. Subfolders will contain:
                                        RNAcifs/                Full structures containing RNA, in mmCIF format
                                        rna_mapped_to_Rfam/     Extracted 'pure' RNA chains
                                        datapoints/             Final results in CSV file format.
--seq-folder=…                  Path to a folder to store the sequence and alignment files.
                                        rfam_sequences/fasta/   Compressed hits to Rfam families
                                        realigned/              Sequences, covariance models, and alignments by family
--no-homology                   Do not try to compute PSSMs and do not align sequences.
                                Allows to yield more 3D data (consider chains without a Rfam mapping).

--all                           Build chains even if they already are in the database.
--only                          Ask to process a specific chain label only
--ignore-issues                 Do not ignore already known issues and attempt to compute them
--update-homologous             Re-download Rfam and SILVA databases, realign all families, and recompute all CSV files
--from-scratch                  Delete database, local 3D and sequence files, and known issues, and recompute.
--archive                       Create a tar.gz archive of the datapoints text files, and update the link to the latest archive

Typical usage:

nohup bash -c 'time ~/Projects/RNANet/RNAnet.py --3d-folder ~/Data/RNA/3D/ --seq-folder ~/Data/RNA/sequences -s --archive' &

Post-computation task: estimate quality

The file statistics.py is supposed to give a summary on the produced dataset. See the results/ folder. It can be run automatically after RNANet if you pass the -s option.

How to further filter the dataset

You may want to build your own sub-dataset by querying the results/RNANet.db file. Here are quick examples using Python3 and its sqlite3 package.

Filter on 3D structure resolution

We need to import sqlite3 and pandas packages first.

import sqlite3
import pandas as pd

Step 1 : We first get a list of chains that are below our favorite resolution threshold (here 4.0 Angströms):

with sqlite3.connect("results/RNANet.db) as connection:
    chain_list = pd.read_sql("""SELECT chain_id, structure_id, chain_name
                                FROM chain JOIN structure 
                                ON chain.structure_id = structure.pdb_id
                                WHERE resolution < 4.0 
                                ORDER BY structure_id ASC;""",
                            con=connection)

Step 2 : Then, we define a template string, containing the SQL request we use to get all information of one RNA chain, with brackets { } at the place we will insert every chain_id. You can remove fields you are not interested in.

req = """SELECT index_chain, old_nt_resnum, position, nt_name, nt_code, nt_align_code, is_A, is_C, is_G, is_U, is_other, freq_A, freq_C, freq_G, freq_U, freq_other, dbn, paired, nb_interact, pair_type_LW, pair_type_DSSR, alpha, beta, gamma, delta, epsilon, zeta, epsilon_zeta, chi, bb_type, glyco_bond, form, ssZp, Dp, eta, theta, eta_prime, theta_prime, eta_base, theta_base,
v0, v1, v2, v3, v4, amlitude, phase_angle, puckering 
FROM 
(SELECT chain_id, rfam_acc from chain WHERE chain_id = {})
NATURAL JOIN re_mapping
NATURAL JOIN nucleotide
NATURAL JOIN align_column;"""

Step 3 : Finally, we iterate over this list of chains and save their information in CSV files:

with sqlite3.connect("results/RNANet.db) as connection:
    for chain in chain_list.iterrows():
        df = pd.read_sql(req.format(chain.chain_id), connection)
        filename = chain.structure_id + '-' + chain.chain_name + '.csv'
        df.to_csv(filename, float_format="%.2f", index=False)

Filter on 3D structure publication date

You might want to get only the dataset you would have had in a past year, to compare yourself with the competitors of a RNA-Puzzles problem for example. We will simply modify the Step 1 above:

with sqlite3.connect("results/RNANet.db) as connection:
    chain_list = pd.read_sql("""SELECT chain_id, structure_id, chain_name
                                FROM chain JOIN structure 
                                ON chain.structure_id = structure.pdb_id
                                WHERE date < "2018-06-01" 
                                ORDER BY structure_id ASC;""",
                            con=connection)

Then proceed to steps 2 and 3.

Filter to avoid chain redundancy when several mappings are available

Some chains can be mapped to two (or more) RNA families, and exist several times in the database. If you want just one example of each RNA 3D chain, use in Step 1:

with sqlite3.connect("results/RNANet.db) as connection:
    chain_list = pd.read_sql("""SELECT UNIQUE chain_id, structure_id, chain_name
                                FROM chain JOIN structure
                                ON chain.structure_id = structure.pdb_id
                                ORDER BY structure_id ASC;""",
                            con=connection)

More about the database structure

To help you design your own requests, here follows a description of the database tables and fields.

Table family, for Rfam families and their properties

  • rfam_acc: The family codename, from Rfam's numbering (Rfam accession number)
  • description: What RNAs fit in this family
  • nb_homologs: The number of hits known to be homologous downloaded from Rfam to compute nucleotide frequencies
  • nb_3d_chains: The number of 3D RNA chains mapped to the family (from Rfam-PDB mappings, or inferred using the redundancy list)
  • nb_total_homol: Sum of the two previous fields, the number of sequences in the multiple sequence alignment, used to compute nucleotide frequencies
  • max_len: The longest RNA sequence among the homologs (in bases)
  • comput_time: Time required to compute the family's multiple sequence alignment in seconds,
  • comput_peak_mem: RAM (or swap) required to compute the family's multiple sequence alignment in megabytes,
  • idty_percent: Average identity percentage over pairs of the 3D chains' sequences from the family

Table structure, for 3D structures of the PDB

  • pdb_id: The 4-char PDB identifier
  • pdb_model: The model used in the PDB file
  • date: The first submission date of the 3D structure to a public database
  • exp_method: A string to know wether the structure as been obtained by X-ray crystallography ('X-RAY DIFFRACTION'), electron microscopy ('ELECTRON MICROSCOPY'), or NMR (not seen yet)
  • resolution: Resolution of the structure, in Angstöms

Table chain, for the datapoints: one chain mapped to one Rfam family

  • chain_id: A unique identifier
  • structure_id: The pdb_id where the chain comes from
  • chain_name: The chain label, extracted from the 3D file
  • pdb_start: Position in the chain where the mapping to Rfam begins (absolute position, not residue number)
  • pdb_end: Position in the chain where the mapping to Rfam ends (absolute position, not residue number)
  • pdb_start: Position in the chain where the mapping to Rfam begins (absolute position, not residue number)
  • pdb_start: Position in the chain where the mapping to Rfam begins (absolute position, not residue number)
  • reversed: Wether the mapping numbering order differs from the residue numbering order in the mmCIF file (eg 4c9d, chains C and D)
  • issue: Wether an issue occurred with this structure while downloading, extracting, annotating or parsing the annotation. Chains with issues are removed from the dataset (Only one known to date: 1gsg, chain T, which is too short)
  • rfam_acc: The family which the chain is mapped to
  • inferred: Wether the mapping has been inferred using the redundancy list (value is 1) or just known from Rfam-PDB mappings (value is 0)
  • chain_freq_A, chain_freq_C, chain_freq_G, chain_freq_U, chain_freq_other: Nucleotide frequencies in the chain
  • pair_count_cWW, pair_count_cWH, ... pair_count_tSS: Counts of the non-canonical base-pair types in the chain (intra-chain counts only)

Table nucleotide, for individual nucleotide descriptors

  • nt_id: A unique identifier
  • chain_id: The chain the nucleotide belongs to
  • index_chain: its absolute position within the portion of chain mapped to Rfam, from 1 to X. This is completely uncorrelated to any gene start or 3D chain residue numbers.
  • nt_position: relative position within the portion of chain mapped to RFam, from 0 to 1
  • old_nt_resnum: The residue number in the 3D mmCIF file (it's a string actually, some contain a letter like '37A')
  • nt_name: The residue type. This includes modified nucleotide names (e.g. 5MC for 5-methylcytosine)
  • nt_code: One-letter name. Lowercase "acgu" letters are used for modified "ACGU" bases.
  • nt_align_code: One-letter name used for sequence alignment. Contains "ACGUN-" only first, and then, gaps may be replaced by the most common letter at this position (default)
  • is_A, is_C, is_G, is_U, is_other: One-hot encoding of the nucleotide base
  • dbn: character used at this position if we look at the dot-bracket encoding of the secondary structure. Includes inter-chain (RNA complexes) contacts.
  • paired: empty, or comma separated list of index_chain values referring to nucleotides the base is interacting with. Up to 3 values. Inter-chain interactions are marked paired to '0'.
  • nb_interact: number of interactions with other nucleotides. Up to 3 values. Includes inter-chain interactions.
  • pair_type_LW: The Leontis-Westhof nomenclature codes of the interactions. The first letter concerns cis/trans orientation, the second this base's side interacting, and the third the other base's side.
  • pair_type_DSSR: Same but using the DSSR nomenclature (Hoogsteen edge approximately corresponds to Major-groove and Sugar edge to minor-groove)
  • alpha, beta, gamma, delta, epsilon, zeta: The 6 torsion angles of the RNA backabone for this nucleotide
  • epsilon_zeta: Difference between epsilon and zeta angles
  • bb_type: conformation of the backbone (BI, BII or ..)
  • chi: torsion angle between the sugar and base (O-C1'-N-C4)
  • glyco_bond: syn or anti configuration of the sugar-base bond
  • v0, v1, v2, v3, v4: 5 torsion angles of the ribose cycle
  • form: if the nucleotide is involved in a stem, the stem type (A, B or Z)
  • ssZp: Z-coordinate of the 3’ phosphorus atom with reference to the5’ base plane
  • Dp: Perpendicular distance of the 3’ P atom to the glycosidic bond
  • eta, theta: Pseudotorsions of the backbone, using phosphorus and carbon 4'
  • eta_prime, theta_prime: Pseudotorsions of the backbone, using phosphorus and carbon 1'
  • eta_base, theta_base: Pseudotorsions of the backbone, using phosphorus and the base center
  • phase_angle: Conformation of the ribose cycle
  • amplitude: Amplitude of the sugar puckering
  • puckering: Conformation of the ribose cycle (10 classes depending on the phase_angle value)

Table align_column, for positions in multiple sequence alignments

  • column_id: A unique identifier
  • rfam_acc: The family's MSA the column belongs to
  • index_ali: Position of the column in the alignment (starts at 1)
  • freq_A, freq_C, freq_G, freq_U, freq_other: Nucleotide frequencies in the alignment at this position

There always is an entry, for each family (rfam_acc), with index_ali = zero and nucleotide frequencies set to freq_other = 1.0. This entry is used when the nucleotide frequencies cannot be determined because of local alignment issues.

Table re_mapping, to map a nucleotide to an alignment column

  • remapping_id: A unique identifier
  • chain_id: The chain which is mapped to an alignment
  • index_chain: The absolute position of the nucleotide in the chain (from 1 to X)
  • index_ali The position of that nucleotide in its family alignment

Contact

louis.becquey@univ-evry.fr