Command Line Interface¶
Two Command Line Interface CLI) are accessible after the installation.
- aria2: interface for setting up and running an ARIA project
- ariaec [1]: interface for converting and analyze contact maps
ARIA2¶
Please refer to the ARIA documentation for more explanations.
ARIAEC¶
ariaec COMMAND ARGS [OPTIONS]
Commands
| Name | Short Description |
|---|---|
| setup | Setup ARIA project with EC data |
| bbconv | Translate BBcontacts as distance restraints |
| maplot | Contact map visualisation tool |
| pdbqual | Call PDB quality tools |
| analysis | Analyze results from an ARIA project |
| tbl2xml | Convert TBL restraints in ARIA XML format |
| pdbdist | Extract distance from a culled list of PDBs |
| pdbstat | Statistical analysis of pdbdist results |
| iniconv | Convert a INI file as csv for easy readability |
Options
| Name | Short Description |
|---|---|
-h, --help |
show help message and exit |
Setup¶
Translate contact maps as distance restraints and initialize a new ARIA XML project.
ariaec setup SEQFILE INFILE [INFILE ...] -o OUTPUT_DIRECTORY [OPTIONS] -t INTYPE [INTYPE ...]
Arguments
| Name | Short Description |
|---|---|
seq |
Sequence file [FASTA] |
infile [infile ...] |
Contact or pdb file(s) used to build aria distance restraints |
Options
| Name | Short Description |
|---|---|
-h, --help |
show help message and exit |
-d, --debug |
Increase output verbosity (default: False) |
--nolog |
Don’t generate log files (default: False) |
-o OUTPUT_DIRECTORY, --output OUTPUT_DIRECTORY |
Output directory (default: None) |
-c CONF_FILE, --conf CONF_FILE |
configuration file (default: None) |
-t intype [intype ...] |
Contact Map file format:sup:* |
-d DISTFILE, --distfile DISTFILE |
Pdb or distance matrix iif distance_type set to distfile in conf file, use distances in the given file as target distance to build distance restraints |
-s SSPRED, --ssfile SSPRED |
Secondary structure prediction file. Supported formats are psipred, psipred2, psipred3, ss2 and indextableplus |
-p ARIAPROJECT, --ariaproject ARIAPROJECT |
ARIA project file. This project will be updated with data generated during the ariaec setup call |
-r SEQRANGE, --range SEQRANGE |
Index range if we don’t want tu use the whole sequence and map |
-n REF, --native REF |
Native pdb. Allow TP/FP detection |
--hb HB |
H-bonds contact file (eg: metapsicov.hb) |
--no-filter |
Do not filter contact map |
--extract-all |
Extract data or all data and parameters if an ARIA project is defined with -p option |
--ssidx |
* Accepted contact map formats combining formats supported by ConKit with few supplementary formats: gremlin, pconsc1, pconsc3, pconsc2, bbcontacts, metapsicov_stg1, membrain, metapsicovhb, comsat, casprr, ccmpred, plm, bclcontact, epcmap, evfold, native, pconsc, psicov, freecontact, genericstructure, ncont, plmc, plmdca, metapsicov_stg2, native_full, metapsicov, evcoupling, contactlist, plmev, mmcif, casp, pdb, flib |
Warning
The contact map format option needs to have the same number of format that the number of contact of pdb files. Since this is a greedy option, it needs to be at the end of the command in order to work correctly.
Bbconv¶
Translate BBcontacts as distance restraints which can be used during setup.
ariaec bbconv CONTACTFILE SSPRED SEQ [MSA] [OPTIONS] -t CONTACTYPE
Arguments
| Name | Short description |
|---|---|
contactfile |
contacts file |
sspred |
PSIPRED secondary structure prediction file |
seq |
sequence file [FASTA] |
msa |
MSA [FASTA] used to compute diversityvalue (optional) |
Options
| Name | Description |
|---|---|
-o OUTPUT_DIRECTORY, --output OUTPUT_DIRECTORY |
Output directory (default: None) |
-c CONF_FILE, --conf CONF_FILE |
configuration file (default: None) |
--nolog |
Don’t generate log files (default: False) |
-d, --debug |
Increase output verbosity (default: False) |
-t intype |
Contact Map file format:sup:* |
* Accepted contact map formats combining formats supported by ConKit with few supplementary formats: gremlin, pconsc1, pconsc3, pconsc2, bbcontacts, metapsicov_stg1, membrain, metapsicovhb, comsat, casprr, ccmpred, plm, bclcontact, epcmap, evfold, native, pconsc, psicov, freecontact, genericstructure, ncont, plmc, plmdca, metapsicov_stg2, native_full, metapsicov, evcoupling, contactlist, plmev, mmcif, casp, pdb, flib |
|
Maplot¶
Contactmap analysis and visualisation tool.
ariaec maplot SEQ SSPRED INFILE [INFILE ...] [OPTIONS] -t INTYPE [INTYPE ...] --merge MERGETYPE [MERGETYPE ...]
Arguments
| Name | Short description |
|---|---|
seq |
Sequence file [FASTA] |
sspred |
Secondary structure prediction file |
infile [infile ...] |
Contact or pdb file(s) used to build aria distance restraints |
Options
| Name | Description |
|---|---|
-o OUTPUT_DIRECTORY, --output OUTPUT_DIRECTORY |
Output directory (default: None) |
-c CONF_FILE, --conf CONF_FILE |
configuration file (default: None) |
--nolog |
Don’t generate log files (default: False) |
-d, --debug |
Increase output verbosity (default: False) |
-t intype [intype ...] |
Contact Map file format:sup:* |
--merge mergetype [mergetype ...] |
Merge given contact types with other maps |
--filter |
Use contact list filter and top n contacts selection |
--onlyreport |
Generate only report file |
--no-filter |
Do not filter contact map |
--ssidx |
Use secondary structure index |
--prefix |
Generate prefix for file names |
--prefixname PREFIXNAME |
Prefix name for file names |
* Accepted contact map formats combining formats supported by ConKit with few supplementary formats: gremlin, pconsc1, pconsc3, pconsc2, bbcontacts, metapsicov_stg1, membrain, metapsicovhb, comsat, casprr, ccmpred, plm, bclcontact, epcmap, evfold, native, pconsc, psicov, freecontact, genericstructure, ncont, plmc, plmdca, metapsicov_stg2, native_full, metapsicov, evcoupling, contactlist, plmev, mmcif, casp, pdb, flib |
|
Analysis¶
Supplementary analysis results for a specific iteration from an ARIA project.
ariaec analysis [-h] [-r REF] [-d RESTRAINT] [-p PREFIXNAME] project iteration_path list_name
Arguments
| Name | Short description |
|---|---|
project |
ARIA project file [XML] |
iteration_path |
Iteration path used to run violation analysis |
list_name |
Name of restraint list analyzed in the tbl file |
Options
| Name | Description |
|---|---|
-o OUTPUT_DIRECTORY, --output OUTPUT_DIRECTORY |
Output directory (default: None) |
-c CONF_FILE, --conf CONF_FILE |
configuration file (default: None) |
--nolog |
Don’t generate log files (default: False) |
-d, --debug |
Increase output verbosity (default: False) |
-r REF, --ref REF |
Native pdb. Allow TP/FP detection. |
-d RESTRAINT |
Distance restraint file (XML) used for violation analysis. Otherwise, use restraints of the current iteration |
-p PREFIXNAME, --prefixname PREFIXNAME |
Prefix name for file names |
PDBQual¶
Call PDB quality tools.
ariaec pdbqual [-h] infile [infile ...]
Arguments
| Name | Short description |
|---|---|
infile [infile ...] |
PDB file(s) used to run quality tools with aria API |
TBL2XML¶
Convert TBL restraints in ARIA XML format.
ariaec tbl2xml [-h] molecule.xml list_name infile.tbl [infile.tbl ...]
Arguments
| Name | Short description |
|---|---|
molecule.xml |
ARIA molecule file [XML] |
list_name |
Restraint list name in the tbl file |
infile.tbl |
TBL distance restraint file(s) |
PDBDist¶
Extract distance from a culled list of PDBs.
ariaec pdbdist [-h] [--cullist CULLED_PDB_LIST] [--pdbdir PDB_FOLDER]
Options
| Name | Description |
|---|---|
--cullist CULLED_PDB_LIST |
Culled list of pdb files from PISCES server * |
--pdbdir PDB_FOLDER |
Folder containing pdb file entries |
| * : G. Wangand R. L. Dunbrack, Jr. PISCES: a protein sequence culling server. Bioinformatics, 19:1589-1591, 2003. | |
PDBStat¶
Statistical analysis of pdbdist results.
ariaec pdbstat [-h] [-j N_JOBS] [--min] pdbdists
Arguments
| Name | Short description |
|---|---|
pdbdists |
PDB distance file in csv format |
Options
| Name | Description |
|---|---|
-j N_JOBS |
Number of cpus used to run mixture in parallel. By default, use max of available cpus |
--min |
Compute stats only on a minimized list of atom (CA, CB and 1 SC) |