MIToS' Scripts
The MIToS_Scripts.jl package offers a set of easy-to-use scripts for command-line execution without requiring Julia coding. It includes several scripts designed for various bioinformatics tasks, such as measuring estimating residue conservation and inter-residue coevolution, calculating distances between residues in a protein structure, and more.
Installation
To install MIToS_Scripts.jl, you only need Julia 1.9 or later installed on your system. Executing julia in the terminal to open the Julia REPL, and finally, run the following command:
using Pkg
Pkg.add(url = "https://github.com/MIToSOrg/MIToS_Scripts.jl")Then, you can get the location of the installed scripts by running the following command:
using MIToS_Scripts
scripts_folder = joinpath(pkgdir(MIToS_Scripts), "scripts")You can run them from that location. Alternatively, you can add the location to your PATH environment variable, or copy the scripts to a folder already in your PATH to run them from anywhere.
Usage
You can execute each provided script from your command line. For example, to run the Buslje09.jl script—if you are located in the folder where it is the scripts—use:
julia Buslje09.jl input_msa_fileRefer to the documentation of each script for specific usage instructions; you can access it by running the script with the --help or -h flag:
julia Buslje09.jl -hScripts
Buslje09.jl
usage: Buslje09.jl [-l] [-o OUTPUT] [-p PARALLEL] [-f FORMAT]
[-L LAMBDA] [-c] [-i THRESHOLD] [-g MAXGAP] [-a]
[-s SAMPLES] [-G] [-F] [--version] [-h] [FILE]
This takes a MSA file as input. It calculates and saves on
*.buslje09.csv a Z score and a corrected MI/MIp as described on:
Buslje, C. M., Santos, J., Delfino, J. M., & Nielsen, M. (2009).
Correction for phylogeny, small number of observations and data
redundancy improves the identification of coevolving amino acid pairs
using mutual information. Bioinformatics, 25(9), 1125-1131.
positional arguments:
FILE File name. If it is not used, the script reads
from STDIN.
optional arguments:
-l, --list The input is a list of file names. If -p is
used, files will be processed in parallel.
-o, --output OUTPUT Name of the output file. Output will be gzip
if the extension is ".gz". If it starts with a
dot, the name is used as a suffix or extension
of the input filename. If it ends with a dot,
is used as a prefix. If the output name starts
and ends with dots, it's used as an interfix
before the extension.If a single file is used
and there is not a file name (STDIN), the
output will be print into STDOUT, unless a
output filename is used. You can use "STDOUT"
to force print into STDOUT. STDOUT can not be
use with --list. (default: ".buslje09.csv")
-p, --parallel PARALLEL
Number of worker processes. (type: Int64,
default: 1)
-f, --format FORMAT Format of the MSA: Stockholm, Raw or FASTA
(default: "Stockholm")
-L, --lambda LAMBDA Low count value (type: Float64, default: 0.05)
-c, --clustering Sequence clustering (Hobohm I)
-i, --threshold THRESHOLD
Percent identity threshold for sequence
clustering (Hobohm I) (type: Float64, default:
62.0)
-g, --maxgap MAXGAP Maximum fraction of gaps in positions included
in calculation (type: Float64, default: 0.5)
-a, --apc Use APC correction (MIp)
-s, --samples SAMPLES
Number of samples for Z-score (type: Int64,
default: 100)
-G, --usegap Use gaps on statistics
-F, --fixedgaps Fix gaps positions for the random samples
--version show version information and exit
-h, --help show this help message and exit
MIToS 3.0.6
Bioinformatics Unit
Leloir Institute Foundation
Av. Patricias Argentinas 435, CP C1405BWE, Buenos Aires, ArgentinaBLMI.jl
usage: BLMI.jl [-l] [-o OUTPUT] [-p PARALLEL] [-f FORMAT] [-b BETA]
[-i THRESHOLD] [-g MAXGAP] [-a] [-s SAMPLES] [-F]
[--version] [-h] [FILE]
This takes a MSA file as input. Calculates and saves on *.BLMI.csv a Z
score and a corrected MI/MIp. The script uses BLOSUM62 based pseudo
frequencies and sequences clustering (Hobohm I).
positional arguments:
FILE File name. If it is not used, the script reads
from STDIN.
optional arguments:
-l, --list The input is a list of file names. If -p is
used, files will be processed in parallel.
-o, --output OUTPUT Name of the output file. Output will be gzip
if the extension is ".gz". If it starts with a
dot, the name is used as a suffix or extension
of the input filename. If it ends with a dot,
is used as a prefix. If the output name starts
and ends with dots, it's used as an interfix
before the extension.If a single file is used
and there is not a file name (STDIN), the
output will be print into STDOUT, unless a
output filename is used. You can use "STDOUT"
to force print into STDOUT. STDOUT can not be
use with --list. (default: ".BLMI.csv")
-p, --parallel PARALLEL
Number of worker processes. (type: Int64,
default: 1)
-f, --format FORMAT Format of the MSA: Stockholm, Raw or FASTA
(default: "Stockholm")
-b, --beta BETA β for BLOSUM62 pseudo frequencies (type:
Float64, default: 8.512)
-i, --threshold THRESHOLD
Percent identity threshold for sequence
clustering (Hobohm I) (type: Float64, default:
62.0)
-g, --maxgap MAXGAP Maximum fraction of gaps in positions included
in calculation (type: Float64, default: 0.5)
-a, --apc Use APC correction (MIp)
-s, --samples SAMPLES
Number of samples for Z-score (type: Int64,
default: 50)
-F, --fixedgaps Fix gaps positions for the random samples
--version show version information and exit
-h, --help show this help message and exit
MIToS 3.0.6
Bioinformatics Unit
Leloir Institute Foundation
Av. Patricias Argentinas 435, CP C1405BWE, Buenos Aires, ArgentinaConservation.jl
usage: Conservation.jl [-l] [-o OUTPUT] [-p PARALLEL] [-f FORMAT] [-c]
[-i THRESHOLD] [--version] [-h] [FILE]
This takes a MSA file as input and it calculates and saves on
*.conservation.csv the Shannon entropy (H) and Kullback-Leibler
divergence (KL) values for each column (Johansson and Toh 2010).
It is possible to do a sequence clustering using the Hobohm I
algorithm to avoid the effect of sequence redundancy in the
conservation scores. Each sequence in a cluster is weighted using the
inverse of the number of elements in that cluster.
Shannon entropy is a common measure of the residue variability of a
particular MSA column. For each column, we consider the frequency of
the 20 natural protein residues. This uses the Euler's number e as the
base of the logarithm, so the entropy is measured in nats.
The Kullback-Leibler divergence, also called relative entropy, is a
measure of residue conservation. It measures how much a probability
distribution differs from a background distribution. In particular,
this implementation measures the divergence between the residue
distribution of an MSA column and the probabilities derived from the
BLOSUM62 substitution matrix.
Johansson, F., Toh, H., 2010. A comparative study of conservation and
variation scores. BMC Bioinformatics 11, 388.
positional arguments:
FILE File name. If it is not used, the script reads
from STDIN.
optional arguments:
-l, --list The input is a list of file names. If -p is
used, files will be processed in parallel.
-o, --output OUTPUT Name of the output file. Output will be gzip
if the extension is ".gz". If it starts with a
dot, the name is used as a suffix or extension
of the input filename. If it ends with a dot,
is used as a prefix. If the output name starts
and ends with dots, it's used as an interfix
before the extension.If a single file is used
and there is not a file name (STDIN), the
output will be print into STDOUT, unless a
output filename is used. You can use "STDOUT"
to force print into STDOUT. STDOUT can not be
use with --list. (default:
".conservation.csv")
-p, --parallel PARALLEL
Number of worker processes. (type: Int64,
default: 1)
-f, --format FORMAT Format of the MSA: Stockholm, Raw or FASTA
(default: "Stockholm")
-c, --clustering Sequence clustering (Hobohm I)
-i, --threshold THRESHOLD
Percent identity threshold for sequence
clustering (Hobohm I) (type: Float64, default:
62.0)
--version show version information and exit
-h, --help show this help message and exit
MIToS 3.0.6
Bioinformatics Unit
Leloir Institute Foundation
Av. Patricias Argentinas 435, CP C1405BWE, Buenos Aires, ArgentinaDownloadPDB.jl
usage: DownloadPDB.jl [-c CODE] [-l LIST] [-f FORMAT] [--version] [-h]
Download gzipped files from PDB.
optional arguments:
-c, --code CODE PDB code
-l, --list LIST File with a list of PDB codes (one per line)
-f, --format FORMAT Format. It should be PDBFile (pdb) or PDBML
(xml) (default: "PDBML")
--version show version information and exit
-h, --help show this help message and exit
MIToS 3.0.6
Bioinformatics Unit
Leloir Institute Foundation
Av. Patricias Argentinas 435, CP C1405BWE, Buenos Aires, ArgentinaDistances.jl
usage: Distances.jl [-l] [-o OUTPUT] [-p PARALLEL] [-d DISTANCE]
[-f FORMAT] [-m MODEL] [-c CHAIN] [-g GROUP] [-i]
[--version] [-h] [FILE]
Calculates residues distance and writes them into a *.distances.csv.gz
gzipped file.
positional arguments:
FILE File name. If it is not used, the script reads
from STDIN.
optional arguments:
-l, --list The input is a list of file names. If -p is
used, files will be processed in parallel.
-o, --output OUTPUT Name of the output file. Output will be gzip
if the extension is ".gz". If it starts with a
dot, the name is used as a suffix or extension
of the input filename. If it ends with a dot,
is used as a prefix. If the output name starts
and ends with dots, it's used as an interfix
before the extension.If a single file is used
and there is not a file name (STDIN), the
output will be print into STDOUT, unless a
output filename is used. You can use "STDOUT"
to force print into STDOUT. STDOUT can not be
use with --list. (default:
".distances.csv.gz")
-p, --parallel PARALLEL
Number of worker processes. (type: Int64,
default: 1)
-d, --distance DISTANCE
The distance to be calculated, options: All,
Heavy, CA, CB (default: "All")
-f, --format FORMAT Format of the PDB file: It should be PDBFile
or PDBML (default: "PDBFile")
-m, --model MODEL The model to be used, use All for all
(default: "1")
-c, --chain CHAIN The chain to be used, use All for all
(default: "All")
-g, --group GROUP Group of atoms to be used, should be ATOM,
HETATM or All for all (default: "All")
-i, --inter Calculate inter chain distances
--version show version information and exit
-h, --help show this help message and exit
MIToS 3.0.6
Bioinformatics Unit
Leloir Institute Foundation
Av. Patricias Argentinas 435, CP C1405BWE, Buenos Aires, ArgentinaMSADescription.jl
usage: MSADescription.jl [-l] [-o OUTPUT] [-p PARALLEL] [-f FORMAT]
[-e] [--version] [-h] [FILE]
Creates an *.description.csv from a Stockholm file with: the number of
columns, sequences, clusters after Hobohm clustering at 62% identity
and mean percent identity. Also the mean, standard deviation and
quantiles of: sequence coverage of the MSA, gap percentage.
positional arguments:
FILE File name. If it is not used, the script reads
from STDIN.
optional arguments:
-l, --list The input is a list of file names. If -p is
used, files will be processed in parallel.
-o, --output OUTPUT Name of the output file. Output will be gzip
if the extension is ".gz". If it starts with a
dot, the name is used as a suffix or extension
of the input filename. If it ends with a dot,
is used as a prefix. If the output name starts
and ends with dots, it's used as an interfix
before the extension.If a single file is used
and there is not a file name (STDIN), the
output will be print into STDOUT, unless a
output filename is used. You can use "STDOUT"
to force print into STDOUT. STDOUT can not be
use with --list. (default: ".description.csv")
-p, --parallel PARALLEL
Number of worker processes. (type: Int64,
default: 1)
-f, --format FORMAT Format of the MSA: Stockholm, Raw or FASTA
(default: "Stockholm")
-e, --exact If it's true, the mean percent identity is
exact (using all the pairwise comparisons).
--version show version information and exit
-h, --help show this help message and exit
MIToS 3.0.6
Bioinformatics Unit
Leloir Institute Foundation
Av. Patricias Argentinas 435, CP C1405BWE, Buenos Aires, ArgentinaPercentIdentity.jl
usage: PercentIdentity.jl [-l] [-o OUTPUT] [-p PARALLEL] [-f FORMAT]
[-s] [--version] [-h] [FILE]
Calculates the percentage identity between all the sequences of an MSA
and creates an *.pidstats.csv file with: The number of columns and
sequences. The mean, standard deviation, median, minimum and maximum
values and first and third quantiles of the percentage identity. It
could also create and pidlist.csv file with the percentage identity
for each pairwise comparison.
positional arguments:
FILE File name. If it is not used, the script reads
from STDIN.
optional arguments:
-l, --list The input is a list of file names. If -p is
used, files will be processed in parallel.
-o, --output OUTPUT Name of the output file. Output will be gzip
if the extension is ".gz". If it starts with a
dot, the name is used as a suffix or extension
of the input filename. If it ends with a dot,
is used as a prefix. If the output name starts
and ends with dots, it's used as an interfix
before the extension.If a single file is used
and there is not a file name (STDIN), the
output will be print into STDOUT, unless a
output filename is used. You can use "STDOUT"
to force print into STDOUT. STDOUT can not be
use with --list. (default: ".pidstats.csv")
-p, --parallel PARALLEL
Number of worker processes. (type: Int64,
default: 1)
-f, --format FORMAT Format of the MSA: Stockholm, Raw or FASTA
(default: "Stockholm")
-s, --savelist Create and pidlist.csv file with the
percentage identity for each pairwise
comparison.
--version show version information and exit
-h, --help show this help message and exit
MIToS 3.0.6
Bioinformatics Unit
Leloir Institute Foundation
Av. Patricias Argentinas 435, CP C1405BWE, Buenos Aires, ArgentinaAlignedColumns.jl
usage: AlignedColumns.jl [-l] [-o OUTPUT] [-p PARALLEL] [--version]
[-h] [FILE]
Creates a file in Stockholm format with the aligned columns from a
Pfam Stockholm file. Insertions are deleted, as they are unaligned in
a profile HMM. The output file *.aligned.* contains UniProt residue
numbers and original column numbers in its annotations.
positional arguments:
FILE File name. If it is not used, the script reads
from STDIN.
optional arguments:
-l, --list The input is a list of file names. If -p is
used, files will be processed in parallel.
-o, --output OUTPUT Name of the output file. Output will be gzip
if the extension is ".gz". If it starts with a
dot, the name is used as a suffix or extension
of the input filename. If it ends with a dot,
is used as a prefix. If the output name starts
and ends with dots, it's used as an interfix
before the extension.If a single file is used
and there is not a file name (STDIN), the
output will be print into STDOUT, unless a
output filename is used. You can use "STDOUT"
to force print into STDOUT. STDOUT can not be
use with --list. (default: ".aligned.")
-p, --parallel PARALLEL
Number of worker processes. (type: Int64,
default: 1)
--version show version information and exit
-h, --help show this help message and exit
MIToS
Bioinformatics Unit
Leloir Institute Foundation
Av. Patricias Argentinas 435, CP C1405BWE, Buenos Aires, ArgentinaSplitStockholm.jl
usage: SplitStockholm.jl [-p PATH] [--hideprogress] [--version] [-h]
file
Splits a file with multiple sequence alignments in Stockholm format,
creating one compressed file per MSA in Stockholm format:
accessionumber.gz
positional arguments:
file Input file
optional arguments:
-p, --path PATH Path for the output files [default: execution
directory] (default: "")
--hideprogress Hide the progress bar
--version show version information and exit
-h, --help show this help message and exit
MIToS 3.0.6
Bioinformatics Unit
Leloir Institute Foundation
Av. Patricias Argentinas 435, CP C1405BWE, Buenos Aires, Argentina