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myrast

myrast dockerfile This is myrast distribution on a docker file. To use myrast you need a RAST account. BEside upload and retrieve genomes that are the functionalities described here, other myrast commands can be used with this docker distribution.

Download myrast docker distribution

Once you have docker installed, pull the myrast dcker distribution.
docker pull nselem/myrast

Open myRast terminal

docker run -i -t -v $(pwd):/home nselem/myrast /bin/bash

Use myRast

Now you can use myRast:

There are several scripts in my rast distribution, here we explain the corresponding scripts to upload, download and delete jobs to rast servers.

svr__submit_RAST_job
svr_retrieve_RAST_job
svr_delete_RAST_job

To upload fasta/genbank we use this script svr_submit_RAST_job

svr_submit_RAST_job -user <user> -passwd <pass> -fasta <file> -domain Bacteria -bioname "Organism name" -genetic_code 11 -gene_caller rast

This script has several parameters:

Parameter Description
--user username RAST login for the submitting user
--passwd password RAST password for the submitting user
--genbank filename If submitting a genbank file, the file of input data.
--fasta filename If submitting a FASTA file of contigs, the file of input data.
--domain Bacteria or
--domain Archaea Domain of the submitted genome.
--taxon_id taxonomy-id The NCBI taxonomy id of the submitted genome
--bioname "genus species str." Biological name of the submitted genome
--genetic_code ( 11 | 4 ) Genetic code for the submitted genome, either 11 or 4.
--gene_caller Gene caller to use (FigFam-base RAST gene caller or straight Glimmer-3)
--reannotate_only Preserve the original gene calls and use RAST

Note On -bioname it is important that the first letter is capital and all the others lowercase, as on scientific names.

Upload several genomes to RAST

To upload genomes in batch to RAST you can use the following bash script. You will need a file tab-separated where the first column contains the name of the genome files, and the second column the scientific name of the organism. Name this file IdsFile and place yourself where the genome files and the ids files are located. Finally, please substitute your username and password in the corresponding places and copy and paste this script in the terminal inside the myrast docker.

cat IdsFile | while read line; do id=$(echo $line|cut -d' ' -f1); name=$(echo $line|cut -d' ' -f2-5); echo svr_submit_RAST_job -user <usr> -passwd <pass> -genbank $id -domain Bacteria -bioname "${name}" -genetic_code 11 -gene_caller rast; svr_submit_RAST_job -user <usr> -passwd <pass> -genbank $id -domain Bacteria -bioname "$name" -genetic_code 11 -gene_caller rast; done

To retrieve RAST files svr_retrieve_RAST_job.

svr_retrieve_RAST_job <user> <password> <jobId> table_txt > $ID.txt

if you have a list of files, you can process it with bash. For example to download a list of RAST files, store the RAST Id numbers on a file, (Rast_ID on this example) and use a while from bash to retrieve them:

On this case the variable "line" will contain a RAST Id number, and each amino acid file from a RAST Id will be downloaded and stored on "$line.faa"
cut -f1 Rast_ID | while read line; do svr_retrieve_RAST_job <user> <password> $line amino_acid > $line.faa ; done

You can change the format table_txt for whatever format you need.

Attribute Description
genbank GenBank (with SEED function conventions and enhancements)
genbank_stripped GenBank with EC-numbers stripped from functions
embl EMBL (with SEED function conventions and enhancements)
embl_stripped EMBL with EC-numbers stripped from functions
gff3 GFF3
gff3_stripped GFF3 with EC-numbers stripped from functions
gtf GTF
gtf_stripped GTF with EC-numbers stripped from functions
rast_tarball gzipped tar archive of the RAST genome directory
nucleic_acid DNA for genes
amino_acid Protein translations for genes
table_txt Gene data in tab-separated format
table_xls Gene data in EXCEL format

To delete RAST files svr_delete_RAST_job.

svr_delete_RAST_job username password jobnumber`

Extra features included in myrast docker.

  1. Download genomes from NCBI.
  2. Upload genomes to RAST.
  3. Download genomes to RAST.

1 Download genomes from NCBI

Download NCBI genomes using a perl script included in this myrast docker.

Input Files:
Id_NCBI file (File with the genome ids from NCBI you wish to upload to RAST)
1.NCBI_and_RAST script from GitHub
perl /opt/myrast/1.NCBI_and_RAST.pl <yourIdsfile> <yourRASTId> <yourRastPassword>
NOTE: 1.NCBI_and_RAST script, will de run inside the docker.

1.1 Id_NCBI file Prepare the file Id_NCBI. It should be a text file with two columns. The first column filled with NCBI Ids, the second column should contain the organism's genus with the species name. The two columns must be tab separated. Accepted IDs: You can only use ids from the NCBI databases protein, nucleotide and genome.

NOTE: To see the status of the job, type: $svr_status_of_RAST_job user password jobID
If you want to review other options, could visit http://blog.theseed.org/servers/usage/the-rast-batch-interface.html

NCBI id list

Figure 1- File with NCBI Id’s, genus and species names.

You can look for the NCBI ids from the following links:
Assembly NCBI
Genoma NCBI
Note. Please check that your organism name is correctly written. And that is only the First letter of the genus must be capital. Names like CORYNEBACTERIUM ACCOLENS ATCC 49725 won't be accepted, you must write Corynebacterium accolens atcc 49725 instead. You can use in excel or libre office the option Format->Change Capitals (feature not present in google drive).

NCBI id list
To download genomes without using RAST please comment line 20 adding a character # at the beginning of line, Figure 2. Save your changes.

NCBI id list
Figure 3. Modify line 20 if you are not planning to use RAST, and this is if you only want to download genomes from NCBI.

Finally, run the script:
perl 1.NCBI_and_RAST.pl <Ids_NCBI file>

Download genomes using ncbi-genome-download github repo from kblin.

To download some specific bacteria from ncbi we have used ncbi-genome-download. It has to be installed forllowing its github tutorial

After the installation, to visualize a list of the genomes that will be downloaded use the dry-run modifier. For example the following line would show the Clavibacter bacteria with a complete assembly available at MIBiG in the file IDS.
ncbi-genome-download --genus Clavibacter bacteria --parallel 4 --assembly-level complete --format fasta_ --dry-run >IDS

To actually download the organisms just remove the dry-run modifier.
ncbi-genome-download --genus Clavibacter bacteria --parallel 4 --assembly-level complete --format fasta_

2. RAST upload genomes

Input files
Id_NCBI file (File with the genome ids from NCBI you wish to upload to RAST)
1.NCBI_and_RAST script from GitHub
1.NCBI_and_RAST.pl Id_NCBI file user pass

Id_NCBI file Follow the instructions in the page above.

3. RAST retrieve genomes

Input Files:
RAST_id file with your RAST ids
2.Batch_RetrievesFiles.pl script from GitHub
2.Batch_RetrieveFiles.pl RAST_id

3.1. Id_RAST file
From your jobs overview personal website, copy the job, the id and the organism name columns in a text tab separated file. First, from the RAST web site save the jobId, the genome Id and the organism name of your interest.

NCBI id list
Figure 5. Get your job ids, genome Ids and organism names from RAST website.

After that use the information to construct a tab separated file.
NCBI id list
Figure 6. Create a file with your jobs id’s.

Create a tab separated file
1.Copy the table in an excel or google sheet file.
2.Delete the columns you don’t need.
3.Copy the columns you need into a text editor like vi, nano, gedit, etc. (remember word is not a text editor).
4.Save the file.

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