geneID v3

About the App

geneID v3 is a browser-based application that takes user’s defined sequenceID, or a comma-separated list of sequenceIDs, and returns corresponding coding sequences (cds) and polypeptide (pep) sequences in the new tab. User is able to choose to download visualised results either as TAB-separated (.txt) files or FASTA (.fasta) files, or both. Moreover, user can choose to conduct a query across three hierarchical levels of information:

1. Considering representative sequences only
2. Considering alternative and representative sequences
3. All sequences – i.e. alternative, representative and cultivar-specific sequences

At the time, geneID contains potato sequenceIDs and corresponding sequences, however it is organism-agnostic.

   

Fig1: Landing page, one sequenceID query

Fig2: Landing page, comma-separated list query

Fig3: Results Tab

Dependencies

User needs to install:

1. Visual studio code (April 2022, v 1.67)
2. In Visual Studio Code add extension SQL Server (mssql)
3. XAMMP (v 8.1.6, PHP 8.1.6)
   Note: Install just apache server, other things such as MySQL, FileZilla, Mercury and Tomcat are not needed
4. Microsoft SQL Server Management Studio (v 18.11.1)
5. PyCharm (v 2022.1.1)

SetUp

1. Prepare/download table(s) containing sequenceIDs, and the corresponding sequences (e.g. preprocessed CDS and pep)
2. Import tables in Microsoft SQL Server Management Studio
   right click on your database -> Tasks -> Import Flat File -> Select table(s)
3. Download all files for Visual studio code from Scripts directory
4. Deposit all necessary files into htcdocs designated directory in your installation folder for XAMMP
5. Connect database from Microsoft SQL Server Management Studio to Visual studio code
   Note: Follow steps listed at Connect to your database
6. Open XAMMP and press start button (to the right of the module Apache)
7. Open your browser and type localhost/the-name-of-directory in which you saved your Visual studio code files

DB creation

Download all fasta files and download PyCharm

Reformating fasta files to tab delimited files:

out_lines = []
temp_line = ''
with open('path/to/file','r') as fp:
     for line in fp:
         if line.startswith('>'):
             out_lines.append(temp_line)
             temp_line = line.strip() + '\t'
         else:
             temp_line += line.strip()

with open('path/to/new_file', 'w') as fp_out:
    fp_out.write('\n'.join(out_lines))

Replace path/to/file with path to fasta files. replace path/to/new_file with directory where tab delimited files will be written to.
Code taken from: stackoverflow 'convert a fasta file to a tab-delimited file using python script'

In Microsoft SQL Server Management Studio import converted files into designated database.
Right click on your database -> Import flat file -> Pick your file
If needed, modify the names of your columns and types of your data.

Merge all fasta files using:

SELECT * FROM (name_of_your_table)
UNION
SELECT * FROM (name_of_second_table)
(...)

   

Hints section

subset fasta

for f in *fasta; do
    echo $f
    xargs faidx -d ' ' $f \
    < 5cv_weak-components_extract-IDs.txt > \
    ./out/subset_$f 2> ./err/subset_$f.error;
done;

tab to fasta

https://fairdomhub.org/data_files/3420

fasta to tab

https://bioinformatics.stackexchange.com/questions/14818/creating-a-tab-delimited-file

MS SQL MySQL migrations

https://www.mysql.com/products/workbench/migrate/

https://dev.mysql.com/doc/workbench/en/wb-migration-install.html

FLASK

https://blog.appseed.us/flask-react-full-stack-seed-projects/

https://dev.to/dev_elie/connecting-a-react-frontend-to-a-flask-backend-h1o

https://flask.palletsprojects.com/en/2.0.x/

https://dev.to/gajesh/the-complete-flask-beginner-tutorial-124i

other tools

https://igraph.org/

https://cytoscape.org/

https://github.com/neo4j/neo4j

FASTA files

https://fairdomhub.org/assays/1268?graph_view=tree

https://fairdomhub.org/data_files/3424

https://fairdomhub.org/data_files/3415