This is a neat trick in a couple of steps to create a SQLite database from a gzip file.

First, make sure your text file is tab-separated, and has a header row that you would like to use as the table columns.

First, we make a FIFO object and stream the gzip file to that. Note that we background the zcat command here.

mkfifo tempfile
zcat sprot.uniprot.proc.gz > tempfile &

This doesn’t actually uncompress your file, it just sets a 0 byte file object that will read the uncompressed file.

Now, we open SQLIte3 with the name of our (new or existing) database.

sqlite3 db.sqlite

And then set tabs mode for the import and read the tempfile filehandle into a new table.

.mode tabs
.import tempfile newtable

SQLite3 will automatically create the table with column names the same as the headers, and the data will be loaded.

You can check by looking at the .schema

“plus ça change, plus c’est la même chose “

Jean-Baptiste Alphonse Karr

So its 2023 and the new [sequencing] kid on the block, MGI, hasn’t figured out adapter trimming.

Here is a quick primer [pun intended] on the easiest way to remove primers and filter reads.

Use fastp and give it this file of Illumina adapters to trim against.

I use this command to filter and remove adapters from our sequences

mkdir output
fastp -n 1 -l 100 -i fastq/$R1 -I fastq/$R2 -o output/$R1 -O output/$R2 --adapter_fasta IlluminaAdapters.fa

If you have a lot of files, you can easily wrap this in a for loop to process all the files in a directory

mkdir fastq_fastp
for R1 in $(find fastq -name \*R1\* -printf "%f\n"); do
    R2=${R1/R1/R2}
    fastp -n 1 -l 100 -i fastq/$R1 -I fastq/$R2 -o fastq_fastp/$R1 -O fastq_fastp/$R2 --adapter_fasta IlluminaAdapters.fa 
done

In addition to trimming all adapter sequences, this will remove any sequence with an N (yes, one or more), and remove any sequence shorter than 100 bp. fastp will also make sure that your reads are paired as well!

1. Start an instance using nectar or jetstream
2. You don’t need a user account. Possibly
3. Install jupyterhub:

curl -L https://tljh.jupyter.org/bootstrap.py | sudo python3 -  --admin rob

4. Allow users to create usernames and passwords:

tljh-config set auth.type nativeauthenticator.NativeAuthenticator
tljh-config reload

5. Create a username using the web interface
6. Authorize those users:

add /hub/authorize to your URL. e.g.
http://203.101.227.65/hub/authorize

7. Install R and Python

apt install r-base nodejs

8. Start R and install ir-kernel

$ R
> install.packages('IRkernel')
> IRkernel::installspec(user = FALSE)
> quit()

Usermanagement:

If you are having issues with user management you can cheat and get into the SQLIte database

sqlite3  /opt/tljh/state/jupyterhub.sqlite
#find the schema for the user tables
.tables
.schema users_info

CREATE TABLE users_info (
        id INTEGER NOT NULL,
        username VARCHAR(128) NOT NULL,
        password BLOB NOT NULL,
        is_authorized BOOLEAN,
        login_email_sent BOOLEAN,
        email VARCHAR(128),
        has_2fa BOOLEAN,
        otp_secret VARCHAR(16),
        PRIMARY KEY (id)
);

Find out about a user:

select * from users_info;

Authorise a user:

update users_info set is_authorized=1 where username='rob';

select * from users_info;

Should be good to go now!