`tqc-client`

A program for viewing QC statistics of .fasta and .bam files.

TQC is currently running on CLIMB, uploading new data every day. It has QC data going back to the published_date of 2022-03-02.

The tqc-client can retrieve data from TQC with the use of the get command, which will be detailed further below.

Setup

1. Clone this repository

$ git clone https://github.com/CLIMB-COVID/tqc-client.git

2. Create and activate the conda environment

$ conda env create -f environment.yml
$ conda activate tqc-client

3. Set the required environment variables

The environment variables needed to use TQC are:

TQC_IP: this is the hostname for TQC.
TQC_PORT: this is the port number for TQC.

These can be provided by @tombch.

4. Run the TQC client

We are now ready to use tqc-client.

Data cannot be added to TQC by users. It can only be retrieved, using get, which will be detailed further below.

To run TQC and look at its options for retrieving data:

$ python tqc.py get --help

5. [Optional] Bash function for ease of use

To run tqc-client from any directory, this function can be put into your .bashrc file with <PATH-TO-DIR> replaced by the directory for tqc-client.

function tqc() {
    python "<PATH-TO-TQC-DIR>/tqc.py" "$@"
}
export -f tqc

Data stored in TQC

Metadata

central_sample_id: this field is required in all TQC data.
run_name: this field is required in all TQC data.
pag_name: this field is required in all TQC data.
sequencing_org_code
foel_producer
phe_private_provider
phe_site
collection_date
received_date
sequencing_org_received_date
sequencing_submission_date
published_date
fasta_path: path to the .fasta file on CLIMB.
bam_path: path to the .bam file on CLIMB.
library_primers: formatted information on library primers.
library_primers_reported: information on library primers, before formatting.
pag_suppressed: whether the PAG has been suppressed or not.
- Each entry in this field is either VALID or SUPPRESSED.
- NOTE: At the moment, TQC is not regularly reupdating its data.
- This means that PAGs that have been recently suppressed may still be marked as 'VALID' in TQC.
- I am working on implementing regular scans for changed metadata!
pag_basic_qc: whether the PAG passed Majora basic QC.

Fasta QC

num_bases: number of characters in the sequence.
pc_acgt: the percentage of the characters A, C, G and T in the sequence.
pc_masked: the percentage of the characters N and X in the sequence.
pc_ambiguous: the percentage of the characters W, S, M, K, R, Y, B, D, H and V in the sequence.
pc_invalid: the percentage of all other characters in the sequence that are not ACGT, masked or ambiguous.
longest_gap: the length of the longest subsequence of masked and/or invalid bases in the sequence.
longest_ungap: the length of the longest subsequence of ACGT and/or ambiguous bases in the sequence.

Bam QC

num_pos: number of positions (the number of bases in the reference genome).
mean_cov: mean coverage - this is the sum of coverages, divided by num_pos.
pc_pos_cov_gteX: percentage of positions with coverage greater than or equal to X.
- there are fields for X = 1, X = 5, X = 10, X = 20, X = 50, X = 100, and X = 200.

If library_primers information was given (that could be mapped to a .bed file):

pc_tiles_medcov_gteX: the percentage of tiles with a median coverage greater than or equal to X.
- there are fields for X = 1, X = 5, X = 10, X = 20, X = 50, X = 100, and X = 200.
tile_n: the number of tiles.
tile_vector: vector containing the median coverage for each tile.

Retrieving data from TQC

Overview

Data is retrieved and written to stdout as a tab-separated table using the get command of TQC.

Basic commands

The TQC database can be filtered by various arguments provided after get.

Passing multiple arguments to TQC will return only the rows that match all the constraints from the arguments.

For example, the command:

$ python tqc.py --published-date 2022-03-24 --library-primers 3

will return all rows that satisfy the following condition:

(published_date = 2022-03-22) AND (library_primers = 3)

Some arguments can be passed any number of values, and this will return rows that match any of the values within the argument.

For example, the command:

$ python tqc.py --published-date 2022-03-22 --library-primers 2 3 4

will return all rows that satisfy the following condition:

(published_date = 2022-03-22) AND ( (library_primers = 2) OR (library_primers = 3) OR (library_primers = 4) )

and the command:

$ python tqc.py --sequencing-org-code ABCD --published-date 2022-03-22 2022-03-24 --library-primers 2 3 4

will return all rows that satisfy the following condition:

(sequencing_org_code = ABCD) AND ( (published_date = 2022-03-22) OR (published_date = 2022-03-24) ) AND ( (library_primers = 2) OR (library_primers = 3) OR (library_primers = 4) )

By default, TQC returns data only on unsuppressed PAGs that passed basic QC. The types of PAGs returned can be explicitly determined by passing VALID and/or SUPPRESSED to the --pag-suppressed argument, and passing PASS and/or FAIL to the --pag-basic-qc argument.

To return all PAGs, add --all to the command. For example:

$ python tqc.py --all

will return everything.

Matching empty cells

String fields with empty cells can be matched by passing _ to an argument, in place of a value.

For example, the command:

$ python tqc.py --published-date 2022-03-22 --library-primers 3 4 _

will return all rows that satisfy the following condition:

(published_date = 2022-03-22) AND ( (library_primers = 3) OR (library_primers = 4) OR (library_primers = EMPTY) )

where EMPTY denotes a cell in the library_primers column with the empty string as its value.

Numeric fields

Some fields store data as integers or floats, and these can be filtered using various operators. These operators are:

lt: less than
gt: greater than
leq: less than or equal
geq: greater than or equal
eq: equal
neq: not equal

To see which fields can be filtered using these operators, see python tqc.py --help.

For example, the command:

$ python tqc.py --published-date 2022-03-22 --pc-acgt leq 90 --pc-ambiguous gt 0

will return all rows that satisfy the following condition:

(published_date = 2022-03-22) AND (pc_acgt <= 90) AND (pc_ambiguous > 0)

The same numeric field can be passed more than once, unlike non-numeric fields.

For example, the command:

$ python tqc.py --pc-acgt geq 70 --pc-acgt leq 90 --pc-ambiguous gt 0

will return all rows that satisfy the following condition:

(70 <= pc_acgt <= 90) AND (pc_ambiguous > 0)

Date fields

There are five fields that store date information in TQC: collection_date, received_date, sequencing_org_received_date, sequencing_submission_date and published_date.

Rows can be matched by any number of individual dates:

$ python tqc.py --published-date 2022-03-02 2022-03-05 2022-03-06

this will return all rows that satisfy the following condition:

(published_date = 2022-03-02) OR (published_date = 2022-03-05) OR (published_date = 2022-03-06)

or between two dates:

$ python tqc.py --published-date-range 2022-03-02 2022-03-09

this will return all rows that satisfy the following condition:

 2022-03-02 <= published_date <= 2022-03-09

or by any number of individual ISO weeks (given in a YYYY-WW format):

$ python tqc.py --published-iso-week 2022-01 2022-04 2022-05

this will return all rows that satisfy the following condition:

(published_iso_week = 2022-01) OR (published_iso_week = 2022-04) OR (published_iso_week = 2022-05)

or between two ISO weeks:

$ python tqc.py --published-iso-week-range 2022-01 2022-05

this will return all rows that satisfy the following condition:

 2022-01 <= published_iso_week <= 2022-05

Additional metadata

The data returned by TQC can also be merged with additional metadata by giving the path to a .tsv file to the --metadata argument. This will display a left join between the TQC data and the given metadata table.

All arguments for `python tqc.py`

For reference.

$ python -m client.python tqc.py --help
usage: tqc.py get [-h] [--central-sample-id CENTRAL_SAMPLE_ID [CENTRAL_SAMPLE_ID ...]]
                  [--run-name RUN_NAME [RUN_NAME ...]] [--pag-name PAG_NAME [PAG_NAME ...]]
                  [--pag-suppressed PAG_SUPPRESSED [PAG_SUPPRESSED ...]]
                  [--pag-basic-qc PAG_BASIC_QC [PAG_BASIC_QC ...]] [--all]
                  [--sequencing-org-code SEQUENCING_ORG_CODE [SEQUENCING_ORG_CODE ...]]
                  [--foel-producer FOEL_PRODUCER [FOEL_PRODUCER ...]]
                  [--phe-private-provider PHE_PRIVATE_PROVIDER [PHE_PRIVATE_PROVIDER ...]]
                  [--phe-site PHE_SITE [PHE_SITE ...]] [--collection-pillar COLLECTION_PILLAR [COLLECTION_PILLAR ...]]
                  [--collection-date YYYY-MM-DD [YYYY-MM-DD ...] | --collection-date-range YYYY-MM-DD YYYY-MM-DD |
                  --collection-iso-week YYYY-WW [YYYY-WW ...] | --collection-iso-week-range YYYY-WW YYYY-WW]
                  [--received-date YYYY-MM-DD [YYYY-MM-DD ...] | --received-date-range YYYY-MM-DD YYYY-MM-DD |
                  --received-iso-week YYYY-WW [YYYY-WW ...] | --received-iso-week-range YYYY-WW YYYY-WW]
                  [--sequencing-org-received-date YYYY-MM-DD [YYYY-MM-DD ...] | --sequencing-org-received-date-range
                  YYYY-MM-DD YYYY-MM-DD | --sequencing-org-received-iso-week YYYY-WW [YYYY-WW ...] |
                  --sequencing-org-received-iso-week-range YYYY-WW YYYY-WW]
                  [--sequencing-submission-date YYYY-MM-DD [YYYY-MM-DD ...] | --sequencing-submission-date-range
                  YYYY-MM-DD YYYY-MM-DD | --sequencing-submission-iso-week YYYY-WW [YYYY-WW ...] |
                  --sequencing-submission-iso-week-range YYYY-WW YYYY-WW] [--published-date YYYY-MM-DD [YYYY-MM-DD ...]
                  | --published-date-range YYYY-MM-DD YYYY-MM-DD | --published-iso-week YYYY-WW [YYYY-WW ...] |
                  --published-iso-week-range YYYY-WW YYYY-WW] [--fasta-path FASTA_PATH [FASTA_PATH ...]]
                  [--bam-path BAM_PATH [BAM_PATH ...]] [--library-primers LIBRARY_PRIMERS [LIBRARY_PRIMERS ...]]
                  [--library-primers-reported LIBRARY_PRIMERS_REPORTED [LIBRARY_PRIMERS_REPORTED ...]]
                  [--num-bases OPERATOR VALUE] [--pc-acgt OPERATOR VALUE] [--pc-masked OPERATOR VALUE]
                  [--pc-invalid OPERATOR VALUE] [--pc-ambiguous OPERATOR VALUE] [--longest-gap OPERATOR VALUE]
                  [--longest-ungap OPERATOR VALUE] [--num-pos OPERATOR VALUE] [--mean-cov OPERATOR VALUE]
                  [--pc-pos-cov-gte1 OPERATOR VALUE] [--pc-pos-cov-gte5 OPERATOR VALUE]
                  [--pc-pos-cov-gte10 OPERATOR VALUE] [--pc-pos-cov-gte20 OPERATOR VALUE]
                  [--pc-pos-cov-gte50 OPERATOR VALUE] [--pc-pos-cov-gte100 OPERATOR VALUE]
                  [--pc-pos-cov-gte200 OPERATOR VALUE] [--pc-tiles-medcov-gte1 OPERATOR VALUE]
                  [--pc-tiles-medcov-gte5 OPERATOR VALUE] [--pc-tiles-medcov-gte10 OPERATOR VALUE]
                  [--pc-tiles-medcov-gte20 OPERATOR VALUE] [--pc-tiles-medcov-gte50 OPERATOR VALUE]
                  [--pc-tiles-medcov-gte100 OPERATOR VALUE] [--pc-tiles-medcov-gte200 OPERATOR VALUE]
                  [--tile-n OPERATOR VALUE] [--metadata TSV_PATH] [--host HOST] [--port PORT]

operators: lt, gt, leq, geq, eq, neq

options:
  -h, --help            show this help message and exit
  --central-sample-id CENTRAL_SAMPLE_ID [CENTRAL_SAMPLE_ID ...]
  --run-name RUN_NAME [RUN_NAME ...]
  --pag-name PAG_NAME [PAG_NAME ...]
  --pag-suppressed PAG_SUPPRESSED [PAG_SUPPRESSED ...]
                        Default: valid PAGs only
  --pag-basic-qc PAG_BASIC_QC [PAG_BASIC_QC ...]
                        Default: passed PAGs only
  --all                 Ignore defaults regarding PAG suppression and basic QC passing
  --sequencing-org-code SEQUENCING_ORG_CODE [SEQUENCING_ORG_CODE ...]
  --foel-producer FOEL_PRODUCER [FOEL_PRODUCER ...]
  --phe-private-provider PHE_PRIVATE_PROVIDER [PHE_PRIVATE_PROVIDER ...]
  --phe-site PHE_SITE [PHE_SITE ...]
  --collection-pillar COLLECTION_PILLAR [COLLECTION_PILLAR ...]
  --collection-date YYYY-MM-DD [YYYY-MM-DD ...]
  --collection-date-range YYYY-MM-DD YYYY-MM-DD
  --collection-iso-week YYYY-WW [YYYY-WW ...]
  --collection-iso-week-range YYYY-WW YYYY-WW
  --received-date YYYY-MM-DD [YYYY-MM-DD ...]
  --received-date-range YYYY-MM-DD YYYY-MM-DD
  --received-iso-week YYYY-WW [YYYY-WW ...]
  --received-iso-week-range YYYY-WW YYYY-WW
  --sequencing-org-received-date YYYY-MM-DD [YYYY-MM-DD ...]
  --sequencing-org-received-date-range YYYY-MM-DD YYYY-MM-DD
  --sequencing-org-received-iso-week YYYY-WW [YYYY-WW ...]
  --sequencing-org-received-iso-week-range YYYY-WW YYYY-WW
  --sequencing-submission-date YYYY-MM-DD [YYYY-MM-DD ...]
  --sequencing-submission-date-range YYYY-MM-DD YYYY-MM-DD
  --sequencing-submission-iso-week YYYY-WW [YYYY-WW ...]
  --sequencing-submission-iso-week-range YYYY-WW YYYY-WW
  --published-date YYYY-MM-DD [YYYY-MM-DD ...]
  --published-date-range YYYY-MM-DD YYYY-MM-DD
  --published-iso-week YYYY-WW [YYYY-WW ...]
  --published-iso-week-range YYYY-WW YYYY-WW
  --fasta-path FASTA_PATH [FASTA_PATH ...]
  --bam-path BAM_PATH [BAM_PATH ...]
  --library-primers LIBRARY_PRIMERS [LIBRARY_PRIMERS ...]
  --library-primers-reported LIBRARY_PRIMERS_REPORTED [LIBRARY_PRIMERS_REPORTED ...]
  --num-bases OPERATOR VALUE
  --pc-acgt OPERATOR VALUE
  --pc-masked OPERATOR VALUE
  --pc-invalid OPERATOR VALUE
  --pc-ambiguous OPERATOR VALUE
  --longest-gap OPERATOR VALUE
  --longest-ungap OPERATOR VALUE
  --num-pos OPERATOR VALUE
  --mean-cov OPERATOR VALUE
  --pc-pos-cov-gte1 OPERATOR VALUE
  --pc-pos-cov-gte5 OPERATOR VALUE
  --pc-pos-cov-gte10 OPERATOR VALUE
  --pc-pos-cov-gte20 OPERATOR VALUE
  --pc-pos-cov-gte50 OPERATOR VALUE
  --pc-pos-cov-gte100 OPERATOR VALUE
  --pc-pos-cov-gte200 OPERATOR VALUE
  --pc-tiles-medcov-gte1 OPERATOR VALUE
  --pc-tiles-medcov-gte5 OPERATOR VALUE
  --pc-tiles-medcov-gte10 OPERATOR VALUE
  --pc-tiles-medcov-gte20 OPERATOR VALUE
  --pc-tiles-medcov-gte50 OPERATOR VALUE
  --pc-tiles-medcov-gte100 OPERATOR VALUE
  --pc-tiles-medcov-gte200 OPERATOR VALUE
  --tile-n OPERATOR VALUE
  --metadata TSV_PATH
  --host HOST
  --port PORT

CLIMB-COVID / tqc-client

`tqc-client`

Setup

1. Clone this repository

2. Create and activate the conda environment

3. Set the required environment variables

4. Run the TQC client

5. [Optional] Bash function for ease of use

Data stored in TQC

Metadata

Fasta QC

Bam QC

Retrieving data from TQC

Overview

Basic commands

Defaults

Matching empty cells

Numeric fields

Date fields

Additional metadata

All arguments for `python tqc.py`

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