jsrc 0.2.3

Python library for bioinformatics and scientific computing

jsrc

Python library for bioinformatics and scientific computing.

Installation

Recommended (global CLI via uv tool):

uv tool install jsrc

Using uv virtual environment:

uv venv
source .venv/bin/activate
uv pip install jsrc

Using Conda virtual environment + pip:

conda create -n jsrc python=3.11 -y
conda activate jsrc
pip install jsrc

From source (development):

git clone https://github.com/imjiaoyuan/jsrc.git
cd jsrc
uv venv
uv sync --extra dev --extra all

Run jsrc --help to get started.

For detailed usage, see the Documentation. 中文文档请参阅 文档。

Quick Start

jsrc --help
jsrc <module> --help
jsrc <module> <subcommand> --help

Examples:

jsrc seq --help
jsrc analyze phylo --help
jsrc vision extract --help

Module Overview

module	focus	typical use
seq	Sequence extraction, translation, QC, k-mer, sliding window	jsrc seq extract ...
plot	Gene/exon/chromosome/domain and other plots	jsrc plot gene ...
analyze	Phylogeny, motif, consensus, SNP/INDEL, QC	jsrc analyze phylo ...
gs	Genomic selection dataset build/split/train	jsrc gs train ...
grn	GRN conversion, centrality, build packaging, local serve	jsrc grn build ...
vision	Object extraction, morphology traits, EFD	jsrc vision extract ...
job	Background job submit/list/log/kill/history	jsrc job submit "cmd"

Error Output Conventions

• Input and validation failures are reported in unified format: Error: <message>.
• Missing files, invalid parameters, and incompatible inputs follow the same style across subcommands.
• Use --help on the target module/subcommand first when argument combinations are unclear.

A Glance of jsrc's Functions

vision module

jsrc vision extract -i test/leaf1.jpg -o test/efd --channel a --invert --save-mask
jsrc vision efd -i test/efd -o test/efd --harmonics 20

Contour extraction & EFD reconstruction (20 harmonics):

EFD coefficients (first 5 rows):

an,bn,cn,dn
 0.7004,  0.0127, -0.0412,  1.0018
-0.0100, -0.0083, -0.0400,  0.0293
 0.0948, -0.0055, -0.0285, -0.1134
 0.0085, -0.0702,  0.0777, -0.0099

Morphological traits:

jsrc vision traits -i test/leaf1.jpg --channel a --invert

trait	value
area	461833.5
perimeter	3479.84
aspect_ratio	0.671
circularity	0.479
extent	0.535
solidity	0.837

---

grn module

Generate and launch a 1000-gene random network viewer:

jsrc grn net2json -i test/grn/network.tsv -o test/grn/grn.json
jsrc grn anno2json -i test/grn/annotation.tsv -o test/grn/annotation.json
jsrc grn build -d test/grn/public -g test/grn/grn.json -n test/grn/annotation.json -z test/grn/grn-viewer.zip -a -t 200
jsrc grn serve -d test/grn/public -g test/grn/public/json/grn.json -n test/grn/public/json/annotation.json -p 8000 -a -t 200

Centrality ranking (top 5):

jsrc grn centrality -i test/grn/network.tsv --top 5

rank	node	in_degree	out_degree	total_degree
1	GENE_0504	24.14	34.97	59.12
2	GENE_0785	26.37	29.51	55.88
3	GENE_0165	42.81	12.21	55.01
4	GENE_0394	14.82	33.04	47.86
5	GENE_0427	36.50	10.60	47.10

---

seq module

jsrc seq extract -fa test/seq/test.fa -gff test/seq/test.gff -ids test/seq/ids.txt -o test/seq/extracted.fa -feature gene -match ID

Extract sequences by gene ID from FASTA+GFF, rename via CSV map, run QC stats, k-mer counting, and sliding-window analysis.

QC: 2 sequences, 268 bp total, GC 56.7%, N50 160.

k-mer (k=3): top ATC (40), TCG (40), CGA (39).

---

analyze module

jsrc analyze msa_consensus -fa test/analyze/aln.fa --json
jsrc analyze snpindel -fa test/analyze/aln.fa
jsrc analyze motif -fa test/analyze/aln.fa -o test/analyze/motif_out -minw 3 -maxw 5 -nmotifs 3
jsrc analyze phylo -fa test/analyze/aln.fa -o test/analyze/tree.nwk

• Consensus: ATGCTAGCTAGCTAGCTAGC, mean conservation 0.983
• SNP: seq1 vs seq3 has 1 SNP (alignment score 19/20)
• Motif (top): GCT (12), CTA (12), TAG (12)
• Phylogeny: (seq1:0.00000,seq2:0.00000,seq3:0.05000)Inner1:0.00000;

---

job module

Submit, monitor, and inspect background jobs:

Note: RSS/process-state metrics are most complete on Linux (/proc). On macOS/other Unix, job still works with ps fallback but some metrics may be limited.

jsrc job submit "echo 'job module test' && sleep 1 && echo done" -N test-job

job_id	1
pid	90288
log	/home/user/.local/share/jsrc/job-logs/1.log
status	running

jsrc job ls --limit 5

job_id  status  pid    runtime  rss_mb  ...  command
------  ------  -----  -------  ------       ----------------------------------------------
1       exited  90288  4s       0.0         echo 'job module test' && sleep 1 && echo done

jsrc job logs 1

job module test
done