This package provides a unified command line interface to Atgenomix SeqsLab, a cloud-native biomedical informatics (BioMed IT) platform.
Table of Contents
Getting Started
Prerequisites
Install the SeqsLab Report Parser
pip install seqslab-report-parser
Basic Commands
Parse PDF Report (single)
report-parser single -i {INPUT_DIR} --ref {FASTA_PATH} --ref_fa {FASTA_IDX_PATH} --ref_gene {REF_GENE_PATH} --trans_cds {TRANSCRIPT_CDS_PATH} --ens_to_nm {ENS_TO_NM_MAPPING_PATH}
- -m: optional, generate MAF info
- -v: optional, generate VCF file
Parse PDF Report (batch)
report-parser batch -i {INPUT_DIR} -o {OUTPUT_DIR} --ref {FASTA_PATH} --ref_fa {FASTA_IDX_PATH} --ref_gene {REF_GENE_PATH} --trans_cds {TRANSCRIPT_CDS_PATH} --ens_to_nm {ENS_TO_NM_MAPPING_PATH}
- -m: optional, generate MAF info
- -v: optional, generate VCF file
Generate genes.refGene
report-parser gen-ref-gene --output {REF_GENE_PATH}
Generate Transcript CDS
report-parser gen-cds --output {TRANSCRIPT_CDS_PATH} --gen_code {GEN_CODE_PATH} --ref {FASTA_PATH}
Help documentation
To view help documentation, use one of the following:
report-parser -h
Getting Help
The best way to interact with our team is through GitHub. You can open an issue and choose from one of our templates for guidance, bug reports, or feature requests.
Please check for open similar issues before opening another one.
More Resources
Contributing
The repository currently does not accept contributions but will eventually be opened to the community.
1 maintainer
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