seqslab-report-parser 0.2.4

This package provides a unified command line interface to Atgenomix SeqsLab, a cloud-native biomedical informatics (BioMed IT) platform.

Getting Started

Prerequisites

• Python 3.8 or later

• PyMuPDF

• pyfaidx

• pyhgvs

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.