to_gpf_gene_models_format

to_gpf_gene_models_format converts a gene models file to the default GPF gene models format. It reads the input file, loads the gene models and writes them to the output file. Use it to prepare a gene models resource from a RefSeq, CCDS, UCSC knownGene or GTF file.

Examples

to_gpf_gene_models_format refGene.txt.gz gene_models.txt

Converts a gene models file. The tool infers the format of the input file.

to_gpf_gene_models_format --gm-format refseq \
    --chrom-mapping chrom_mapping.txt refGene.txt.gz gene_models.txt

Converts a RefSeq file and renames the chromosomes with a mapping file.

Option reference

usage: to_gpf_gene_models_format [-h] [--gm-format GM_FORMAT]
                                 [--gm-names GM_NAMES]
                                 [--chrom-mapping CHROM_MAPPING]
                                 input_gene_models output_gene_models

Positional Arguments

input_gene_models

input gene models file

output_gene_models

output gene models file

Named Arguments

--gm-format

gene models format (refseq, ccds or knowngene)

--gm-names

gene names mapping file [type None for no mapping]

--chrom-mapping

chromosome names mapping file