cell2net.preprocessing.get_gene_tss_coord#

cell2net.preprocessing.get_gene_tss_coord(gene_gtf, feature_type='gene')#

Extract transcription start site (TSS) coordinates for genes from a GTF file.

This function parses a GTF (Gene Transfer Format) file to extract the transcription start site (TSS) of genes or other specified features. It returns a pandas DataFrame with the chromosome, gene name, strand, and TSS for each gene.

Parameters:

  • gene_gtf (str) – Path to the GTF file. The file can be plain text or gzip-compressed (“.gz”).

  • feature_type (str (default: 'gene')) – The type of feature to extract (e.g., “gene”, “transcript”).

Return type:

DataFrame

Returns:

A DataFrame containing the following columns:

  • chrom: Chromosome name (str).

  • gene_name: Gene name extracted from the “gene_name” attribute (str).

  • strand: Strand of the gene (‘+’ or ‘-’) (str).

  • tss: Transcription start site position (int).

Notes

  • This function assumes that the “gene_name” attribute is present in the GTF file’s attributes field and is enclosed in double quotes.

  • The TSS is calculated as the start position for ‘+’ strand genes and the end position for ‘-’ strand genes.

  • Lines in the GTF file that do not have 9 columns or do not match the specified feature type are skipped.

  • Duplicate gene names are removed, keeping only the first occurrence.

Examples

>>> Extract TSS information for genes from a GTF file:
>>> import pandas as pd
>>> gene_gtf = "path/to/genes.gtf.gz"
>>> df = get_gene_tss_coor(gene_gtf)
>>> print(df.head())
    chrom  gene_name strand    tss
0    chr1      GeneA      +   1000
1    chr1      GeneB      -   2000
2    chr2      GeneC      +   3000
3    chr2      GeneD      -   4000