| Name | gtfparse JSON |
| Version |
2.5.0
JSON |
| download |
| home_page | |
| Summary | Parsing library for extracting data frames of genomic features from GTF files |
| upload_time | 2024-01-17 04:42:08 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.7 |
| license | |
| keywords |
|
| VCS |
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| bugtrack_url |
|
| requirements |
No requirements were recorded.
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gtfparse
========
Parsing tools for GTF (gene transfer format) files.
# Example usage
## Parsing all rows of a GTF file into a Pandas DataFrame
```python
from gtfparse import read_gtf
# returns GTF with essential columns such as "feature", "seqname", "start", "end"
# alongside the names of any optional keys which appeared in the attribute column
df = read_gtf("gene_annotations.gtf")
# filter DataFrame to gene entries on chrY
df_genes = df[df["feature"] == "gene"]
df_genes_chrY = df_genes[df_genes["seqname"] == "Y"]
```
## Getting gene FPKM values from a StringTie GTF file
```python
from gtfparse import read_gtf
df = read_gtf(
"Transcripts.gtf",
column_converters={"FPKM": float})
gene_fpkms = {
gene_name: fpkm
for (gene_name, fpkm, feature)
in zip(df["seqname"], df["FPKM"], df["feature"])
if feature == "gene"
}
```
Raw data
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