gtfparse
Parsing tools for GTF (gene transfer format) files.
Example usage
Parsing all rows of a GTF file into a Pandas DataFrame
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
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"
}
5 maintainers
Release files for gtfparse 2.8.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| gtfparse-2.8.1.tar.gz | 30.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| gtfparse-2.8.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 51.2 kB
Release files / gtfparse-2.8.1.tar.gz
| Download URL | gtfparse-2.8.1.tar.gz |
|---|---|
| Size | 30.9 kB |
| Tags | Source |
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| Size | 20.4 kB |
| Tags | Python 3 |
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