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GTF Parsing

Project Description

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(
    "stringtie-output.gtf",
    column_converters={"FPKM": float})

gene_fpkms = {
    gene_name: fpkm
    for (gene_name, fpkm, feature)
    in zip(df["gene_name"], df["FPKM"], df["feature"])
    if feature == "gene"
}

Release History

This version
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1.0.5

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1.0.4

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1.0.3

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1.0.2

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1.0.1

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1.0.0

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0.3.0

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0.2.4

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0.2.3

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0.2.2

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0.2.1

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0.2.0

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0.0.6

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0.0.5

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0.0.4

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0.0.3

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0.0.2

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0.0.1

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Filename, Size & Hash SHA256 Hash Help File Type Python Version Upload Date
gtfparse-1.0.5.tar.gz
(12.7 kB) Copy SHA256 Hash SHA256
Source None Feb 24, 2018

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