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cell-extract (1.3.1)

Published 2026-05-20 16:17:45 +00:00 by ross in ross/cell-extract

Installation

pip install --index-url  cell-extract

About this package

Extract specific columns from multiple tabular files and merge by row identifier.

cell-extract

Extract specific columns from multiple tabular files and merge them by row identifier.

cell-extract reads CSV, TSV, or custom-delimited files, extracts a user-specified column from each, and produces a single merged output table. Duplicate row IDs within a file are handled by averaging their numeric values.

Installation

pip install -e .

Or with dev dependencies (for testing):

pip install -e ".[dev]"

Quick Start

Given two files:

alpha.csv

gene,expr,pval
BRCA1,2.3,0.01
TP53,5.1,0.001

beta.csv

gene,expr,pval
BRCA1,4.7,0.02
TP53,3.2,0.05

Run:

cell-extract alpha.csv beta.csv --column expr

Output:

Origin,alpha,beta
BRCA1,2.3,4.7
TP53,5.1,3.2

Usage

cell-extract [OPTIONS] FILE [FILE ...]

Required Argument

Option Description
--column COLUMN, -c COLUMN Name of the column to extract from each file

Options

Option Description
--output FILE, -o FILE Write output to FILE instead of stdout
--output-format {csv,tsv}, -f {csv,tsv} Output format (default: csv)
--with-source, -s Add a Source column recording which original column was extracted
--delimiter DELIM, -d DELIM Input delimiter override (e.g. tab, pipe, |, ;)
--skip-lines N Skip N leading lines in each file before parsing headers
--id-column COLUMN, -i COLUMN Column to use as row identifier (default: first column)
--version, -V Show version and exit
--help, -h Show help message

Behavior

  • Row union: All row identifiers from all files are merged. If a row exists in file A but not file B, the cell for file B will be empty.
  • Duplicate rows averaged: If a row identifier appears multiple times within a file, the values are averaged. Non-numeric values in the target column are skipped with a warning.
  • Integer formatting: Averages that are whole numbers display without a decimal point (e.g. 6); fractional results include a decimal (e.g. 1.5).
  • Empty cells: Missing values are written as empty fields.
  • Delimiter detection: .csv → comma; .tsv or .tab → tab. Use --delimiter to override.
  • Output format: CSV by default; use -f tsv for TSV output.
  • Row identifier: Defaults to the first column of each file. Use --id-column to specify a different column.

Examples

Multiple files with different row sets

cell-extract set1.csv set2.csv set3.csv -c expression

TSV input and output

cell-extract -c count -f tsv sample_A.tsv sample_B.tsv

Save to file

cell-extract -c fold_change -o merged.csv *.csv

With source tracing column

cell-extract alpha.csv beta.csv -c expr -s
# Origin,alpha,beta,Source
# BRCA1,2.3,4.7,expr
# TP53,5.1,3.2,expr

Custom delimiter (pipe-delimited files)

cell-extract -c val -d pipe data1.csv data2.csv
cell-extract -c val -d "|" data1.csv data2.csv

Skip metadata header lines

# Files with experiment labels before the column headers:
#   Experiment: RNA-seq
#   Date: 2025-02-14
#   gene,expr,pval
#   BRCA1,2.3,0.01

cell-extract -c expr --skip-lines 2 file1.csv file2.csv

Custom row identifier column

# Use the "label" column instead of the first column as the row key
cell-extract -c val -i label data.csv

Duplicate rows averaged

# input.csv:
# id,val
# X,10
# X,30

cell-extract input.csv -c val
# Origin,input
# X,20        ← average of (10+30)/2

All features together

cell-extract -c result -i sample_id -d pipe --skip-lines 3 -s -f tsv -o out.tsv *.csv

Development

Run tests:

pip install -e ".[dev]"
pytest tests/

License

MIT

Requirements

Requires Python: >=3.9
Details
PyPI
ross/cell-extract
2026-05-20 16:17:45 +00:00
9
MIT
19 KiB
Assets (2)
cell_extract-1.3.1-py3-none-any.whl 7.5 KiB
cell_extract-1.3.1.tar.gz 11 KiB
Versions (6) View all
1.4.0 2026-05-21
1.3.1 2026-05-20
1.3.0 2026-05-05
1.2.0 2026-05-05
1.1.0 2026-05-05
Issues