data-file-profiler-utils 0.1.7

A Python module for simple data file profiling.

Data File Profiler Utils

A Python module for simple data file profiling.

Usage

Installation

pip install data-file-profiler-utils

Integration

from import data_file_profiler_utils import Manager as ProfileManager

pm = ProfileManager()
pm.profile_file("/tmp/patient002.vcf")

Exported Console Script

Contents of sample data file:

cat -n sample.tsv
1  #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
2  1       12345   rs567   A       G       50      PASS    DP=30;AF=0.2;AN=1000;CSQ=missense_variant|HIGH|GeneA|ENSG00000112345|transcriptA|ENST00000234567|protein_coding|1/10|c.123C>T|p.Arg41Trp|123/1000|ensembl
3  2       56789   rs890   T       C       44      PASS    DP=25;AF=0.1;AN=1200;CSQ=synonymous_variant|MEDIUM|GeneB|ENSG00000123456|transcriptB|ENST00000345678|protein_coding|5/20|c.567A>G|p.Ala189Ala|567/1200|ensembl
4  3       98765   rs123   G       T       60      PASS    DP=40;AF=0.3;AN=800;CSQ=splice_acceptor_variant|HIGH|GeneC|ENSG00000134567|transcriptC|ENST00000456789|protein_coding|2/15|c.987+1G>T|p.?|987/800|ensembl
5  1       34567   rs456   C       A       55      PASS    DP=35;AF=0.15;AN=900;CSQ=frameshift_variant|HIGH|GeneX|ENSG00000145678|transcriptX|ENST00000567890|protein_coding|8/25|c.345_346insT|p.Leu116Phefs*12|345/900|ensembl

Invocation of the exported console script:

profile-data-file --infile /tmp/demo-data-file-profiler-utils/sample.tsv --verbose --outdir /tmp/demo-data-file-profiler-utils/
--logfile was not specified and therefore was set to '/tmp/demo-data-file-profiler-utils/profile_data_file.log'
Wrote profile metadata file '/tmp/demo-data-file-profiler-utils/sample.tsv.profile.txt'
The log file is '/tmp/demo-data-file-profiler-utils/profile_data_file.log'
Execution of '/tmp/data-file-profiler-utils/venv/lib/python3.10/site-packages/data_file_profiler_utils/profile_data_file.py' completed

Contents of the profile report:

cat -n /tmp/demo-data-file-profiler-utils/sample.tsv.profile.txt
1  ## method-profiled: /tmp/data-file-profiler-utils/venv/lib/python3.10/site-packages/data_file_profiler_utils/manager.py
2  ## date-profiled: 2025-02-15-142732
3  ## profiled-by: sundaram
4  file: /tmp/demo-data-file-profiler-utils/sample.tsv
5  md5sum: 786b82b2414d3acf7af34c068e358759
6  date_created: 2025-02-15 14:06:37.202165
7  file_size: 776
8  line_count: 5

History

0.1.0 (2024-02-10)

• First release on PyPI.