diff_chains.py - compare to chain formatted files¶
- Tags
Genomics GenomeAlignment CHAIN Comparison
Purpose¶
Compare two genomic alignment files and calculate statistics from the comparison.
Documentation¶
Operates on two chain formatted files.
Outputs a table with the following columns:
Column |
Content |
contig1 |
contig name |
contig2 |
contig name |
strand |
strand |
mapped1 |
mapped residues |
identical1 |
identically mapped residues |
different1 |
differently mapped residues |
unique1 |
residues mapped only from set1 |
pmapped1 |
percentage of mapped residues |
pidentical1 |
percentage of identically mapped residues |
pdifferent1 |
percentage of differently mapped residues |
Similar columns exist for data set 2
Usage¶
Example:
cgat diff_chains.py hg19ToMm10v1.chain.over.gz hg19ToMm10v2.chain.over.gz
This will compare the locations that regions within the genome hg19 map to between two different mappings to the genome mm10.
Type:
python diff_chains.py --help
for command line help.
Command line options¶
usage: diff-chains [-h] [--version] [-m] [-a] [-u] [-r RESTRICT]
[--timeit TIMEIT_FILE] [--timeit-name TIMEIT_NAME]
[--timeit-header] [--random-seed RANDOM_SEED] [-v LOGLEVEL]
[--log-config-filename LOG_CONFIG_FILENAME]
[--tracing {function}] [-? ?] [-I STDIN] [-L STDLOG]
[-E STDERR] [-S STDOUT]
diff-chains: error: argument -?: expected one argument