chain2psl.py - convert a chain file to a psl file¶
- Tags
Genomics Intervals GenomeAlignment PSL CHAIN Conversion
Purpose¶
convert a UCSC chain formatted file to a UCSC psl formatted file.
This tool is equivalent to the UCSC tool chainToPsl except that it will not compute the number of matching, mismatching, etc. bases and thus does not require the sequences.
The nomenclature the UCSC uses for its chain files is
targetToQuery.chain
for mapping query
to target
(reference). According to the UCSC documentation, target
is the
first entry in chain
files.
We have been using the nomenclature QueryToTarget.psl
. In following
this convention, the correct way to converting a psl file is:
python chain2psl.py < targetToQuery.chain > QueryToTarget.psl
If you would like to keep the TargetToQuery convention, you will need to add a pslSwap:
python chain2psl.py < targetToQuery.chain | pslSwap stdin stdout > targetToQuery.psl
Usage¶
For example:
cgat chain2psl.py < in.chain > out.psl
Type:
cgat chain2psl.py --help
for command line help.
Command line options¶
usage: chain2psl [-h] [--version] [--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]
chain2psl: error: argument -?: expected one argument