psl2df: Convert PSL alignment to data.frame

In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

Convert PSL alignment to data.frame

Description

Convert PSL alignment to data.frame

Usage

psl2df(psl, verbose = FALSE, ...)

Arguments

psl	file or other connection compatible with base::readLines() of data in PSL alignment format.
...	additional arguments are ignored.

Details

This function takes PSL alignment format, as produced by BLAT, and converts to data.frame. The driving reason for this function is that current methods to convert PSL to other formats lose some useful information, for example conversion to BED12 format loses the query alignment coordinates, in favor of storing only the reference coordinates.

To supply text as input use base::textConnection() to wrap a text connection around the input text.

See Also

Other jam data import functions: import_juncs_from_bed()

Examples

psls <- c(
   "2252\t0\t0\t0\t0\t0\t5\t56285\t+\tQuery_Sequence\t2252\t0\t2252\tReference_Sequence\t99095\t1992\t60529\t6\t227,86,71,79,77,1712,\t0,227,313,384,463,540,\t1992,6931,11020,39871,45861,58817,",
   "664\t0\t0\t0\t1\t3\t1\t1\t+\tQuery_Sequence\t2252\t1291\t1958\tReference_Sequence\t99095\t58842\t59507\t2\t657,7,\t1291,1951,\t58842,59500,"
   );
psl2df(textConnection(psls), verbose=TRUE)

jmw86069/splicejam documentation built on Nov. 4, 2024, 10:53 a.m.