Via BEDOPS convert2bed (psl2bed) and bedops operations:

$ psl2bed < hits.psl | bedops --range 5 --everything - > answer.bed

The file answer.bed will contain intervals from the PSL input, padded up- and downstream by five bases.

This BED file can be run through samtools faidx or similar to get sequence data.

Via BEDOPS convert2bed (psl2bed) and bedops operations:

$ psl2bed < hits.psl | bedops --range 5 --everything - > answer.bed

The file answer.bed will contain target intervals from the PSL (BLAT) input, padded up- and downstream by five bases.

This BED file can be run through samtools faidx or similar to get sequence data.

References:

• https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/psl2bed.html

• https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html#range-range