mask, remove or keep regions in an alignment
remove_blocks_from_aln is a tool to mask, remove or keep regions in an alignment. The regions are defined in an EMBL style tab-delimited file.
Details for installing remove_blocks_from_aln are provided below. If you encounter an issue when installing remove_blocks_from_aln please contact your local system administrator. If you encounter a bug please log it here or email us at path-help@sanger.ac.uk.
Download the latest release from this github repository, or clone the repository. Then run the tests:
python setup.py test
If the tests all pass, install:
python setup.py install
remove_block_from_aln.py [options]
-a <file name> alignment file name
-o <file name> output file name
-t <file name> tab file name (containing regions to keep/remove)
-r <name> reference name (optional, but required if there are gaps in the reference sequence relative to the tab file)
-k keep regions in tab file (default is to mask them)
-c cut regions in tab file (default is to mask them)
-R do not remove blocks from reference sequence (default is to remove from all sequences)
-s <N|X|?|-> Symbol to use for removed regions (default = N)
-h Show help menu
Alignment file must be in fasta format:
>sequence1
AAAATTTTCCCCGGGG
>sequence2
TTTTGGGGAAAACCCC
Tab file should emulate the EMBL file format, using only feature (FT) lines to define your regions:
FT misc_feature 5070..5095
FT /note="26 bp;mummer_exact"
FT misc_feature 8163..8182
FT /note="20 bp;mummer_exact"
FT misc_feature 9569..9588
FT /note="20 bp;mummer_exact"
Note: while complemented regions can be handled, joins cannot and should be split into separate regions.
remove_blocks_from_aln is free software, licensed under GPLv3.
Please report any issues to the issues page or email path-help@sanger.ac.uk.