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find_gaps
Martin Asser Hansen edited this page Oct 2, 2015
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find_gaps locates stretches of N's (case insensitive) in sequences in the stream. For each stretch of N's a record is output like this:
S_ID: chr1
S_BEG: 123
S_END: 12345
S_LEN: 12222
---
... | find_gaps [options]
[-? | --help] # Print full usage description.
[-m <uint> | --min_len=<uint>] # Minimum gap length - Default=5
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
Here is how you find gaps in a genome read in with read_fasta and the result is written to KISS format with write_kiss:
read_fasta -i genome.fna | find_gaps | write_kiss -x
Martin Asser Hansen - Copyright (C) - All rights reserved.
March 2010
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
find_gaps is part of the Biopieces framework.