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remove_indel_columns
Martin Asser Hansen edited this page Oct 2, 2015
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remove_indel_columns removes columns in alignments containing only indels (~-._ characters)
from sequences in the stream.
... | remove_indel_columns [options]
[-? | --help] # Print full usage description.
[-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.
Consider the following aligned sequences in the FASTA file test.fna:
>test1
_cgta.cgta-ctacg~actcgtacg-
>test2
_cgta.cgta-ctacg~actcgtacg-
>test3
_cgta.cgta-ctacg~actcgtacg-
>test4
_cgta.cgta-ctacg~actcgtacg-
>test5
_cgta.cgtagctacg~actcgtacg-
To remove the indels-only columns, do:
read_fasta -i test.fna | remove_indel_columns
SEQ_NAME: test1
SEQ: cgtacgta-ctacgactcgtacg
SEQ_LEN: 23
---
SEQ_NAME: test2
SEQ: cgtacgta-ctacgactcgtacg
SEQ_LEN: 23
---
SEQ_NAME: test3
SEQ: cgtacgta-ctacgactcgtacg
SEQ_LEN: 23
---
SEQ_NAME: test4
SEQ: cgtacgta-ctacgactcgtacg
SEQ_LEN: 23
---
SEQ_NAME: test5
SEQ: cgtacgtagctacgactcgtacg
SEQ_LEN: 23
---
Martin Asser Hansen - Copyright (C) - All rights reserved.
December 2011
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
remove_indel_columns is part of the Biopieces framework.