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write_align
write_align writes aligned sequence from the data stream as a pretty alignment with a ruler to indicate alignment position and a consensus sequence.
The ruler uses these symbols:
-
.for every 10 residues -
:for every 50 residues -
|for every 100 residues
The consensus is denoted Consensus: 50% and indicates that 50% of the residues
in the column are conserved if there is a letter present.
... | write_align [options]
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-o <file> | --data_out=<file>] # Write result to file.
[-w <uint> | --wrap=<uint>] # Wrap sequences to a given width.
[-R | --no_ruler] # Suppress ruler for multiple alignments.
[-C | --no_consensus] # Suppress consensus for multiple alignments.
[-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 three Biopiece records:
SEQ: ACATAGACAGCACGTAC--GACGACGACG
SEQ_NAME: test2
---
SEQ: ACATCGTCAGCACGTACGGGACGACGACG
SEQ_NAME: test3
---
SEQ: ACATCGACAGCACGTAC----CGACGACG
SEQ_NAME: test1
---
To output these as a pretty alignment just pipe the stream to write_align:
... | write_align -x
. .
test2 ACATAGACAGCACGTAC--GACGACGACG
test3 ACATCGTCAGCACGTACGGGACGACGACG
test1 ACATCGACAGCACGTAC----CGACGACG
Consensus: 50% ACAT-G-CAGCACGTAC--GACGACGACG
If the first sequence in the alignment is a reference sequence you can use invert_align to
emphasize the changes (and disable the consensus with the -C since it is nonsense in this context):
read_fasta -i test.aln | align_seq | invert_align | write_align -Cx
. .
test2 ACATAGACAGCACGTAC__GACGACGACG
test3 ----C-T----------GG----------
test1 ----C--------------__--------
Now, if the stream only had two aligned records, a pairwise alignment would be output:
read_fasta -i test.aln | align_seq | head_records -n 2 | write_align -x
. .
test2 ACATAGACAGCACGTAC--GACGACGACG
|||| | |||||||||| ||||||||||
test3 ACATCGTCAGCACGTACGGGACGACGACG
. .
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
write_align is part of the Biopieces framework.