mview
mview copied to clipboard
Deal with asterisk "*" character in inputs
Hello! I'd like to kindly ask if is it possible to add support to inputs baring asterisk "*" character. This one I tested was made with sam2fasta.py:
raw
$ cat minitestsam2fastapy.fasta
>NC_045512.2_1bp_to_1680bp
ATTAAAGGTTTATACCTTCCCAGGTAACAAACC
>clone1
ATTAAAGGTTTATACC**CCCAGGTAACAAACC
>clone2
-----------------------------AACC
raw fails
$ mview -in fasta minitestsam2fastapy.fasta
Sequence lengths differ for output format 'mview' - aborting
mview: no alignments found
mview: no alignments found
edited
$ cat minitestsam2fastapy-EDIT.fasta
ATTAAAGGTTTATACCTTCCCAGGTAACAAACC
>clone1
ATTAAAGGTTTATACC--CCCAGGTAACAAACC
>clone2
-----------------------------AACC
edited works
$ mview -in fasta minitestsam2fastapy-EDIT.fasta
Identities normalised by aligned length.
cov pid 1 [ . . . ] 33
1 NC_045512.2_1bp_to_1680bp 100.0% 100.0% ATTAAAGGTTTATACCTTCCCAGGTAACAAACC
2 clone1 93.9% 93.9% ATTAAAGGTTTATACC--CCCAGGTAACAAACC
3 clone2 12.1% 100.0% -----------------------------AACC
MView 1.67, Copyright (C) 1997-2020 Nigel P. Brown
(tools) david@NewLinux:/media/david/SSD2a/1-workdir/bam2msa/test$