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Deal with asterisk "*" character in inputs

Open Aciole-David opened this issue 5 months ago • 1 comments

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$

Aciole-David avatar Sep 04 '24 20:09 Aciole-David