mpdunne / alan Goto Github PK
View Code? Open in Web Editor NEWAlignment viewer for linux terminal
Alignment viewer for linux terminal
Hi,
I love this tool! Easy to use and install, output has pretty and useful colors
Would it be possible to allow stdin as input? Bioinformatics tools love to work with streams, would be really nice if I could look at stream output with alan instead of the far-inferior less
I wanted to post a minimal example to demonstrate, sorry for the useless use of cat
printf ">test\nMVVLKR" > test_seq.pep
cat test_seq.pep | alan -
See muscle v5 documentation: https://drive5.com/muscle5/
For OS X OS X 10.13.1, I get this error when running alan
:
sed: illegal option -- r
usage: sed script [-Ealn] [-i extension] [file ...]
sed [-Ealn] [-i extension] [-e script] ... [-f script_file] ... [file ...]
I thought maybe we need to use sed -E
instead of sed -r
to unlock the extended regex feature. however, that just returns this:
usage: grep [-abcDEFGHhIiJLlmnOoqRSsUVvwxZ] [-A num] [-B num] [-C[num]]
[-e pattern] [-f file] [--binary-files=value] [--color=when]
[--context[=num]] [--directories=action] [--label] [--line-buffered]
[--null] [pattern] [file ...]
Running alanpartridge
give me:
usage: grep [-abcDEFGHhIiJLlmnOoqRSsUVvwxZ] [-A num] [-B num] [-C[num]]
[-e pattern] [-f file] [--binary-files=value] [--color=when]
[--context[=num]] [--directories=action] [--label] [--line-buffered]
[--null] [pattern] [file ...]
awk: invalid -v option
awk: invalid -v option
So, I think it may just be an issue of different versions of awk
/sed
/grep
that have different flags/options available.
Hi and thanks for the ingeniously simple tool!
I would love to use it to skim through hundreds of alignments. For this purpose, :n
and :p
shortcuts of less
would be helpful.
Is it possible to enable feeding arbitrary number fasta files as separate input pipes to less
?
Cheers!
Nikita
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