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alan's Issues

Accepting stdin as input

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 -

sed in OS X 10.13.1 doesn't have -r flag for extended regex

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.

Switching between input files as in `less`?

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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