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Predict AMPs in (meta)genomes and peptides

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Merge pull request #2 from luispedro/fix_doc_typos DOC Fix typos in the documentation

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DOC Fix typos in the documentation

Fix some minor typos in the docs and add a message about how this is all very experimental so that people don't start using it while expecting it to be polished (we will want people to use it, but not yet)

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issue openedngless-toolkit/ngless

error message write ofile

The error message was: /fast/temp/reads_block_selected_mapped_HG38_progenomesmasked.1.fq14697-12.gz: renameFile:renamePath:rename: does not exist (No such file or directory)

Was due to the path given in my human_samples.txt file: RAWseq/P01-A01-H1H RAWseq/P01-A02-H9H RAWseq/P01-A03-H20H ... But I find the error message a bit misleading. Maybe you can enhance the error message.

import "mocat" version "2.0.1"
local import "motus" version "2.5"
import "parallel" version "1.0"

#load samples attention! here mocat structure (each sample one directory is expected while "Paired-end reads are assumed to be split into two files, with matching names with .1/.2 appended. _1/_2 as is used by the European Nucleotide Archive (ENA) is also accepted."
samples = readlines('human_samples.txt')
current = lock1(samples)
input = paired( current + "_R1.fastq",  current + "_R2.fastq")
RESULTS = "PreProc"
qc_reads = preprocess(input, keep_singles=False) using |read|:
    read = substrim(read, min_quality=25)
    if len(read) < 45:
        discard
human_mapped = map(qc_reads, fafile='/fast/AG_Forslund/shared/references/HG38_progenomesmasked.fa')
collect(count(human_mapped,features=['seqname']),
current=current,
allneeded=samples,
ofile='filterhuman.txt')

non_human = select(human_mapped) using |mr|:
    mr = mr.filter(min_match_size=45, min_identity_pc=90, action={unmatch})
    if mr.flag({mapped}):
        
non_human_reads = as_reads(
write(non_human_reads,ofile=RESULTS</>current + 'filtered_qc.fq.gz')

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PR opened BigDataBiology/big-data-biology_org

Bump nokogiri from 1.10.10 to 1.11.1

Bumps nokogiri from 1.10.10 to 1.11.1. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/sparklemotion/nokogiri/releases">nokogiri's releases</a>.</em></p> <blockquote> <h2>v1.11.1 / 2021-01-06</h2> <h3>Fixed</h3> <ul> <li>[CRuby] If <code>libxml-ruby</code> is loaded before <code>nokogiri</code>, the SAX and Push parsers no longer call <code>libxml-ruby</code>'s handlers. Instead, they defensively override the libxml2 global handler before parsing. [<a href="https://github-redirect.dependabot.com/sparklemotion/nokogiri/issues/2168">#2168</a>]</li> </ul> <h3>SHA-256 Checksums of published gems</h3> <pre><code>a41091292992cb99be1b53927e1de4abe5912742ded956b0ba3383ce4f29711c nokogiri-1.11.1-arm64-darwin.gem d44fccb8475394eb71f29dfa7bb3ac32ee50795972c4557ffe54122ce486479d nokogiri-1.11.1-java.gem f760285e3db732ee0d6e06370f89407f656d5181a55329271760e82658b4c3fc nokogiri-1.11.1-x64-mingw32.gem dd48343bc4628936d371ba7256c4f74513b6fa642e553ad7401ce0d9b8d26e1f nokogiri-1.11.1-x86-linux.gem 7f49138821d714fe2c5d040dda4af24199ae207960bf6aad4a61483f896bb046 nokogiri-1.11.1-x86-mingw32.gem 5c26111f7f26831508cc5234e273afd93f43fbbfd0dcae5394490038b88d28e7 nokogiri-1.11.1-x86_64-darwin.gem c3617c0680af1dd9fda5c0fd7d72a0da68b422c0c0b4cebcd7c45ff5082ea6d2 nokogiri-1.11.1-x86_64-linux.gem 42c2a54dd3ef03ef2543177bee3b5308313214e99f0d1aa85f984324329e5caa nokogiri-1.11.1.gem </code></pre> <h2>v1.11.0 / 2021-01-03</h2> <h3>Notes</h3> <h4>Faster, more reliable installation: Native Gems for Linux and OSX/Darwin</h4> <p>"Native gems" contain pre-compiled libraries for a specific machine architecture. On supported platforms, this removes the need for compiling the C extension and the packaged libraries. This results in <strong>much faster installation</strong> and <strong>more reliable installation</strong>, which as you probably know are the biggest headaches for Nokogiri users.</p> <p>We've been shipping native Windows gems since 2009, but starting in v1.11.0 we are also shipping native gems for these platforms:</p> <ul> <li>Linux: <code>x86-linux</code> and <code>x86_64-linux</code> -- including musl platforms like alpine</li> <li>OSX/Darwin: <code>x86_64-darwin</code> and <code>arm64-darwin</code></li> </ul> <p>We'd appreciate your thoughts and feedback on this work at <a href="https://github-redirect.dependabot.com/sparklemotion/nokogiri/issues/2075">#2075</a>.</p> <h3>Dependencies</h3> <h4>Ruby</h4> <p>This release introduces support for Ruby 2.7 and 3.0 in the precompiled native gems.</p> <p>This release ends support for:</p> <ul> <li>Ruby 2.3, for which <a href="https://www.ruby-lang.org/en/news/2019/03/31/support-of-ruby-2-3-has-ended/">official support ended on 2019-03-31</a> [<a href="https://github-redirect.dependabot.com/sparklemotion/nokogiri/issues/1886">#1886</a>] (Thanks <a href="https://github.com/ashmaroli"><code>@​ashmaroli</code></a>!)</li> <li>Ruby 2.4, for which <a href="https://www.ruby-lang.org/en/news/2020/04/05/support-of-ruby-2-4-has-ended/">official support ended on 2020-04-05</a></li> <li>JRuby 9.1, which is the Ruby 2.3-compatible release.</li> </ul> <h4>Gems</h4> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/sparklemotion/nokogiri/blob/main/CHANGELOG.md">nokogiri's changelog</a>.</em></p> <blockquote> <h2>v1.11.1 / 2021-01-06</h2> <h3>Fixed</h3> <ul> <li>[CRuby] If <code>libxml-ruby</code> is loaded before <code>nokogiri</code>, the SAX and Push parsers no longer call <code>libxml-ruby</code>'s handlers. Instead, they defensively override the libxml2 global handler before parsing. [<a href="https://github-redirect.dependabot.com/sparklemotion/nokogiri/issues/2168">#2168</a>]</li> </ul> <h2>v1.11.0 / 2021-01-03</h2> <h3>Notes</h3> <h4>Faster, more reliable installation: Native Gems for Linux and OSX/Darwin</h4> <p>"Native gems" contain pre-compiled libraries for a specific machine architecture. On supported platforms, this removes the need for compiling the C extension and the packaged libraries. This results in <strong>much faster installation</strong> and <strong>more reliable installation</strong>, which as you probably know are the biggest headaches for Nokogiri users.</p> <p>We've been shipping native Windows gems since 2009, but starting in v1.11.0 we are also shipping native gems for these platforms:</p> <ul> <li>Linux: <code>x86-linux</code> and <code>x86_64-linux</code> -- including musl platforms like alpine</li> <li>OSX/Darwin: <code>x86_64-darwin</code> and <code>arm64-darwin</code></li> </ul> <p>We'd appreciate your thoughts and feedback on this work at <a href="https://github-redirect.dependabot.com/sparklemotion/nokogiri/issues/2075">#2075</a>.</p> <h3>Dependencies</h3> <h4>Ruby</h4> <p>This release introduces support for Ruby 2.7 and 3.0 in the precompiled native gems.</p> <p>This release ends support for:</p> <ul> <li>Ruby 2.3, for which <a href="https://www.ruby-lang.org/en/news/2019/03/31/support-of-ruby-2-3-has-ended/">official support ended on 2019-03-31</a> [<a href="https://github-redirect.dependabot.com/sparklemotion/nokogiri/issues/1886">#1886</a>] (Thanks <a href="https://github.com/ashmaroli"><code>@​ashmaroli</code></a>!)</li> <li>Ruby 2.4, for which <a href="https://www.ruby-lang.org/en/news/2020/04/05/support-of-ruby-2-4-has-ended/">official support ended on 2020-04-05</a></li> <li>JRuby 9.1, which is the Ruby 2.3-compatible release.</li> </ul> <h4>Gems</h4> <ul> <li>Explicitly add racc as a runtime dependency. [<a href="https://github-redirect.dependabot.com/sparklemotion/nokogiri/issues/1988">#1988</a>] (Thanks, <a href="https://github.com/voxik"><code>@​voxik</code></a>!)</li> <li>[MRI] Upgrade mini_portile2 dependency from <code>~> 2.4.0</code> to <code>~> 2.5.0</code> [<a href="https://github-redirect.dependabot.com/sparklemotion/nokogiri/issues/2005">#2005</a>] (Thanks, <a href="https://github.com/alejandroperea"><code>@​alejandroperea</code></a>!)</li> </ul> <h3>Security</h3> <p>See note below about CVE-2020-26247 in the "Changed" subsection entitled "XML::Schema parsing treats input as untrusted by default".</p> <h3>Added</h3> <ul> <li>Add Node methods for manipulating "keyword attributes" (for example, <code>class</code> and <code>rel</code>): <code>#kwattr_values</code>, <code>#kwattr_add</code>, <code>#kwattr_append</code>, and <code>#kwattr_remove</code>. [<a href="https://github-redirect.dependabot.com/sparklemotion/nokogiri/issues/2000">#2000</a>]</li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/sparklemotion/nokogiri/commit/7be6f04aa2700e818f8a3bfe82801b5bd6e8c4f4"><code>7be6f04</code></a> version bump to v1.11.1</li> <li><a href="https://github.com/sparklemotion/nokogiri/commit/aa0c3991953c5955b0c2e778af961a2ca3225467"><code>aa0c399</code></a> dev: overhaul .gitignore</li> <li><a href="https://github.com/sparklemotion/nokogiri/commit/3d90c6d1bc871ad41c117efbd95c7d7b5a63344d"><code>3d90c6d</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/sparklemotion/nokogiri/issues/2169">#2169</a> from sparklemotion/2168-active-support-test-failure</li> <li><a href="https://github.com/sparklemotion/nokogiri/commit/bbf850c6297347461df92b1f208f4e8fc744e1c8"><code>bbf850c</code></a> changelog: update for <a href="https://github-redirect.dependabot.com/sparklemotion/nokogiri/issues/2168">#2168</a></li> <li><a href="https://github.com/sparklemotion/nokogiri/commit/ee697726dc35f2996d5f5cf6b8c8e0516a79eadf"><code>ee69772</code></a> ci: another valgrind suppression</li> <li><a href="https://github.com/sparklemotion/nokogiri/commit/f9a2c4e050f337e30f08ac32f19e1e10f229723a"><code>f9a2c4e</code></a> fix: restore proper error handling in the SAX push parser</li> <li><a href="https://github.com/sparklemotion/nokogiri/commit/35aa88b75e7d8436217471ef6ff58f814466b26e"><code>35aa88b</code></a> fix(cruby): reset libxml2's error handler in sax and push parsers</li> <li><a href="https://github.com/sparklemotion/nokogiri/commit/07459fd0e0db1d488748726d1f4accd9bac18646"><code>07459fd</code></a> fix(test): clobber libxml2's global error handler before every test</li> <li><a href="https://github.com/sparklemotion/nokogiri/commit/b682ac5afeabfc636edf282700f05fd5923fa396"><code>b682ac5</code></a> ci: ensure all tests are running <code>setup</code></li> <li><a href="https://github.com/sparklemotion/nokogiri/commit/007662fc216902a5ae186cb78b0d46f7f48b8d92"><code>007662f</code></a> github: update "installation difficulty" issue template</li> <li>Additional commits viewable in <a href="https://github.com/sparklemotion/nokogiri/compare/v1.10.10...v1.11.1">compare view</a></li> </ul> </details> <br />

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