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              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
atropos-1.1.24+dfsg/doc/installation.rst-13-index) <https://pypi.python.org/pypi/atropos/>`_, and
atropos-1.1.24+dfsg/doc/installation.rst:14:install the atropos binary into ``$HOME/.local/bin``. If an old version of
atropos-1.1.24+dfsg/doc/installation.rst-15-atropos exists on your system, the ``--upgrade`` parameter is required in order
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atropos-1.1.24+dfsg/doc/installation.rst-20-If you want to avoid typing the full path, add the directory
atropos-1.1.24+dfsg/doc/installation.rst:21:``$HOME/.local/bin`` to your ``$PATH`` environment variable.
atropos-1.1.24+dfsg/doc/installation.rst-22-
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atropos-1.1.24+dfsg/paper/containers/docker2singularity.sh-8-   echo "Transferring $container to ${REMOTE_HOST}:${REMOTE_DIR}" \
atropos-1.1.24+dfsg/paper/containers/docker2singularity.sh:9:&& name=`basename $container` \
atropos-1.1.24+dfsg/paper/containers/docker2singularity.sh-10-&& file="${name}.img" \
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atropos-1.1.24+dfsg/paper/manuscript/main/tex/main.tex-97-
atropos-1.1.24+dfsg/paper/manuscript/main/tex/main.tex:98:Often, details of sequencing library construction are not fully communicated from the individual or facility that generated the library to the individual(s) performing data analysis. For example, the majority of datasets in the NCBI Sequence Read Archive (SRA) lack adapter sequence annotations. Manual determination of sequencing adapters and other potential library contaminants can be a tedious and error-prone task. Thus, we implemented in Atropos a command that automatically identifies adapters/contaminants from a sample of read sequences. First, a profile is built of $k$-mers (where $k$ is a fixed number of consecutive nucleotides, defaulting to $k=12$) within $N$ read sequences (where $N$ defaults to 10,000). When at least 8 consecutive A bases are detected, those bases along with all subsequent bases (in the 3' direction) are first trimmed, as that pattern is a strong indicator that the sequencer scanned past the end of the template (i.e. the length of the fragment + adapter is less than the read length; Figure~\ref{fig:overview}E). Additionally, low-complexity reads are excluded, where complexity $X(S)$ is defined as follows. Let $C(i,S)$ be the number of elements of a nucleotide sequence $S = s_{1}, ..., s_{n}$, that are nucleotide $i \in {A,C,G,T}$.
atropos-1.1.24+dfsg/paper/manuscript/main/tex/main.tex-99-
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atropos-1.1.24+dfsg/paper/manuscript/main/tex/main.tex-111-
atropos-1.1.24+dfsg/paper/manuscript/main/tex/main.tex:112:where $l$ is the read length and $O=100$ by default. Finally, high-abundance $k$-mers of all lengths are merged to eliminate shorter sequences that are fully contained in longer sequences.
atropos-1.1.24+dfsg/paper/manuscript/main/tex/main.tex-113-
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atropos-1.1.24+dfsg/paper/workflow/bin/summarize_slurm_job.sh-1-#!/bin/bash
atropos-1.1.24+dfsg/paper/workflow/bin/summarize_slurm_job.sh:2:jobId=`cat $1`
atropos-1.1.24+dfsg/paper/workflow/bin/summarize_slurm_job.sh-3-sacct -P -o ALL -j $jobId
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atropos-1.1.24+dfsg/versioneer.py-76-
atropos-1.1.24+dfsg/versioneer.py:77:`_version.py` also contains `$Revision$` markers, and the installation
atropos-1.1.24+dfsg/versioneer.py-78-process marks `_version.py` to have this marker rewritten with a tag name
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atropos-1.1.24+dfsg/debian/createmanpages-4-
atropos-1.1.24+dfsg/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
atropos-1.1.24+dfsg/debian/createmanpages-6-NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`