<commit_before>### Muscato (Multi-Genome Scalable Alignment Tool)

Muscato is a software tool for matching a collection of read sequences
into a collection of target sequences (e.g. gene sequences).  The
approach scales efficiently to hundreds of millions of reads and
target sequences.  A major goal of Muscato is to perform exhaustive
multi-mapping, meaning that each read is mapped to as many gene
sequences as possible, subject to specified match quality constraints.

__Installation__

Muscato is written in [Go](https://golang.org) and uses several of the
[Gnu core
utilities](http://www.gnu.org/software/coreutils/coreutils.html).  It
should run on any Unix-like system on which the [Go
tool](https://golang.org/dl) and Gnu utilities are available.

In most cases, installation of Muscato should only require running the
following commands in the shell:

```
go get github.com/kshedden/muscato/...

go get github.com/kshedden/sztool/...
```

The executables for muscato and its auxiliary scripts should appear in
your GOBIN directory (usually ${HOME}/go/bin if installed in a user
account).  You will need to add GOBIN to your PATH environment
variable when using the tool.

__Basic usage__

Before running Muscato, you should prepare a version of your target
sequence file using the `muscato_prep_targets` program.  If your
targets are in a fasta format file, you can simply run:
<commit_msg>Added PATH instructions to README<commit_after>### Muscato (Multi-Genome Scalable Alignment Tool)

Muscato is a software tool for matching a collection of read sequences
into a collection of target sequences (e.g. gene sequences).  The
approach scales efficiently to hundreds of millions of reads and
target sequences.  A major goal of Muscato is to perform exhaustive
multi-mapping, meaning that each read is mapped to as many gene
sequences as possible, subject to specified match quality constraints.

__Installation__

Muscato is written in [Go](https://golang.org) and uses several of the
[Gnu core
utilities](http://www.gnu.org/software/coreutils/coreutils.html).  It
should run on any Unix-like system on which the [Go
tool](https://golang.org/dl) and Gnu utilities are available.

In most cases, installation of Muscato should only require running the
following commands in the shell:

```
go get github.com/kshedden/muscato/...

go get github.com/kshedden/sztool/...
```

The executables for Muscato and its auxiliary scripts should appear in
your GOBIN directory (usually ${HOME}/go/bin if installed in a user
account).  You will need to add GOBIN to your PATH environment
variable when using Muscato.  If you are using the Bash shell enter
the following lines at the shell prompt, or add them to your .bashrc
file to make the changes permanent.

```
export GOPATH=${HOME}/go
export GOBIN=${GOPATH}/bin
export PATH=${GOBIN}:${PATH}
```

__Basic usage__

Before running Muscato, you should prepare a version of your target
sequence file using the `muscato_prep_targets` program.  If your
targets are in a fasta format file, you can simply run:

{'fraction_non_alphanumeric': 0.06714706845725515, 'fraction_numerical': 0.0, 'mean_word_length': 4.583180987202925, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 4, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '693146', 'n_tokens_mistral': 873, 'n_tokens_neox': 825, 'n_words': 418}