<commit_before>
What is NINJA-OPS?

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NINJA is Not Just Another - OTU Picking Solution. Making use of BWT-enabled aligners, NINJA quickly generates an OTU map
and table from a given fasta file of sequence reads. NINJA also allows for convenient quality control on your data, such
as fast reverse complementing, base pair trimming, and a specialized denoising transformation. 

Moreover, NINJA is entirely free and open source. 

The latest NINJA version can always be found on Github (https://github.umn.edu/algh0022/NINJA-OPS or https://github.com/GabeAl/NINJA-OPS).



Version

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1.0 (July 17th, 2015)



Dependencies
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Python 2.7 for wrapper (no additional libraries, such as numpy, are necessary)
Bowtie2



Installation

- - - - - - - - - 



0) To use the wrapper, make sure you have the a version of Python 2.7 installed on your computer. Python can be found at https://www.python.org/downloads/
1) Download and unzip the ninja package.
2) Download and unzip bowtie2 ( http://sourceforge.net/projects/bowtie-bio/files/bowtie2/ ). If you wish to use a different sequence aligner, you cannot run the wrapper ninja.py. Instructions below.
3) Take the executable "bowtie-2-align-s" and copy it to the main folder ninja_package.

IMPORTANT: Do NOT copy "bowtie-2-align-s" to any other folder (for instance, bt2db). Ninja.py looks for bowtie only in the same folder ninja.py is located in.



Instructions (wrapper)

- - - - - - - - - 


With the NINJA wrapper, simply run "python ninja.py" in your command line to put your data through the entire NINJA pipeline. 

Sample commands are as follows:



# Takes a fasta file as input (-i) and outputs its OTU map, OTU table and a list of sequences culled by NINJA to the default output folder ninja_output in your current working directory

> python ninja.py -i seqs.fna 



# Takes a fasta file as input (-i), reverse complements it (-r) and outputs its OTU map, OTU table and a list of sequences culled by NINJA to the folder seqs_output (-o)

> python ninja.py -i seqs.fna -o seqs_output -r


<commit_msg>Clarification to reverse complement behavior<commit_after>
What is NINJA-OPS?

- - - - - - - - - 


NINJA is Not Just Another - OTU Picking Solution. Making use of BWT-enabled aligners, NINJA quickly generates an OTU map
and table from a given fasta file of sequence reads. NINJA also allows for convenient quality control on your data, such
as fast reverse complementing, base pair trimming, and a specialized denoising transformation. 

Moreover, NINJA is entirely free and open source. 

The latest NINJA version can always be found on Github (https://github.umn.edu/algh0022/NINJA-OPS or https://github.com/GabeAl/NINJA-OPS).



Version

- - - - - - - - - 


1.0 (July 17th, 2015)



Dependencies
- - - - - - - - - 


Python 2.7 for wrapper (no additional libraries, such as numpy, are necessary)
Bowtie2



Installation

- - - - - - - - - 



0) To use the wrapper, make sure you have the a version of Python 2.7 installed on your computer. Python can be found at https://www.python.org/downloads/
1) Download and unzip the ninja package.
2) Download and unzip bowtie2 ( http://sourceforge.net/projects/bowtie-bio/files/bowtie2/ ). If you wish to use a different sequence aligner, you cannot run the wrapper ninja.py. Instructions below.
3) Take the executable "bowtie-2-align-s" and copy it to the main folder ninja_package.

IMPORTANT: Do NOT copy "bowtie-2-align-s" to any other folder (for instance, bt2db). Ninja.py looks for bowtie only in the same folder ninja.py is located in.



Instructions (wrapper)

- - - - - - - - - 


With the NINJA wrapper, simply run "python ninja.py" in your command line to put your data through the entire NINJA pipeline. 

Sample commands are as follows:



# Takes a fasta file as input (-i) and outputs its OTU map, OTU table and a list of sequences culled by NINJA to the default output folder ninja_output in your current working directory

> python ninja.py -i seqs.fna 



# Takes a fasta file as input (-i), reverse complements all reads within it (-r) and outputs its OTU map, OTU table and a list of sequences culled by NINJA to the folder seqs_output (-o)

> python ninja.py -i seqs.fna -o seqs_output -r



{'fraction_non_alphanumeric': 0.0814225549836219, 'fraction_numerical': 0.012166588675713618, 'mean_word_length': 3.1585603112840466, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 7, 'https://': 6, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 16, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1712369', 'n_tokens_mistral': 1448, 'n_tokens_neox': 1300, 'n_words': 595}