Welcome to smallBixTools’s documentation!

Contents:

smallBixTools.smallBixTools.try_call(cmd, logging=None)

Try a subprocess call on a string cmd. Raises an error on exceptions. Logging is allowed. :param cmd: The string to try calling. :param logging: Can optionally take a logging arg. This is the default logging for Python. :return: Returns the return code from calling the string command.

smallBixTools.smallBixTools.convert_count_to_frequency_on_fasta(source_fasta_fn, target_fasta_fn)

when running vsearch as such: vsearch –cluster_fast {} –id 0.97 –sizeout –centroids {} We get a centroids.fasta file with seqid header lines like: >ATTCCGGTATCT_9;size=1432; >CATCATCGTAAG_14;size=1; etc. This method converts those count values into frequencies. Notes: The delimiter between sections in the sequence id must be “;”. There must be a section in the sequence id which has exactly: “size=x” where x is an integer. This must be surrounded by ; :param source_fasta_fn: the input fasta file. Full path required. :param target_fasta_fn: the output fasta file. Full path required. If this is the same as the input, the input will

be over-written.
Returns:No return value.
smallBixTools.haplotype_aligned_file.haplo_aligned_file(infile, outfile)

Haplotypes an aligned fasta file. Each sequence which is the same is only included once. The last sequence id in the file associated with this sequence is used as the seqid in the outfile. :param infile: The .fasta formatted file to be haplotyped :param outfile: The place to write the haplotyped .fasta file to on disc. :return: No return.

Indices and tables

install smallBixTools you can use pip: pip install smallbixtools (or update: python /home/dave/anaconda3/bin/pip install smallBixTools –upgrade)

How to install with conda: identify what python your anaconda is using: (how do..) python3.5 /home/<username>/anaconda3/bin/pip install smallbixtools

Or, if you have it installed already, you can simply update: python3.5 /home/dave/anaconda3/bin/pip install smallBixTools –upgrade