presto.Applications

External application wrappers

presto.Applications.makeUSearchDb(ref_file, usearch_exec='/usr/local/bin/usearch')

Makes a usearch database file for ublast

Arguments: ref_file = the path to the reference database file usearch_exec = the path to the usearch executable

Returns: a handle to the named temporary file containing the database file

presto.Applications.runBlastnAlignment(seq, ref_file, evalue=1e-05, max_hits=100, blastn_exec='/usr/bin/blastn')

Aligns a sequence against a reference database using BLASTN

Arguments: seq = a SeqRecord objects to align ref_dict = a dictionary of reference SeqRecord objects evalue = the E-value cut-off for ublast maxhits = the maxhits output limit for ublast blastn_exec = the path to the usearch executable

Returns: a DataFrame of alignment results

presto.Applications.runMuscle(seq_list, muscle_exec='/usr/local/bin/muscle')

Multiple aligns a set of sequences using MUSCLE

Arguments: seq_list = a list of SeqRecord objects to align muscle_exec = the MUSCLE executable

Returns: a MultipleSeqAlignment object containing the alignment

presto.Applications.runUBlastAlignment(seq, ref_file, evalue=1e-05, max_hits=100, usearch_exec='/usr/local/bin/usearch')

Aligns a sequence against a reference database using the UBLAST algorithm of USEARCH

Arguments: seq = a SeqRecord object to align ref_file = the path to the reference database file evalue = the E-value cut-off for ublast max_hits = the maxhits output limit for ublast usearch_exec = the path to the usearch executable

Returns: a DataFrame of alignment results

presto.Applications.runUClust(seq_list, ident=0.9, seq_start=0, seq_end=None, usearch_exec='/usr/local/bin/usearch')

Cluster a set of sequences using the UCLUST algorithm from USEARCH

Arguments: seq_list = a list of SeqRecord objects to align ident = the sequence identity cutoff to be passed to usearch seq_start = the start position to trim sequences at before clustering seq_end = the end position to trim sequences at before clustering usearch_exec = the path to the usearch executable

Returns: a dictionary object containing {sequence id: cluster id}