presto.Applications¶
External application wrappers
-
presto.Applications.
makeBlastnDb
(ref_file, db_exec='makeblastdb')¶ Makes a blastn database file
- Parameters
ref_file – the path to the reference database file
db_exec – the path to the makeblastdb executable
- Returns
(name and location of the database, handle of the tempfile.TemporaryDirectory)
- Return type
-
presto.Applications.
makeUBlastDb
(ref_file, db_exec='usearch')¶ Makes a ublast database file
- Parameters
ref_file – path to the reference database file.
db_exec – path to the usearch executable.
- Returns
(location of the database, handle of the tempfile.NamedTemporaryFile)
- Return type
-
presto.Applications.
runBlastn
(seq, database, evalue=1e-05, max_hits=100, aligner_exec='blastn')¶ Aligns a sequence against a reference database using BLASTN
- Parameters
seq – a list of SeqRecord objects to align.
database – the path and name of the blastn database.
evalue – the E-value cut-off.
maxhits – the maximum number of hits returned.
aligner_exec – the path to the blastn executable.
- Returns
Alignment results.
- Return type
pandas.DataFrame
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presto.Applications.
runCDHit
(seq_list, ident=0.9, length_ratio=0.0, seq_start=0, seq_end=None, max_memory=3000, threads=1, cluster_exec='cd-hit-est')¶ Cluster a set of sequences using CD-HIT
- Parameters
seq_list (list) – a list of SeqRecord objects to align.
ident (float) – the sequence identity cutoff to be passed to cd-hit-est.
length_ratio (float) – cd-hit-est parameter defining the minimum short/long length ratio allowed within a cluster.
seq_start (int) – the start position to trim sequences at before clustering.
seq_end (int) – the end position to trim sequences at before clustering.
max_memory (int) – cd-hit-est max memory limit (Mb)
threads (int) – number of threads for cd-hit-est.
cluster_exec (str) – the path to the cd-hit-est executable.
- Returns
{cluster id: list of sequence ids}.
- Return type
-
presto.Applications.
runMuscle
(seq_list, aligner_exec='muscle')¶ Multiple aligns a set of sequences using MUSCLE
- Parameters
seq_list – a list of SeqRecord objects to align
aligner_exec – the MUSCLE executable
- Returns
Multiple alignment results.
- Return type
Bio.Align.MultipleSeqAlignment
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presto.Applications.
runUBlast
(seq, database, evalue=1e-05, max_hits=100, aligner_exec='usearch')¶ Aligns a sequence against a reference database using the usearch_local algorithm of USEARCH
- Parameters
seq – a list of SeqRecord objects to align.
database – the path to the ublast database or a fasta file.
evalue – the E-value cut-off.
maxhits – the maximum number of hits returned.
aligner_exec – the path to the usearch executable.
- Returns
Alignment results.
- Return type
pandas.DataFrame
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presto.Applications.
runUClust
(seq_list, ident=0.9, length_ratio=0.0, seq_start=0, seq_end=None, threads=1, cluster_exec='usearch')¶ Cluster a set of sequences using the UCLUST algorithm from USEARCH
- Parameters
seq_list (list) – a list of SeqRecord objects to align.
ident (float) – the sequence identity cutoff to be passed to usearch.
length_ratio (float) – usearch parameter defining the minimum short/long length ratio allowed within a cluster.
seq_start (int) – the start position to trim sequences at before clustering.
seq_end (int) – the end position to trim sequences at before clustering.
threads (int) – number of threads for usearch.
cluster_exec (str) – the path to the usearch executable.
- Returns
{cluster id: list of sequence ids}.
- Return type