API Reference¶

Build the argument parser for probe design CLIs.

Calculate the cost of the oligo library

Main function for HCR Probe design. Called when used directly from cmdline

Batch probe design for multi-record FASTA inputs.

Formats tile output for direct ordering using IDT template

Print run parameters to stderr.

Formats tile output and writes to outHandle

Given a sequence, a name for the sequence, a step size, and a tile size, scanSequence will return a list of Tile objects that tile across the sequence

Manual test harness with hard-coded parameters and FASTA file.

For each read in the sam file, add 1 to the count of hits for that read

Run Bowtie2 to align probe tiles and write a SAM file to disk.

Download and extract a prebuilt Bowtie2 index into the package indices.

Quick manual test for Bowtie2 masking and SAM parsing.

Build a Bowtie2 index from the provided FASTA files.

Resolve FASTA inputs from files and directories.

Format an index prefix relative to the package when possible.

Load the HCRconfig.yaml file.

CLI entry point for building and registering a reference genome index.

Register a species and its Bowtie2 index prefix in the config file.

Write configuration data to HCRconfig.yaml.

Generator function to iterate over fasta records in : Use in a loop to apply to each Seq record contained in a .fasta file Input: record handle as obtained by handle = open(,'r') Returns an iterator across Sequences in file

Generate a random sequence of DNA or RNA of a given length

Return a list of all indices of a substring in a string

Return the complement of a DNA sequence

Draw a random value from the distribution, where values with a higher probability are drawn more often

Find all occurences of a substring in a string

Given a DNA sequence, return the percentage of G's and C's in the sequence

Generates a random sequence of length 'length' drawing from a distribution of base frequencies in a dictionary

The function getGC(seq) takes a string of DNA sequence as input and returns the GC content of the sequence

The function getTm(seq) takes a sequence as an argument and returns the melting temperature of the sequence

Given a list of sequences, return a dictionary of the counts of each seed

Returns dictionary of k,v = kmer:'list of kmer start positions in seq'

Returns a dictionary of k,v = kmer:'count of kmer in seq'

Takes as argument a kmer string, a dictionary with kmers as keys from kmer_dictionary_counts, and a dictionary of genomic frequencies with kmers as keys. Returns a dictionary of stats for kmer ("Signal2Noise Ratio, Z-score")

Given a dictionary of character frequencies, return a list of cumulative frequencies

Sums the counts of appearances of each char in chars

Given a sequence and a background GC probability, what is the probability of getting that sequence

Does same thing as reverse_complement only cooler

Return the reverse complement of a DNA sequence

Seed the random number generator with system entropy.

The function transcribe() takes a DNA sequence and replaces each instance of the nucleotide T with a uracil (U) in the transcribed RNA sequence

The function calculates the melting temperature of a sequence

Given a sequence, the function returns the Tm of the sequence using the SantaLucia 98 parameters

Check whether a string contains any of the given characters.

Calc Gibbs Free Energy in cal/mol from enthaply, entropy, and temperature

Arguments: dH -- enthalpy in kcal/mol dS -- entropy in cal/(mol * Kelvin) temp -- temperature in celcius (default 37 degrees C)

Return [enthalpy, entropy] list with units kcal/mol and cal/(mol*Kelvin) for DNA/DNA duplex initiation for the input DNA sequence (actg 5'->3'). Values from SantaLucia 1998. Argument is DNA

Return [enthalpy, entropy] list in kcal/mol and cal/(mol*Kelvin) for RNA/DNA duplex initiation. Values from Sugimoto et al 1995

Calculates the melting temperature of a DNA sequence.

Return Gibbs free energy at 37degC (in kcal/mol) contribution from single base overhang in DNA/DNA duplex.

Arguments: inseq - 2bp DNA sequence (5' -> 3') end - specifies which end the over hang is on (valid values: 3 or 5)

Table 2 in Bommarito, S. (2000). Nucleic Acids Research

Return Gibbs free energy at 37degC (in kcal/mol) contribution from single base overhang in RNA/RNA duplex.

Arguments: inseq - 2bp RNA sequence (5' -> 3') uracil->thymidine end - specifies which end the over hang is on (valid values: 3 or 5)

Table 3 in Freier et al, Biochemistry, 1986

Adjust Gibbs Free Energy from 1M Na+ for another concentration

Arguments: delG -- Gibbs free energy in kcal/mol nbases -- number of bases in the sequence saltconc -- desired Na+ concentration for new Gibbs free energy calculation

Equation 7 SantaLucia 1998

Calculate thermodynamic values for DNA/DNA hybridization.

Input Arguments: inseq -- the input DNA sequence of the DNA/DNA hybrid (5'->3') temp -- in celcius for Gibbs free energy calc (default 37degC) salt -- salt concentration in units of mol/L (default 0.33M)

Return [enthalpy, entropy] list in kcal/mol and cal/(mol*Kelvin)

Calculate RNA/DNA base stack thermodynamic values (Sugimoto et al 1995)

Sugimoto 95 parameters for RNA/DNA Hybridization (Table 3) "Thermodynamic Parameters To Predict Stability of RNA/DNA Hybrid Duplexes" in Biochemistry 1995

Input Arguments: inseq -- RNA sequence of the RNA/DNA hybrid ( 5'->3' uracil->thymidine)

Return [enthalpy, entropy] list in kcal/mol and cal/(mol*Kelvin)

Generator function to iterate over fasta records in : Use in a loop to apply to each sequence record contained in a .fasta file Input: record handle as obtained by handle = open(,'r') Returns an iterator across sequences in file

Generate random DNA tags with optional restriction site filtering.

Print to stderr with the same signature as print().

Estimate sequence length after tag insertion.

Return a list of unique Tile objects from the input list.

Check if a sequence contains restriction sites.

Check whether a sequence contains only nucleic characters.

wrapper around pretty_print that prints to stdout

Pretty-print nested structures to a file handle.

Print a warning if restriction sites are found in a sequence.

Submit a BLASTN job for the given FASTA string.

Report the number of hits for each record in a BLAST response.

This function takes a sequence and returns a masked sequence with help from RepeatMasker

Placeholder for a local RepeatMasker wrapper.

Simple smoke test for the remote RepeatMasker flow.