mpa.ScanModel

Overview

The scan model class can scan a model over all sequences embedde within larger contigs.

Usage

>>> import mpathic as mpa
>>> model = mpa.io.load_model("./mpathic/data/sortseq/full-0/crp_model.txt")
>>> fastafile = "./mpathic/examples/genome_ecoli_1000lines.fa"
>>> contig = mpa.io.load_contigs_from_fasta(fastafile,model)
>>> mpa.ScanModel(model_df = model, contig_list = contig)

Example Output Table:

    val                     seq   left  right ori     contig
0  2.040628  GGTCGTTTGCCTGCGCCGTGCA  11710  11731   +  MG1655.fa
1  2.006080  GGAAGTCGCCGCCCGCACCGCT  74727  74748   -  MG1655.fa
2  1.996992  TGGGTGTGGCGCGTGACCTGTT  45329  45350   +  MG1655.fa
3  1.920821  GGTATGTGTCGCCAGCCAGGCA  38203  38224   +  MG1655.fa
4  1.879852  GGTGATTTTGGCGTGGTGGCGT  73077  73098   -  MG1655.fa
5  1.866188  GTTCTTTTCCGCGGGCTGGGAT  35967  35988   -  MG1655.fa
...

Class Details

class scan_model.ScanModel(model_df, contig_list, numsites=10, verbose=False)

Parameters:

model_df: (pandas dataframe)

The dataframe containing a model of the binding energy and a wild type sequence.

contig_list: (list)

list containing contigs. Can be loaded from fasta file via mpathic.io.load_contigs

numsites: (int)

Number of sites

verbose: (bool)

A value of True will force the ‘flush’ the buffer and everything will be written to screen.