PeptidesSearch 0.2.5

Search a list of peptides in a fasta file (or proteome) and returns exact matches or hits with one mismatch

A useful tools to search a list of peptides in a fasta file (a list of proteins, or a proteome)

Description

This tool consists one module:

• PeptideSearch: this tool searches for peptides in a fasta file including proteins, it can find Exact Match or Marches with up to One Mismatch

Installation

Normal installation

pip install PeptideSearch

Development installation

git clone https://github.com/khaledianehdieh/PeptidesSearch.git

Usage

python3
>>> from PeptideSearch import PeptideSearch as PS 
>>> P=PS.PeptideSearch(Peptides, Fasta_File) #Peptides is a .txt file that has one peptide per line, and Fasta_File is a fasta file containing the proteins

#you might use the function as you need in three different ways:
#1- Find Exact Matches
>>> df_EM, pList= P.ExactMatch()  # returns all Exact Matches (df_EM) for each peptide and a list of peptides (pList) that didn't find any

#2- Find One MisMatches
>>> peptides= P.read_Peptides()
df_OM, NotFoundList= P.OneMismatch(peptides) #returns all One  Mis Matches (df_OM) for each peptide and list of peptides (NotFoundList) that couldn't find any match.

#3- Combine one and two, first find a list of exacxt matches and then look for one mismatch for the peptides that we diddnt find any match
#Also saves the result in a CSV file
>>> df_all, NotFounPeptides = P.MatchFinder()   #returns All Matches (df_all) including exact matches, and one mismatched for each peptide and a list of peptides (NotFounPeptides) that couldn't find any match. This part first applies the exact match, and if there is not any exact match for a peptide, then it looks for one mismatch. 

#4- Find a peptide in one sequence
result,index=PS.PeptideSearch.SequenceSearch(peptide, sequence) # result=0 means exact match, result= 1 means one mismatch,  result= -1 means no match, and index is the start location of the peptide in the sequence.

Change log

[0.1] - 2021-08-02

• Created

[0.2.1] - 2021-08-02

• Added usage

[0.2.2] - 2021-08-02

-Added SequenceSearch()