A useful tools to search a list of peptides in a fasta file (a list of proteins, or a proteome)
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
pip install PeptidesSearchpip install PeptidesSearch --upgradegit clone https://github.com/khaledianehdieh/PeptidesSearch.gitpython3
>>> from PeptideSearch import PeptideSearch as PS
>>> P=PS.PeptideSearch(Peptides, Fasta_File)
#Peptides is a List or 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() #or df_EM, pList= P.ExactMatch(List_of_Peptides)
# 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 1 and 2, first find a list of exacxt matches and then look
#for one mismatch for the peptides that we didn't find any match
>>> 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.
#Also saves the result in a CSV file
#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.