%global _empty_manifest_terminate_build 0 Name: python-PeptidesSearch Version: 0.3.5 Release: 1 Summary: Search a list of peptides in a fasta file (or proteome) and returns exact matches or hits with one mismatch License: MIT URL: https://github.com/khaledianehdieh/PeptidesSearch Source0: https://mirrors.aliyun.com/pypi/web/packages/db/0a/6002bc021d5742b4c2d950db9964fe791a97cf487ec7a620fc8b71293ebc/PeptidesSearch-0.3.5.tar.gz BuildArch: noarch Requires: python3-pandas Requires: python3-numpy Requires: python3-more-itertools %description 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 ```bash pip install PeptidesSearch ``` ## Upgrade installation ```bash pip install PeptidesSearch --upgrade ``` ## Development installation ```bash 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 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. ``` # Change log ## [0.1] - 2021-08-02 - Created ## [0.2.1] - 2021-08-02 - Added usage ## [0.2.2] - 2021-08-02 -Added SequenceSearch() ## [0.2.7] - 2021-08-02 -Added search for also a list passed as a parameter ## [0.3.0] - 2021-08-02 -Added progress bar %package -n python3-PeptidesSearch Summary: Search a list of peptides in a fasta file (or proteome) and returns exact matches or hits with one mismatch Provides: python-PeptidesSearch BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-PeptidesSearch 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 ```bash pip install PeptidesSearch ``` ## Upgrade installation ```bash pip install PeptidesSearch --upgrade ``` ## Development installation ```bash 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 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. ``` # Change log ## [0.1] - 2021-08-02 - Created ## [0.2.1] - 2021-08-02 - Added usage ## [0.2.2] - 2021-08-02 -Added SequenceSearch() ## [0.2.7] - 2021-08-02 -Added search for also a list passed as a parameter ## [0.3.0] - 2021-08-02 -Added progress bar %package help Summary: Development documents and examples for PeptidesSearch Provides: python3-PeptidesSearch-doc %description help 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 ```bash pip install PeptidesSearch ``` ## Upgrade installation ```bash pip install PeptidesSearch --upgrade ``` ## Development installation ```bash 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 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. ``` # Change log ## [0.1] - 2021-08-02 - Created ## [0.2.1] - 2021-08-02 - Added usage ## [0.2.2] - 2021-08-02 -Added SequenceSearch() ## [0.2.7] - 2021-08-02 -Added search for also a list passed as a parameter ## [0.3.0] - 2021-08-02 -Added progress bar %prep %autosetup -n PeptidesSearch-0.3.5 %build %py3_build %install %py3_install install -d -m755 %{buildroot}/%{_pkgdocdir} if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi pushd %{buildroot} if [ -d usr/lib ]; then find usr/lib -type f -printf "\"/%h/%f\"\n" >> filelist.lst fi if [ -d usr/lib64 ]; then find usr/lib64 -type f -printf "\"/%h/%f\"\n" >> filelist.lst fi if [ -d usr/bin ]; then find usr/bin -type f -printf "\"/%h/%f\"\n" >> filelist.lst fi if [ -d usr/sbin ]; then find usr/sbin -type f -printf "\"/%h/%f\"\n" >> filelist.lst fi touch doclist.lst if [ -d usr/share/man ]; then find usr/share/man -type f -printf "\"/%h/%f.gz\"\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . mv %{buildroot}/doclist.lst . %files -n python3-PeptidesSearch -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Thu Jun 08 2023 Python_Bot - 0.3.5-1 - Package Spec generated