path: root/python-peptidessearch.spec

%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.nju.edu.cn/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
* Tue May 30 2023 Python_Bot <Python_Bot@openeuler.org> - 0.3.5-1
- Package Spec generated