baliaga31 / mapping

Projet mapping HMIN113 BCD

Mapping Project

Projet mapping HMIN113 BCD

NAME:

SamReader

VERSION:

0.1.1

DESCRIPTION:

SamReader is a parser program for samtools files (extension: .sam). It analyze only Paired-End dataset. 

This software will return several files:

 - Final_Flag_table.txt
    
    This text file contains a table which summarize the whole flag combination (read 1 and read2). Their numbers and percentages are computed. 

 - 5 fasta files are returned by SamReader:

    * only_partially_mapped.fasta This file contains the reads (not paired) which are partially mapped.

    * only_unmapped.fasta This file contains the reads (not paired) which are unmapped.

    * read1_unmapped_read2_unmapped.fasta This file contains the both reads (Read 1 and Read 2) which are unmapped. 

    * read1_mapped_read2_partially.fasta
    This file contains one read (Read 1 or Read 2) which are mapped and the other one (Read 1 or Read 2) which are partially mapped.

    * read1_mapped_read2_unmapped.fasta This file contains one read (Read1 or Read 2) which are mapped and the other one (Read 1 or Read 2) which are unmapped.

- A summary file is returned too. In this document, more information is available as mapper programm, version ...

- This software analyze only Paired-End (PE) dataset. Contact us if you want a new version with the Single-End (Authors).

More information about SAM file, please visit this website: https://samtools.github.io/hts-specs/SAMv1.pdf

REQUIREMENT:

Python3 is necessary to launch the programm. If you don't have Python 3, you can download here: https://www.python.org/downloads/

This software works with Linux. We are not sure this programm works with windows.

INSTALLATION AND LAUNCH THE SOFTWARE:

Download SamReader.py from our Github page (https://github.com/wanaga3166/Mapping/tree/main). 

Move the SamReader.py in your tool directory.

Open your terminal, go to your tool directory. 

Use this command:

python3 SamReader.py - h 

Please see the help menu as showed above to read the full option list or check the next paragraph below.

OPTION LIST:

-h or --help : help information
-i or --input: input file (.sam)
-o or --output: output name files

EXAMPLES:

python3 SamReader.py -h # Launch the help
python3 SamReader.py -i <file> # Launch SamReader to analyze a samtools file (.sam) and print the result in the terminal
python3 SamReader.py -i <file> -o <name> # If this option is present with a name, several files will be created (fasta files, table, summary) and print the result into the terminal.  
python3 SamReader.py --input <file>
python3 SamReader.py --help
python3 SamReader.py --input <file> --output <name>  

TROUBLESHOOTINGS:

If you encounter one or several malfunctions when you execute this software, please contact us (see our e-mail addresses below).

AUTHORS:

Benoit ALIAGA ([email protected])
Matthieu ANGLES ([email protected])

MORE INFORMATIONS:

https://github.com/wanaga3166/Mapping

LICENCE:

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
 You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.