Used to extract simple data from a .sam file.
A Python script that extracts simple data from a .sam file. It needs a .sam file (see samformat.info for more info) in parameter. When running the script, it will ask the user to input a certain threshold for filtering reads with a certain mapping quality. It will generate a .txt file that sums up simple data.
Input:
- a single .sam file
Output:
- a .txt file containing:
- the total number of reads
- the number of different reads
- the number of paired reads
- the number of reads mapped in proper pair
- the number of reads matched at 100% (CIGAR)
- The number of reads with a mapping quality higher than a certain threshold (threshold can be set manually)
- Linux-derived OS
- Python3
./sam_reader.py sam_file.sam
Elian Strozyk elian.strozyk@etu.umontpellier.fr at Université de Montpellier
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/."
- 0.0.1 (2022-12-06)
- Initial Release
- Anna-Sophie Fiston-Lavier
- Arnaud Soulier and Allyson Moureaux