Reading Multiple GenBank Files and Count feature | Python for Bioinformatics
#bioinformatics #datascience #python
This tutorial shows you how to read a genbank file and count the number of sequence features using the python bioinformatics package, biopython.
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Course Materials
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Commands used
from Bio import SeqIO
SeqIO.parse
SeqIO.read
SeqIO.write
Biopython Tutorial
Download the genbank files using the links here
M48 https://www.ncbi.nlm.nih.gov/nuccore/...
P10 https://www.ncbi.nlm.nih.gov/nuccore/...
AR465 https://www.ncbi.nlm.nih.gov/nuccore/...
R50 https://www.ncbi.nlm.nih.gov/nuccore/...
V521 https://www.ncbi.nlm.nih.gov/nuccore/...
Notebook can be found here
https://github.com/vappiah/Python-Bio...
Install Python libraries using pip
• Install python packages using pip
• Installing python packages using pip ...
Install python libraries using anaconda
• How I Install python packages on ANY ...
How to use Functions to analyze multiple sequences
• Python for Bioinformatics | Beginners...
Count features in multiple genbank files- Part-1
• How to count number of sequence featu...
How to count features in a single genbank file
• Reading GenBank Files and Count featu...
Description of genbank files : https://www.ncbi.nlm.nih.gov/Sitemap/...
Chapters
00:00 introduction and motivation for this video
01:15 summary of the exercises to be done
01:41 PC requirement
02:10 Exercise begins
02:14 download the genbank files
04:20 import python libraries
04:57 set the path of the directory containing the genbank files
05:35 get the filenames of the downloaded genbank data
06:53 count genbank features
07:18 create functions to count features
09:47 get all features in the genbank files
11:09 create a list to store the feature counts
11:33 using 'for' loop to count the features in all the genbank files
14:07 examine the result
16:00 create a dataframe to store the counts
20:50 remove unwanted columns
23:04 making queries / extract information from a pandas dataframe
24:43 save dataframe to an output file
26:19 open the output file
BioPython Tutorial for Bioinformatics - Count features in multiple genbank files | Part 2
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