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Using Interval Trees to Query Genome Annotations by Position

Rahul Agarwal — Sun, 17 Aug 2014 08:28:23 -0500

To work on query related to overlapping genomic features: use IntervalTree python pkg

http://informatics.malariagen.net/2011/07/07/using-interval-trees-to-query-genome-annotations-by-position/

http://hackmap.blogspot.de/2008/11/python-interval-tree.html

http://en.wikipedia.org/wiki/Interval_tree#Construction

Rahul Agarwal — Sun, 17 Aug 2014 07:59:32 -0500

Subprocess is one of simplest way of running linux command from within python code

Example:

if you want to run fastqc for QC of fastq file:

from subprocess import Popen,PIPE,call

p=Popen(["fastqc","-f","fastq","-o", "/home/name/result/","/dev/stdin"],stdin=fopen("read.fastq","r") ,stdout=PIPE,stderr=PIPE)

print p.stderr

p.stdout.close()

http://pymotw.com/2/subprocess/