Python List Comprehension

Python list comprehension enables for easy manipulation of a list variable.  For example, list comprehension can be used to convert from a string to an integer or float as well as do some common operation on a list.  Below is an example script that shows the syntax for list comprehension and how to utilize the code in Python.  Hope its helpful.

Sort BAM File in Samtools

Samtools does a host of useful operations for .bam files.  One such operation is sorting.  Below is a simple example script to show how to use samtools to sort an unsorted BAM file.


This script will sort the unsorted.bam using 8 threads that allocates 12G of memory per thread.  The resulting sorted .bam file will be called sorted.bam.

To confirm a .bam file is sorted, check the header (samtools view -H sorted.bam) for the line:
SO:coordinate.

Additionally, here is the usage information for Samtools sort:

Usage:   samtools sort [options]

Options: -n        sort by read name
         -f        use as full file name instead of prefix
         -o        final output to stdout
         -l INT    compression level, from 0 to 9 [-1]
         -@ INT    number of sorting and compression threads [1]
         -m INT    max memory per thread; suffix K/M/G recognized [768M]

Unix Sort by Column Number

I always forget the flags to use when using UNIX sort.  Here is a list of common useful flags.

Flags

-k: selects the column number to sort

-n: indicates you are sorting numeric values so use numeric ordering (ex: 10, 11, not 10, 100)

-r: sort in reverse (descending) order for this column

An example line of code that sorts by numeric values in column 2 in descending order would be as follows.