Pysam Fetch Behavior
1
1
Entering edit mode
7.7 years ago

I wanted to fetch only certain columns from a tabix indexed file. Using Pysam's fetch command, I get the entire row in a string format. However, I would like to query only the exact column. Is there a quick way to accomplish this?

tabix • 5.6k views
ADD COMMENT
0
Entering edit mode

Could you be more specific? Do you want to fetch only certain columns from a subset of rows, or do you just want certain columns from the whole data?

ADD REPLY
0
Entering edit mode

Use awk on pysam output for exact column .

ADD REPLY
1
Entering edit mode

If the OP is using pysam, it's a good guess that they are already in a Python environment. awk, while extremely useful, is a worse fit than simply accessing the AlignedRead object returned by the IteratorRow object returned by Samfile.fetch().

region = Samfile.fetch('chr1:1-1000')
positions = [read.pos for pos in region]
ADD REPLY
0
Entering edit mode

I am specifically working with TSV files. So, I here is an example of TSV file: chr\tpos\tjudgement 1\t2389\tTrue 1\t2399\tTrue When I use fetch to get row for chr 1 and pos 2399, I get the following: 1\t2399\tTrue However, I want a way to directly access judgement value for chr 1 and pos 2399. I'd like to directly call the exact column value. I cannot use awk. I was wondering if there is a direct way of doing so using Pysam. Thank you for all your help.

ADD REPLY
1
Entering edit mode
7.7 years ago
row = Tabixfile.fetch(reference='chr1', start=2399, end=2399, parser=asTuple)
judgement = row[2]
ADD COMMENT
0
Entering edit mode
import pysam
tabixfile = pysam.Tabixfile( "/usr/local/xyz.vcf" )

and now when I m doing this:

row = tabixfile.fetch(reference='chr1', start=249240539, end=249240539)

but while doing

x = row[2]

I am getting this error. 

Where I am going wrong actually ? Any pointer ? 

ADD REPLY

Login before adding your answer.

Traffic: 2608 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6