What linux spreadsheet program can you open .sam files in?

[lindenb]

Visualize Bam

FYI: I wrote a simple java-based GUI to visualize some BAMS: https://github.com/lindenb/jvarkit/wiki/BamViewGui

[LeightonP]

You might want to consider the pysam module: http://wwwfgu.anat.ox.ac.uk/~andreas...tools/api.html and https://code.google.com/p/pysam/

(EDIT: I see Devon already suggested this - apologies for the duplication0

[KnowNothing2]

Glad I could help. BTW, I didn't deal with the header in my example. You might check "if(len(line) > 5): stuff" or check for a @ as the first character to get past the header (unless you want to parse it).

Right, I'll have to figure out some of the details. Right now, I just have an idea what I want to perform, but no real idea how to execute. But I did just read through a tutorial that kind of went over the sort of info you presented, I was just unaware that you could do this directly to a sam file.

[dpryan]

Glad I could help. BTW, I didn't deal with the header in my example. You might check "if(len(line) > 5): stuff" or check for a @ as the first character to get past the header (unless you want to parse it).

[KnowNothing2]

Generally something like the following will work:

import csv

sam = csv.reader(open("foo.sam","r"), dialect="excel-tab")
for line in sam :
    print("QNAME: %s" % (line[0]))
    print("Sequence: %s" % (line[9]))

So, just use the column number. You can also use pysam, which makes some things much easier. If you're comfortable with C, I can also recommend the samtools C API. If you need higher performance, you'll find it quite useful.

So that's basically exactly what I was looking for. Thanks!

[dpryan]

Generally something like the following will work:

import csv

sam = csv.reader(open("foo.sam","r"), dialect="excel-tab")
for line in sam :
    print("QNAME: %s" % (line[0]))
    print("Sequence: %s" % (line[9]))

So, just use the column number. You can also use pysam, which makes some things much easier. If you're comfortable with C, I can also recommend the samtools C API. If you need higher performance, you'll find it quite useful.

[KnowNothing2]

You really don't want to write macros to deal with data of this size. Try python/perl/C/whatever. You can use R, if you prefer, but I think it usually reads everything into memory too.

I'm actually trying to write in python. How do I notate a certain variable in a sam file (I'm very new to python bioinformatics).

[dpryan]

You really don't want to write macros to deal with data of this size. Try python/perl/C/whatever. You can use R, if you prefer, but I think it usually reads everything into memory too.

[KnowNothing2]

Well, you can probably open it in libre office if it's small enough (it does read it into memory). Why you would actually want to do that is beyond me.

Basically to write a program

[dpryan]

Well, you can probably open it in libre office if it's small enough (it does read it into memory). Why you would actually want to do that is beyond me.

[GenoMax]

Are we talking about an alignment file? Why do you want to open it in a spreadsheet program? If you need to make a change there may be an alternate option available.

[KnowNothing2]

Tried opening it in libre office calc but the program just freezes