Tried opening it in libre office calc but the program just freezes
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Originally posted by dpryan View PostYou 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.
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Generally something like the following will work:
Code: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]))
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Originally posted by dpryan View PostGenerally something like the following will work:
Code: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]))
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Originally posted by dpryan View PostGlad 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).
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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
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Visualize Bam
FYI: I wrote a simple java-based GUI to visualize some BAMS: https://github.com/lindenb/jvarkit/wiki/BamViewGui
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