def sam2bam_alt(infile,outfile):
#requires *fas file I think? this from google doc
#convert to unsorted bam file
cmd1= sam_pth+"./samtools import "+infile+ " tmp.bam"
#sort this file
cmd2 = sam_pth+"./samtools sort tmp.bam "+ outfile
#index
cmd3 = sam_pth+"./samtools index "+outfile
linux_controller(cmd1)
print cmd1
linux_controller(cmd2)
print cmd2
linux_controller(cmd3)
print cmd3
def sam2bam(sam_file,outfile):
infile = sam_file
#sam to sorted bam, memory eff, instrunctions from bowtie tutorial
#http://bowtie-bio.sourceforge.net/tutorial.shtml
#usage:sam2bam("VVadult_BS_m1_all_mapped.sam","testttt.bam")
if outfile.find("."):
#remove *.bam as this iwll be added automatically
fix = outfile.split(".")
outfile = fix[0]
cmd1 = sam_pth+"./samtools view -bS -o tmp.bam " + infile
print cmd1
linux_controller(cmd1)
print "sorting..."
cmd2 = sam_pth+"./samtools sort tmp.bam " + outfile
print cmd2
linux_controller(cmd2)
cmd3 = sam_pth+"./samtools index "+outfile+".bam"
print cmd3
print "indexing (creating *.bai file....."
linux_controller(cmd3)
print "check "+ outfile + ".bam and "+outfile+".bai"