Comments (5)
What OS/shell are you using? I don't think the issue is on the python side -- my suspicion is that for whatever reason the shell is not treating the single quotes correctly in the awk part of the pipe. Try replacing the awk bit so that the commands are enclosed by double quotes (& escape the internal double quotes with a backslash):
... | awk "$6 < 0.75 {print $1\"\t\"$2}" >allSites
(also try correction below)
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Whoops, you my also need to escape the dollar signs in this case (at least, that's necessary in bash):
... | awk "\$6 < 0.75 {print \$1\"\t\"\$2}" >allSites
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