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Date: Thu, 10 Apr 2014 03:23:03 +0800 (SGT)
From: rohan bareja <rohan_1925@yahoo.co.in>
Subject: CommandLine Option in Python for filtering values from Column
To: "python-list@python.org" <python-list@python.org>
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I want to write a function in Python for a tab delimited file I am dealing =
with,to filter out values from a column, and put that parameter as a comman=
d line option while running the script.=0A=0ASo,if the limit is 10,the filt=
er out all the rows with values less than 10.=0AAlso,I want to check if the=
 number entered is numeric or not else display the message "its not numeric=
".=0A=0A=0ASo,the command line would be:=0A=0A=A0 =A0 python script.py file=
 --quality [limit]=0A=0A=A0 =A0=A0=0A=A0 The Python script:=0A=0A=A0 =A0 im=
port sys=0A=A0 =A0 arg =3D []=0A=A0 =A0 =A0 =A0 for a in sys.argv:=0A =A0 =
=A0arg.append(a)=A0=0A=A0 =A0 =A0 =A0 =A0 =A0 quality =3D arg[2]=0A=0A=0ATo=
 be more specific,the file I am dealing with is a Samfile,and using package=
=A0=0APysam,which has mapping quality limits in the 5th column.=0A=0Ahttps:=
//media.readthedocs.org/pdf/pysam/latest/pysam.pdf=0A=0ACommandline:=0A=0A=
=A0 =A0 =A0 python script.py samfile --quality [limit]=0A=0A=A0I am reading=
 the samfile using this:=0A=0A=A0 =A0 =A0samfile =3D pysam.Samfile(arg[1], =
"rb" )=0A=A0 =A0 =A0mapqlim =3D arg[2]=0A=0AI am a Python beginner,but saw =
one of the modules,argparse. How can I accomplish this using argparse in Py=
thon?
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<html><body><div style=3D"color:#000; background-color:#fff; font-family:ti=
mes new roman, new york, times, serif;font-size:12pt"><div><div>I want to w=
rite a function in Python for a tab delimited file I am dealing with,to fil=
ter out values from a column, and put that parameter as a command line opti=
on while running the script.</div><div><br></div><div>So,if the limit is 10=
,the filter out all the rows with values less than 10.</div><div>Also,I wan=
t to check if the number entered is numeric or not else display the message=
 "its not numeric".</div><div><br></div><div><br></div><div>So,the command =
line would be:</div><div><br></div><div>&nbsp; &nbsp; python script.py file=
 --quality [limit]</div><div><br></div><div>&nbsp; &nbsp;&nbsp;</div><div>&=
nbsp; The Python script:</div><div><br></div><div>&nbsp; &nbsp; import sys<=
/div><div>&nbsp; &nbsp; arg =3D []</div><div>&nbsp; &nbsp; &nbsp; &nbsp; fo=
r a in sys.argv:</div><div><span class=3D"Apple-tab-span"
 style=3D"white-space:pre">=09</span> &nbsp; &nbsp;arg.append(a)&nbsp;</div=
><div>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; quality =3D arg[2]</div><di=
v><br></div><div><br></div><div>To be more specific,the file I am dealing w=
ith is a Samfile,and using package&nbsp;</div><div>Pysam,which has mapping =
quality limits in the 5th column.</div><div><br></div><div>https://media.re=
adthedocs.org/pdf/pysam/latest/pysam.pdf</div><div><br></div><div>Commandli=
ne:</div><div><br></div><div>&nbsp; &nbsp; &nbsp; python script.py samfile =
--quality [limit]</div><div><br></div><div>&nbsp;I am reading the samfile u=
sing this:</div><div><br></div><div>&nbsp; &nbsp; &nbsp;samfile =3D pysam.S=
amfile(arg[1], "rb" )</div><div>&nbsp; &nbsp; &nbsp;mapqlim =3D arg[2]</div=
><div><br></div><div>I am a Python beginner,but saw one of the modules,argp=
arse. How can I accomplish this using argparse in Python?</div><div><br></d=
iv><div><br></div></div></div></body></html>
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