Hello everybody,
I'm still slowly treading my way into bash scripting (without any prior programming experience) and hence my code is mostly what some might call "creative" if they meant well
I have created a script that serves its purpose but it does so very slowly, since it needs to work its way through ~1million lines of text file input and does so with a "while read line" loop, which slows down the process terribly.
If it's in any way possible I'd like to speed up the script and would appreciate any suggestions you may have.
Code:
x=0
MOLprev=0
while read line
do
MOLcur=$(echo $line | awk '{print $5}')
if [[ "$MOLprev" -eq 9999 && "$MOLprev" -ne "$MOLcur" ]]
then
x=$((x+1))
SCALE=$((x*10000))
fi
echo $line | awk -v var1=`echo $MOLprev` -v var2=`echo $SCALE` '{
if (var1 -ge $5)
printf("%4s%7s%5s%4s%6s%12s%8s%8s\n",$1,$2,$3,$4,$5+var2,$6,$7,$8)
else
printf("%4s%7s%5s%4s%6s%12s%8s%8s\n",$1,$2,$3,$4,$5,$6,$7,$8);
}'
MOLprev=$MOLcur
done < atoms_done > $OUTPUT
It is supposed to work through a text file (.pdb - protein data bank file) called "atoms_done" in column 5, which consists of integer values that represent a molecule number. There are several molecule types (column 4) in the file (see example below).
The molecule number (column 4) increases until the value 9999 is reached, after which the number jumps back to 0 and is incremented again until 9999. I want to rewrite or edit the existing file and correct just that and have the numbering increase above 9999 until the end of the file is reached.
ATOM 11393 OW SOL 1997 10.570 25.370 66.140
ATOM 11394 HW1 SOL 1997 10.990 24.510 65.850
ATOM 11395 HW2 SOL 1997 11.260 25.970 66.540
ATOM 11396 OW SOL 1998 26.270 16.020 58.330
ATOM 11397 HW1 SOL 1998 27.210 16.140 58.670
ATOM 11398 HW2 SOL 1998 25.800 16.900 58.370
ATOM 11399 OW SOL 1999 7.760 28.120 61.090
ATOM 11400 HW1 SOL 1999 6.970 28.740 61.090
ATOM 11401 HW2 SOL 1999 8.260 28.210 61.950
ATOM 11402 OW SOL 2000 36.170 4.250 62.330
ATOM 11403 HW1 SOL 2000 35.280 3.810 62.490
ATOM 11404 HW2 SOL 2000 36.030 5.100 61.830
ATOM 11405 C1 MeO 2001 19.100 14.520 124.300
ATOM 11406 O1 MeO 2001 19.850 14.620 123.120
ATOM 11407 HO1 MeO 2001 19.520 15.360 122.630
ATOM 11408 HC1 MeO 2001 18.190 13.930 124.210
ATOM 11409 HC2 MeO 2001 19.740 14.210 125.120
ATOM 11410 HC3 MeO 2001 18.730 15.500 124.600
ATOM 11411 C1 MeO 2002 19.280 3.410 94.800
ATOM 11412 O1 MeO 2002 20.380 3.410 95.710
ATOM 11413 HO1 MeO 2002 21.020 3.970 95.290
ATOM 11414 HC1 MeO 2002 18.320 3.220 95.290
Thank you for any helpful comments and suggestions.
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Can any of you explain me about the below line of code?
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Im not able to understand, what exactly it is doing :confused:
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LEARN ABOUT FREEBSD
xsetwmprotocols
XSetWMProtocols(3) XLIB FUNCTIONS XSetWMProtocols(3)NAME
XSetWMProtocols, XGetWMProtocols - set or read a window's WM_PROTOCOLS property
SYNTAX
Status XSetWMProtocols(Display *display, Window w, Atom *protocols, int count);
Status XGetWMProtocols(Display *display, Window w, Atom **protocols_return, int *count_return);
ARGUMENTS
display Specifies the connection to the X server.
count Specifies the number of protocols in the list.
count_return
Returns the number of protocols in the list.
protocols Specifies the list of protocols.
protocols_return
Returns the list of protocols.
DESCRIPTION
The XSetWMProtocols function replaces the WM_PROTOCOLS property on the specified window with the list of atoms specified by the protocols
argument. If the property does not already exist, XSetWMProtocols sets the WM_PROTOCOLS property on the specified window to the list of
atoms specified by the protocols argument. The property is stored with a type of ATOM and a format of 32. If it cannot intern the WM_PRO-
TOCOLS atom, XSetWMProtocols returns a zero status. Otherwise, it returns a nonzero status.
XSetWMProtocols can generate BadAlloc and BadWindow errors.
The XGetWMProtocols function returns the list of atoms stored in the WM_PROTOCOLS property on the specified window. These atoms describe
window manager protocols in which the owner of this window is willing to participate. If the property exists, is of type ATOM, is of for-
mat 32, and the atom WM_PROTOCOLS can be interned, XGetWMProtocols sets the protocols_return argument to a list of atoms, sets the
count_return argument to the number of elements in the list, and returns a nonzero status. Otherwise, it sets neither of the return argu-
ments and returns a zero status. To release the list of atoms, use XFree.
XGetWMProtocols can generate a BadWindow error.
PROPERTIES
WM_PROTOCOLS
List of atoms that identify the communications protocols between the client and window manager in which the client is willing to
participate.
DIAGNOSTICS
BadAlloc The server failed to allocate the requested resource or server memory.
BadWindow A value for a Window argument does not name a defined Window.
SEE ALSO XAllocClassHint(3), XAllocIconSize(3), XAllocSizeHints(3), XAllocWMHints(3), XFree(3), XSetCommand(3), XSetTransientForHint(3), XSet-
TextProperty(3), XSetWMClientMachine(3), XSetWMColormapWindows(3), XSetWMIconName(3), XSetWMName(3), XSetWMProperties(3), XStringListTo-
TextProperty(3)
Xlib - C Language X Interface
X Version 11 libX11 1.5.0 XSetWMProtocols(3)
05-31-2011
