[Tutor] Fwd: arrangement of datafile

[Keith Winston]

oops, I see Steven pointed out a much cleaner approach. Oh well. Shock &
surprise ;)

Keith


On Mon, Jan 6, 2014 at 3:27 AM, Keith Winston <keithwins at gmail.com> wrote:

> Hi Amrita: I tried to figure out, for kicks, how to do what I THINK is
> what you're trying to do... I've never even opened a .txt file in Python
> before, so you can take all this with a big grain of salt... Anyway, if you
> take your example of your original database:
>
> 1 GLY HA2=3.7850 HA3=3.9130
> 2 SER H=8.8500 HA=4.3370 N=115.7570
> 3 LYS H=8.7530 HA=4.0340 HB2=1.8080 N=123.2380
>  4 LYS H=7.9100 HA=3.8620 HB2=1.7440 HG2=1.4410 N=117.9810
> 5 LYS H=7.4450 HA=4.0770 HB2=1.7650 HG2=1.4130 N=115.4790
> 6 LEU H=7.6870 HA=4.2100 HB2=1.3860 HB3=1.6050 HG=1.5130 HD11=0.7690
> HD12=0.7690 HD13=0.7690 N=117.3260
> 7 PHE H=7.8190 HA=4.5540 HB2=3.1360 N=117.0800
> 8 PRO HD2=3.7450
> 9 GLN H=8.2350 HA=4.0120 HB2=2.1370 N=116.3660
> 10 ILE H=7.9790 HA=3.6970 HB=1.8800 HG21=0.8470 HG22=0.8470 HG23=0.8470
> HG12=1.6010 HG13=2.1670 N=119.0300
> 11 ASN H=7.9470 HA=4.3690 HB3=2.5140 N=117.8620
> 12 PHE H=8.1910 HA=4.1920 HB2=3.1560 N=121.2640
> 13 LEU H=8.1330 HA=3.8170 HB3=1.7880 HG=1.5810 HD11=0.8620 HD12=0.8620
> HD13=0.8620 N=119.1360
>
> I put it in a file ashift.txt. Then:
>
> f = open('ashift.txt', 'r')
> lines = f.readlines()
>
> Now I could iterate through lines (it is a list of strings, one per line),
> but I just shortcut to play with a single line:
>
> tshift = lines[0]
> tshift = tshift.replace("=", ":")
> tshift = tshift.splitlines()  # remove the final \n
> tshift = tshift.split(" ")
>
> At which point we have something like this:
>
> ['1', 'GLY', 'HA2:3.7850', 'HA3:3.9130']
>
> I am out of time, plus I'm very conscious of doing this INCREDIBLY
> ineptly. I have spent a bit of time trying to sort out the right way, there
> might be some approach involving dialects associated with the csv module,
> but I couldn't sort that out. If one could massage the above line (or the
> original file) into
>
> [1, 'GLY', {'HA2' : 3.7850, 'HA3' : 3.9130}]
>
> This is what I'd talked about before, and would make reaching your final
> output pretty easy, following the stuff I said above.
>
> I KNOW there's a much, much easier way to do this, probably a one-liner
> (at least for the file parsing).
>
> You talked about printing this stuff out, but if you are going to process
> it further (analyzing it in some way, for example) there might be
> implications as to how you proceed with this.
>
> Keith
>
>


-- 
Keith
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