MATLAB Central Newsreader - Reading textfile

Reading textfile

Bryan Heit — Thu, 17 Sep 2009 00:01:03 -0400

I am having trouble reading in a text file. What I want is to
generate an array of strins, 1 column wide by as many rows long as
there is lines in the dataset. The dataset is an HTML page saved as
text, containing bioinformatic information. I'm working on a script
that'll pull specific species data out of the dataset, but cannot make
much progress. I've tried several ways of reading the data
(importdata, textscan, etc) to no avail. At best the first 4-5 lines
get read in, then the read process is terminated (there are thousands
of lines). The data itself looks as follows:

--------------------------------------------------------------------------------
NPSA gnl|sp|P0C9I2 (1107L_ASFK5) Protein MGF 110-7L OS=African swine
fever virus (isolate Pig/Kenya/KEN-50/1950) GN=Ken-016 PE=3 SV=1

*****› PATTERN 1
Site : 56- 64, Identity
   tyvescrfcw_DCEDGVCTS_riwgnnstsi
--------------------------------------------------------------------------------
NPSA gnl|sp|P0C9I3 (1107L_ASFM2) Protein MGF 110-7L OS=African swine
fever virus (isolate Tick/Malawi/Lil 20-1/1983) GN=Mal-013 PE=3 SV=1

*****› PATTERN 1
Site : 56- 64, Identity
   tyvescrfcw_DCEDGVCTS_rvwgnnstsi
--------------------------------------------------------------------------------
NPSA gnl|sp|P0C9I4 (1107L_ASFP4) Protein MGF 110-7L OS=African swine
fever virus (isolate Tick/South Africa/Pretoriuskop Pr4/1996)
GN=Pret-017 PE=3 SV=1

*****› PATTERN 1
Site : 56- 64, Identity
   tyvescrfcw_DCEDGICTS_rvwgnnstsi
--------------------------------------------------------------------------------

This goes on and on - I would like to read every line; even the
'-----' ones and blank ones, into the data array.

Any help would be greatly appreciated.

Bryan

Re: Reading textfile

dpb — Thu, 17 Sep 2009 00:12:02 -0400

Bryan Heit wrote:
> I am having trouble reading in a text file. What I want is to
> generate an array of strins, 1 column wide by as many rows long as
> there is lines in the dataset. ...
> This goes on and on - I would like to read every line; even the
> '-----' ones and blank ones, into the data array.
>
> Any help would be greatly appreciated.

doc fgetl

--

Re: Reading textfile

Rune Allnor — Thu, 17 Sep 2009 07:45:25 -0400

On 17 Sep, 02:01, Bryan Heit <bryans.spam.t...@gmail.com> wrote:
> I am having trouble reading in a text file. What I want is to
> generate an array of strins, 1 column wide by as many rows long as
> there is lines in the dataset. The dataset is an HTML page saved as
> text, containing bioinformatic information. I'm working on a script
> that'll pull specific species data out of the dataset, but cannot make
> much progress. I've tried several ways of reading the data
> (importdata, textscan, etc) to no avail. At best the first 4-5 lines
> get read in, then the read process is terminated (there are thousands
> of lines). The data itself looks as follows:
...
> Any help would be greatly appreciated.

You will have to write your own parser from scratch.

You should take some time to find out exactly what you
want to use these data for, and how, and come up with a
data structure that fits this use.

Once that's done, scan the file to extract (possibly
multi line) data items. Then scan the lines and extract
whatever data you want. Store the data in structures
or cell arrays.

My point is that this is a somewhat involved task that
might not be easily solved with canned routines. If you
think the above sounds daunting, find/hire somebody that
can help you - it is a standard programming task that any
computer science student can help with. Expect to spend
a bit of time explaining a helper how to separate the
data, though.

Rune

Re: Reading textfile

Lucio Cetto — Thu, 17 Sep 2009 09:39:02 -0400

Bryan:
textscan does it; if the file is too large you should increase buffersize, if every record in the file always have the same number of rows you could reshape the output cell array or play a little more with the format string and you will get the data aranged into columns very easily...

fid = fopen('mcen.txt','r');
strs = textscan(fid,'%s','delimiter','\n')
strs{1}
fclose(fid)

HTH
Lucio

Re: Reading textfile

Bryan — Thu, 17 Sep 2009 15:29:09 -0400

On Sep 17, 5:39 am, "Lucio Cetto" <lce...@nospam.mathworks.com> wrote:
> Bryan:
> textscan does it; if the file is too large you should increase buffersize, if every record in the file always have the same number of rows you could reshape the output cell array or play a little more with the format string and you will get the data aranged into columns very easily...
>
> fid = fopen('mcen.txt','r');
> strs = textscan(fid,'%s','delimiter','\n')
> strs{1}
> fclose(fid)
>
> HTH
> Lucio

Thanx everyone for your impost. Lucio, your method worked perfectly -
the array is huge, but it loads the whole file and I can parse it
easily to extract the data I want.

Once again, thank you everyone.

Bryan