This question already has answers here:
How to save a structure array to a text file
(3 answers)
Closed 8 years ago.
I am an R user: I don't use Matlab. However, I am working with a genomic file from the Broad Institute called "hg18_with_miR_20080407.mat". You can find it at: http://genepattern.broadinstitute.org/ftp/distribution/genepattern/dev_archive/GISTIC/broad.mit.edu:cancer.software.genepattern.module.analysis/00125/1.1/
I tried to use the R package R.matlab (table <- readMat("~/desktop/hg18_with_miR_20080407.mat")), but it keeps loading in definitively. Hence, since I need that file today, I used a friend's computer with Matlab. I have a struct <1x26835> called rg
Each variable has the following values:
refseq 'NM_003585'
gene 'double C2...'
symb 'DOC2B'
locus_id 8447
...
Is there a way that I can print each entry into a text file that I could easily parse? Is there a better way? I am reading the Matlab documentation but would appreciate if someone could give me a one-liner. If not possible, how could I search each variable for a specific gene entry? I keep getting errors. For example:
find(rg == 'Met')
Error: The expression to the left of the equals sign is not a valid target for an assignment.
Thank you!
I recommend trying YAML files (site).
There are libraries for writing matlab data into it here that I have used and liked and googling shows me that there appear to be libraries for R as well.
YAML is basically a newer version of XML files that is human readable, simpler, and less extensible.
Related
I am a rather new user and I am running a simulation experiment. I would like to learn how to write output data to file. I am considering buying the the Big Book of Simulation Modeling which is based on AnyLogic 6. Are there major differences between AnyLogic 6 and 8 in reading/writing data to file? Unfortunately, they haven't released that chapter for the current version of the book that is online. Are there other resources about writing output data to files? Thanks!
Assuming your question is about writing a csv file and not to excel as per your comments, if you want to make use of the standard AnyLogic objects you can easily follow the instructions from the help here
https://anylogic.help/anylogic/connectivity/text-file.html
If you prefer to be in full control of the writing to the CSV file you can also easily use some standard Java functionalities and create a function like this.
The String input can then be any piece of string, with what ever separators you want, comma ,, pipe |, tab "\t" etc, and you simply need to add in line breaks "\n" in your string to write new lines in your output.
This question already has answers here:
List all files in a directory given a regular expression / a set of extensions (Matlab)
(3 answers)
Matlab equivalent of `endsWith`: How to filter list of filenames regarding their extension?
(1 answer)
Closed 7 years ago.
I want to be able to detect a file by looking at its extension:
.m,
.fig,
.mdl,
.slx
but not
.mat
or others.
The final use will be to call DIR with a regular expression that filters out all the unnecessary files.
My first obstacle was to define a word of a single character "m". I couldn't figure out which expression should I use for REGEXP, and the documentation of Matlab was not clear enough.
An example of usage will be helpful, and a reference to a more understandable place will be very appreciated.
I downloaded some data in DAF "transfer" format, which NASA completely
fails to explain here:
http://naif.jpl.nasa.gov/pub/naif/toolkit_docs/C/req/daf.html#Conversion%20and%20Transfer%20of%20DAF%27s
How do I read this file. Here are the first few lines I'm trying to comprehend:
DAFETF NAIF DAF ENCODED TRANSFER FILE
'DAF/SPK '
'2'
'6'
'NIO2SPK '
BEGIN_ARRAY 1 3895604
'URA111 '
'-BC186A96D0E76^8'
'BC0DDF032F041^8'
'2BD'
'7'
'1'
'3'
1024
'-BC18166^8'
'FD2^4'
'-DA4A19AC2BCD18^4'
'-4D5E7E1A67739^4'
'1D46248537C30E^5'
'EBA587DFA5E3B^3'
'-26885CE73CB0D^4'
'-BF0DC6EDB5B2C8^2'
'129C1CFEABE48^3'
'5594FC676368^1'
'-472EBF2225A^1'
'-2198AE1963D^0'
'79CC4CA0C^-1'
'FDD9792D82^-2'
'2001D81A^-2'
'333BCEE2BDD724^4'
'-D78AA10831D9C8^4'
'-6D712677574DF8^4'
'283A14783CDC^4'
'90AC22194ABF6^3'
'-1DEF6219F664FE^3'
'-47318F604096^2'
'9B805F405B1C^1'
'1275B947E2AC^1'
'-16A664664D^0'
'-2F614B9F5^-1'
'-B7C3E41D^-3'
'2F3D71F8^-3'
According to NASA, this is/was a popular format for Fortran programs,
but google was not at all helpful (wikipedia doesn't have an entry
either).
OK, I think I finally figured it out at least part of this. For
reference, the original file (a whopping 162M in size) is the
ura111.bsp file in:
http://naif.jpl.nasa.gov/pub/naif/generic_kernels/spk/satellites/
and converted to ura111.xsp using the toxfr program in:
http://naif.jpl.nasa.gov/pub/naif/utilities/SunIntel_32bit/
The small files:
http://naif.jpl.nasa.gov/pub/naif/generic_kernels/spk/satellites/ura111.cmt
http://naif.jpl.nasa.gov/pub/naif/generic_kernels/spk/satellites/ura111.inp
explain more about the main file.
Things like "-BC18166^8" really are double precision numbers, written
in modified hexadecimal IEEE-754 format. Wikipedia sort of explains
this format here:
http://en.wikipedia.org/wiki/IEEE-754
and there are IEEE-754-to-decimal convertors like this:
http://www.h-schmidt.net/FloatConverter/ (and many others)
However, these don't explain/convert the exact format NASA uses, which
was one reason for my confusion.
For reference "-BC18166^8" is converted as follows:
The decimal value of "BC18166" is 197230950
We now divide by 16 repeatedly until the result is less than 1 (in
other words, we divide by 16^(length of "BC18166")), yielding
0.734742544591427
The '^8' means we multiply by 16**8 to get 3155695200
the leading "-" just means we add a minus sign to get -3155695200
Of course, we could've combined steps 2 and 3 and just multiplied
197230950 by 16.
#klugerama, to answer your question, yes, I am trying to write a file
parser, this time in Perl, as part of a program that accurately
identifies the positions of various objects in our solar system.
I've already parsed the NASA files relating to planets (and Earth's
own moon) here:
ftp://ssd.jpl.nasa.gov/pub/eph/planets/ascii/
but these are in a much different and far easier-to-parse format.
This document (hosted at ucla.edu) has a complete description of the file format.
Addtionally, check out this python project on Github. It appears to provide the DAFTB function you're looking for.
Edit For the record (cough), it doesn't look like this format was ever intended to be read, per se, by humans. It's a transfer format intended to be converted back to usable binary in whatever executable code is appropriate.
You didn't explain why you want to do this. So unless you are writing a file parser (which has been done already in at least two languages), I'm not sure what the benefit is of being able to read the raw values.
Strictly speaking, the answer to your question is that you use software (see link above) to read it.
This question already has answers here:
How to get all files under a specific directory in MATLAB?
(8 answers)
Closed 8 years ago.
I have my data in multiple folders. Let's say I have a folder containing 100 subfolders at the moment that look like this:
/folder/Re0001/vitesse
/folder/Re0002/vitesse
/folder/Re000N/vitesse
/folder/Re000N+1/vitesse
/folder/Re0100/vitesse
I want to import the vitesse file into a cell array. This is the code that i am using at the moment:
numfiles=100;
mydata=cell(1,numfiles);
for i=1:numfiles
mydata{i}=uiimport;
end
It is a working solution.
However, if it involves 100 or more files I have to specify each folders and files manually, which is very troublesome.
By the way I am new to Matlab so can you please incorporate example code with the directory given.
I did something similar few days ago. Have a look at the matlab function ls. If you are using windows system, you are all set. If your are using linux, you may need to split the results. However newer version of matlab have the strsplit function that will do the job, or you will use regular expressions.
In your case,
list = ls('/folder/*/vitesse');
will give you a list of your files.
i am a newbie learning sml and the question i am thrown with involves IO functions that i have no idea how it works even after reading it. Here is the 2 questions that i really need help with to get me started, please provide me with codings and some explaination, i will be able to trial and error with the code given for the other questions.
Q1) listdir(filename,directoryname), which given the name of a directory, list its contents in a text file. The listing is in a form that makes it easy to seperate filenames, dates and sizes from each other. (similar to what msdos does with "dir" but instead of just listing it out, it places all the files and details into a text file.
Q2) readlist(filename) which reads a list of filenames (each of which were produced by listdir in (Q1) and combines them into one large list. (reads from the text file in Q1 and then assigning the contents into 1 big list containing all the information)
Thing is, i only learned from the lecturer in school on the introduction section, there isnt even a system input or output example shown, not even the "use file" function is taught. if anyone that knows sml sees this, please help. Thanks to anyone who took the effort helping me.
Thanks for the reply, current I am using SMLNJ to try and do this. Basically, Q1 requires me to list the directory's files of the "directoryname" provided into a text file in "filename". The Q2 requires me to read from the "filename" text file and then place the contents into one large list.
Duplicate of: smlnj listdir
As a hint I will say that you have to make use of these functions:
OS.FileSys.OpenDir(directoryname) - this will open directory stream for you (Q1)
TextIO.openOut(filename) - this will open the file stream (Q2)
TextIO.openIn(filename)- this will open the file (Q2)
If you are stuck and dont' know how to do the progs then I will post the full code here, but i suggest you first give a try.
zubair sheikh