I executed make all --print-data-base and I see many lines containing:
...could not be stat'd
What is that?
your command to to print data base catches all, and some of the files are not of the type to return specific information as requested, so such files return a null because of invalid type: meaning no information of such files; not an error just a debugging concept
Related
I'm new in Bioinformatics and Biopython, so I have some difficulties with it.
I was reading the Biopython (SeqIO) documentation, but when I try to execute some SeqIO.parse() commands I get FileNotFoundError.
For example, I want to get "example.fasta" file (which I don't have it on my PC). I try to do it with this command:
for record in SeqIO.parse("example.fasta", "fasta"):
print(record.id)
But, all I get is FileNotFoundError: [Errno 2] No such file or directory
Can someone help me with this?
My understanding is that FileNotFoundError occurs when the code tries to open a file on your computer and does not find it.
This can happen either because you simply do not have this file, or you gave the name with a typo, or the path to the file is not correct (This is an important notion: the path to the file should be absolute, or relative to the current working directory (usually the one from which you executed the python script)).
As suggested in the comments to your question, you seem to be expecting SeqIO.parse to get the file for you. This is not the case. The first argument you give to this function (in the example "example.fasta") is the path to an existing file that you want to "parse", that is, interpret its information content and make this content available to the rest of your program in a convenient form.
So in order to get this example working, you first need to get a fasta file. If you do not already have one, you can download some manually from genbank, or find one in the biopython installation (if you installed it from source and know where the source code is located), for instance in Tests/Quality/example.fasta.
Can you give me a sample on how to filter a certain keyword like for example "error" in the /var/log/messages and then send email if it finds real-time word for error.
I would just like to watch for error keyword in the /var/log/messages and then send it to my email address.
simply grepit.
tail -f log.log | grep error
This will list you all error you can then mail them
What you can do is this:
On a regular basis (which you decide), you:
copy the main file to another file
you DIFF on that file, only taking out the newly added parts (if the file is sequentially written, this will be a nice and clean block of lines, at the end of the file)
you copy the main file to the other file, again (this sets the new reference for the next check)
then you GREP on whatever you want, in the block of lines you've found 2 steps back
you report the found lines, using the wanted method (mail,..)
I have just started using Laravel and cannot get my head around how it throws errors. It doesn't show the line where the error is so I don't know how to locate it. Can anyone help?
htmlentities() expects parameter 1 to be string, array given (View:
M:\webserver\www\app\views\products\admin\create.blade.php)
This file is incredibly long and I cannot see where this array is being sent.
It's obviously coming from a Form::text() but I am passing a null as the second param in all that I can see. Why doesn't Laravel simply tell me the line that is erroring. The error it puts out is no use to me.
check the error file:
app/storage/logs/laravel.log
you can watch changes in the file (on Mac and *NIX) using command line:
tail -f app/storage/logs/laravel.log
remember that the storage directory must be writable by the webserver/PHP process because it's used as scratch space (for blade views, logs, etc.)
Build Rules are documented in the Xcode Build System Guide
They are well adapted to the common case where one input file is transformed into a fixed number (usually one) of output files.
The output files must be described in the "Output Files" area of the build rule definition; one line per output file. Typically the output files have the same name as the input file but have different extensions.
In my case, one single input file is transformed into a variable number of files with the same extensions. The number and the names of the output files depend on the content of the input file and are not known in advance.
The output files will have to be further processed later on (they are in this case C files to be compiled).
How can I set up a build rule for such a case?
Any suggestions welcome.
(I asked the same question on the Apple developer forum, but I figured it'd be a good idea to ask here too).
I dealt with this by, instead of generating multiple C files, just concatenating them all together into one file (e.g. "AUTOGENERATED.c"), and specifying that as the output file.
So long as your output files don't contain anything that will conflict (static functions with the same name, conflicting #defines etc.) this works well.
See this article on Cocoa With Love:
http://cocoawithlove.com/2010/02/custom-build-rules-generated-tables-and.html
This has an example of generating custom C code and using that as input to the normal build process. He's using ${} variable syntax in the output
The best way I found to add any number of files to my xcode project (and make some processing) is to write a little php script. The script can simply copy files into the bundle. The tricky part is the integration with xcode. It took me some time to find a clean way. (You can use the script language you like with this method).
First, use "Add Run Script" instead of "Add Copy File"
Shell parameter:
/bin/sh
Command parameter:
${SRCROOT}/your_script.php -s ${SRCROOT} -o ${CONFIGURATION_BUILD_DIR}/${UNLOCALIZED_RESOURCES_FOLDER_PATH}
exit $?
(screenshot in xcode)
${SRCROOT} is your project directory.
${CONFIGURATION(...) is the bundle directory. Exactly what you need :)
This way, your script return code can stop xcode build (use die(0) for success and die(1) for failures) and the output of script will be visible in xcode's build log.
Your script will look like that: (don't forget chmod +x on it)
#!/usr/bin/php
<?php
error_reporting(E_ALL);
$options = getopt("s:o:");
$src_dir = $options["s"]."/";
$output_dir = $options["o"]."/";
// process_files (...)
die(0);
?>
BONUS: here my 'add_file' function.
Note the special treatment for PNG (use apple's png compression)
Note the filemtime/touch usage to prevent copy files each times.
l
define("COPY_PNG", "/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/usr/bin/copypng -compress");
function add_file_to_bundle($output_dir, $filepath) {
// split path
$path_info = pathinfo($filepath);
$output_filepath = $output_dir.$path_info['basename'];
// get file's dates of input and output
$input_date = filemtime($filepath);
$output_date = #filemtime($output_filepath);
if ($input_date === FALSE) { echo "can't get input file's modification date"; die(1); }
// skip unchanged files
if ($output_date === $input_date) {
//message("skip ".$path_info['basename']);
return 0;
}
// special copy for png with apple's png compression tool
if (strcasecmp($path_info['extension'], "png") == 0) {
//message($path_info['basename']." is a png");
passthru(COPY_PNG." ".escapeshellarg($filepath)." ".escapeshellarg($output_filepath), $return_var);
if ($return_var != 0) die($return_var);
}
// classic copy
else {
//message("copy ".$path_info['basename']);
passthru("cp ".escapeshellarg($filepath)." ".escapeshellarg($output_filepath), $return_var);
if ($return_var != 0) die($return_var);
}
// important: set output file date with input file date
touch($output_filepath, $input_date, $input_date);
return 1;
}
Is there a system call (C API function, not assembler) to rename a file in Microware OS-9 3.03?
If not, is there an accepted way to accomplish this task?
To answer the second part: I worked around this by doing an open on the file. If the open succeeded then I infer the file exists. If the open failed then I check the error in errno. If it's EOS_PNNF, then I infer the file does not exist. Anything else is an error.
I would still like to know about the first part of the question.