I want to patch kohana with a file called request.patch, which I have in the root directory of my Kohana install. I am using cygwin in windows 7. The patch reads as follows:
820a821,823
> // Convert dashes to underscores
> $controller = strtr($this->controller, '-', '');
>
822c825
< $class = new ReflectionClass($prefix.$this->controller);
---
> $class = new ReflectionClass($prefix.$controller);
831a835,837
>
> // Convert action dashes to underscores
> $action = strtr($action, '-', '');
However when I cd to the kohana root and then try and apply this patch:
/cygdrive/c/cygwin/bin/patch.exe -p0 < request.patch
I receive the following error:
can't find file to patch at input line 1
Perhaps you used the wrong -p or --strip option?
File to patch:
I mean I'd even just do this manually if I knew what files the numbers were refering to?
Honestly, I'm not sure that's a proper patch file. It doesn't have the filenames or anything (hence the error). Might better to grab the patch from github. You can append .patch on the end of a commit to get a proper patch file.
The numbers would be the line numbers in the file.
Related
I am trying to iterate through every file in a specific directory (called sequences), and perform two functions on each file. I know that the functions (the 'blastp' and 'cat' lines) work, since I can run them on individual files. Ordinarily I would have a specific file name as the query, output, etc., but I'm trying to use a variable so the loop can work through many files.
(Disclaimer: I am new to coding.) I believe that I am running into serious problems with trying to use my file names within my functions. As it is, my code will execute, but it creates a bunch of extra unintended files. This is what I intend for my script to do:
Line 1: Iterate through every file in my "sequences" directory. (All of which end with ".fa", if that is helpful.)
Line 3: Recognize the filename as a variable. (I know, I know, I think I've done this horribly wrong.)
Line 4: Run the blastp function using the file name as the argument for the "query" flag, always use "database.faa" as the argument for the "db" flag, and output the result in a new file that is has the same name as the initial file, but with ".txt" at the end.
Line 5: Output parts of the output file from line 4 into a new file that has the same name as the initial file, but with "_top_hits.txt" at the end.
for sequence in ./sequences/{.,}*;
do
echo "$sequence";
blastp -query $sequence -db database.faa -out ${sequence}.txt -evalue 1e-10 -outfmt 7
cat ${sequence}.txt | awk '/hits found/{getline;print}' | grep -v "#">${sequence}_top_hits.txt
done
When I ran this code, it gave me six new files derived from each file in the directory (and they were all in the same directory - I'd prefer to have them all in their own folders. How can I do that?). They were all empty. Their suffixes were, ".txt", ".txt.txt", ".txt_top_hits.txt", "_top_hits.txt", "_top_hits.txt.txt", and "_top_hits.txt_top_hits.txt".
If I can provide any further information to clarify anything, please let me know.
If you're only interested in *.fa files I would limit your input to only those matching files like this:
for sequence in sequences/*.fa;
do
I can propose you the following improvements:
for fasta_file in ./sequences/*.fa # ";" is not necessary if you already have a new line for your "do"
do
# ${variable%something} is the part of $variable
# before the string "something"
# basename path/to/file is the name of the file
# without the full path
# $(some command) allows you to use the result of the command as a string
# Combining the above, we can form a string based on our fasta file
# This string can be useful to name stuff in a clean manner later
sequence_name=$(basename ${fasta_file%.fa})
echo ${sequence_name}
# Create a directory for the results for this sequence
# -p option avoids a failure in case the directory already exists
mkdir -p ${sequence_name}
# Define the name of the file for the results
# (including our previously created directory in its path)
blast_results=${sequence_name}/${sequence_name}_blast.txt
blastp -query ${fasta_file} -db database.faa \
-out ${blast_results} \
-evalue 1e-10 -outfmt 7
# Define a file name for the top hits
top_hits=${sequence_name}/${sequence_name}_top_hits.txt
# alternatively, using "%"
#top_hits=${blast_results%_blast.txt}_top_hits.txt
# No need to cat: awk can take a file as argument
awk '/hits found/{getline;print}' ${blast_results} \
| grep -v "#" > ${sequence_name}_top_hits.txt
done
I made more intermediate variables, with (hopefully) meaningful names.
I used \ to escape line ends and allow putting commands in several lines.
I hope this improves code readability.
I haven't tested. There may be typos.
You should be using *.fa if you only want files with a .fa ending. Additionally, if you want to redirect your output to new folders you need to create those directories somewhere using
mkdir 'folder_name'
then you need to redirect your -o outputs to those files, something like this
'command' -o /path/to/output/folder
To help you test this script out, you can run each line one by one to test them. You need to make sure each line works by itself before combining.
One last thing, be careful with your use of colons, it should look something like this:
for filename in *.fa; do 'command'; done
Ok so I kinda dropped the ball. I was trying to understand how things work. I had a few html files on my computer that I was trying to rename as txt files. This was strictly a learning exercise. Following the instructions I found here using this code:
for file in *.html
do
mv "$file" "${file%.html}.txt"
done
produced this error:
mv: rename *.html to *.txt: No such file or directory
Long story short I ended up going rogue and renaming the html files, as well as a lot of other non html files as txt files. So now I have files labeled like
my_movie.mp4.txt
my_song.mp3.txt
my_file.txt.txt
This may be a really dumb question but.. Is there a way to check if a file has two extensions and if yes remove the last one? Or any other way to undo this mess?
EDIT
Doing this find . -name "*.*.txt" -exec echo {} \; | cat -b seems to tell me what was changed and where it is located. The cat -b part is not necessary but I like it. This still doesn't fix what I broke though.
I'm not sure if terminal can check for extensions "twice", but you can check for . in every name an if there's more than one occurence of ., then your file has more extensions. Then you can cut the extension off with finding first occurence of . in a string when going backwards... or last one if checking characters in string in a normal way.
I have a faster option for you if you can use python. You can strip the extension with:
for file in list_of_files:
os.rename(file,os.path.splitext(file)[0])
which can give you from your file.txt.txt your file.txt
Example:
You wrote that your command tells you what has changed, so just take those changed files and dump them into a file(path to file per line). Then you can easily run this:
with open('<path to list>') as f:
list_of_files = f.readlines()
for file in list_of_files:
os.rename(file.strip('\n'), os.path.splitext(file.strip('\n'))[0])
If not, then you'd need to get the list from python:
import os
results = []
for root, folder, filenames in os.walk(<your path to folder>):
for filename in filenames:
if filename.endswith('.txt.txt'):
results.append(os.path.join(root, filename))
With this you got a list of files ending with .txt.txt like this <your folder>\\<path_to_file>.
Get a path to your directory used in os.walk() without folder's name(it's already in list) so it'll be like this:
e.g. os.walk('/home/me/directory') -> path='/home/me/' and res is item already in a list, which looks like directory/...
for res in results:
path = '' # set the path here
file = os.path.join(path,r)
os.rename(file, os.path.splitext(file)[0])
Depending on what files you want to find change .txt.txt in if filename.endswith('...') to whatever you like and os.rename() will take file's name without extension which in your case means it strips the additional extension you don't want to have.
I have been using ns2 and nam for a long time on my ubuntu. Now I have to apply a patch (OSPF) to it. I have been searching for how to apply a patch in linux (as I'm kind of new in it) and all I got was:
1) $ tar xvf ns-allinone-2.35.tar.gz
2) $ cd ns-allinone-2.35/
3) $ ln -s ns-2.35/ ns-2.34
... Then the patch will work, except for one line. (commom/packet.h).
4) $ patch -p0 < 10-ospf4ns2.34-base.patch
http://sourceforge.net/projects/ospf4ns/
5) Replace commom/packet.h with the attached "packet.h" : Edited by hand.
6) export CC=gcc44 CXX=g++44 && ./install
I untared the tar file, copied the .patch file in the ns-allinone-2.35 folder called 10-ospf4ns2.34-base.patch, gone to the directory in a terminal, used ln -s ns-2.35/ ns-2.34 and then patched using line 4. After that I have these messages:
The next patch would create the file ns-2.34/classifier/classifier-mtopology.cc,
which already exists! Assume -R? [n] y
patching file ns-2.34/classifier/classifier-mtopology.cc
The next patch would create the file ns-2.34/classifier/classifier-mtopology.h,
which already exists! Assume -R? [n] y
patching file ns-2.34/classifier/classifier-mtopology.h
can't find file to patch at input line 92
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- ns-2.34.old/common/agent.cc 2009-06-14 18:35:45.000000000 +0100
|+++ ns-2.34/common/agent.cc 2010-02-26 23:34:33.161063590 +0000
--------------------------
File to patch:
After this I don't know what to do. What file should I patch? There is no classifier-mtopology.h in ns-2.34.
And after that, which packet.h should I replace with the specified new packet.h? Because there are several common folders. Any help would be much appreciated cause I'm a novice in linux.
It looks like you already applied the patch before (at least partially) and that you are not in the correct directory.
Start again, also you can avoid the symlink with the following instructions:
Extract ns-allinone-2.35.tar.gz in a fresh directory.
cd ns-allinone-2.35/ns-2.35
Apply the patch with:
patch -p1 < 10-ospf4ns2.34-base.patch
I'm totally new to bash scripting but i want to solve this problem..
the command is:
objfil=`echo ${srcfil} | sed -e "s,c$,o,"`
the idea about the bash script program is to check for the source files, and check if there is an adjacent object file in the OBJ directory, if so, the rest of the program runs smoothly, if not, the iteration terminates and skips the current source file, and moves on to the next one.. it works with .c files but not on the headers, since the object filenames depend on .c files.. i want to write this command so it checks the object files not just the .c but the .h files too.. but without skipping them. i know i have to do something else too, but i need to understand what this line of command does exactly to move on. Thanks. (Sorry for my english)
UPDATE:
if test -r ${curOBJdir}/${objfil}
then
cp -v ${srcfil} ./SAVEDSRC/${srcfil}
fdone="NO"
linenums=ALL
else
fdone="YES"
err="${curOBJdir}/${objfil} is missing - ${srcfil} skipped)"
echo ${err}
echo ${err} >>${log}
fi
while test ${fdone} == "NO"
do
#rest of code ...
here is the rest of the program.. i tried to comment out the "test" part to ignore the comparison just because i only want my script to work on .h files, but without checking the e.g abc.h files has an abc.o file.. (the object file generation is needed because the end of the script there's a comparison between the hexdump of the original and modified object files). The whole script is for changing the basic types with typedefs like int to sint32_t for example.
This concrete command will substitute all c's right before line-end to o:
srcfill=abcd.c
objfil=`echo ${srcfil} | sed -e "s,c$,o,"`
echo $objfil
Output:
abcd.o
P.S. It uses a different match/replace separator: default is / but it uses ,.
I'm having trouble applying a patch to my source tree, and it's not the usual -p stripping problem. patch is able to find the file to patch.
Specifically, my question is how to read / interpret the .rej files patch creates when it fails on a few hunks. Most discussions of patch/diff I have seen don't include this.
A simple example:
$ echo -e "line 1\nline 2\nline 3" > a
$ sed -e 's/2/b/' <a >b
$ sed -e 's/2/c/' <a >c
$ diff a b > ab.diff
$ patch c < ab.diff
$ cat c.rej
***************
*** 2
- line 2
--- 2 -----
+ line b
As you can see: The old file contains line 2 and the new file should contain line b. However, it actually contains line c (that's not visible in the reject file).
In fact, the easiest way to resolve such problems is to take the diff fragment from the .diff/.patch file, insert it at the appropriate place in the file to be patched and then compare the code by hand to figure out, what lines actually cause the conflict.
Or - alternatively: Get the original file (unmodified), patch it and run a three way merge on the file.
Wiggle is a great tool for applying .rej files when patch does not succeed.
I'm not an expert on dealing with patch files, but I'd like to add some clarity on how to read them based on my understanding of the information they contain.
Your .rej files will tell you:
the difference between the original and the .rej file;
where the problem code starts in the original file, how many lines it goes on
for in that file;
and where the code starts in the new file, and how many lines it goes on for in that file.
So given this message, noted in the beginning of my .rej file:
diff a/www/js/app.js b/www/js/app.js (rejected hunks)
## -4,12 +4,24 ##
I see that for my problem file (www/js/app), the difference between the original (noted as a/www/js/app.js on the first line) and the .rej file (noted as b/www/js/) starts on line 4 of the original and goes on for 12 lines (the part before the comma in ## -4,12, +4,24 ## on line two), and starts on line 4 of the new version of the file and goes on for 24 lines (the part after the comma in ## -4,12, +4,24 ##.
For further information, see the excellent overview of patch files (containing the information I note above, as well as details on lines added and/or between file versions) at http://blog.humphd.org/vocamus-906/.
Any corrections or clarifications welcome of course.