I'm trying to write a bash script to calculate some biological stuff. I have a problem with regex, bash is a little unfamiliar to me yet. Unfortenly I have no time to learn it that fast coz I need immanently results.
So my files:
RV30.afa
resFilesRV30.fasta
RV30213.afa
resFilesRV30213.fasta
RV30441.afa
resFilesRV30441.fasta
...
Command i have to use:
mscore -cftit RV30.afa resFilesRV30.fasta >FinalRV30.txt'
What i have now:
#!/bin/bash
parallel 'mscore -cftit {} resFile{}.fasta >final{.}.txt' ::: RV*.afa
The problem is:
resFile{}.fasta = is trying to open file like this: resFileXXX.afa.fasta i need to skip extension in second argument (.afa) and ovewritte it by ".fasta".
I didn't find a piece of good advice on google for my problem (or i can't reforge it to my script yet), and my time to get results already ends. So i will be grateful for help in solving this problem. On its basis, I will be able to solve some of the others that appeared in my other scripts
This should work for you by substituting {} with {.} in 2nd argument:
parallel 'mscore -cftit {} resFiles{.}.fasta >final{.}.txt' ::: RV*.afa
As you're using already in your command, the replacement string {.} removes the extension.
Does this not work?
for afafile in *.afa; do number="${afafile#file}"; number="${number%.afa}"; ./mscore -cftit "$afafile" "resFile${number}.fasta" > "file${number}final.txt"; done
Related
I have a small problem I hope you can help me. I want to use "git branch" to get the current branch from the tag I defined so far so good:
I get the following output with the command : git branch --contains TAG
* develop
But now I only want the value : develop Without the star and without spaces, so just develop.
I have read that it seems to be possible with git branch --contains TAG | select-string, but I can't get it to work I hope one of you can help me.
Linux would be nice but i must work on powershell :(
I've been studying content on the regex topic, but am having trouble understanding how to make it work! I need to build a regex to locate a particular string, potentially in multiple places throughout numerous log files. If I were keying the search expression into a text editor, it would look like this...
*Failed to Install*
Following is a typical example of a line containing the string I would like to search for (exit code # will vary)
!!! Failed to install, with exit code 1603
I would really appreciate any help on how to build the regex for this. I suspect I might need the end of line character too?
I plan on using it in a variation of the script that was provided by https://stackoverflow.com/users/3142139/m-hassan in the following thread
Use PowerShell to Quickly Search Files for Regex and Output to CSV
I'm a newbie to powershell scripts, but I'd rather spend the time to figure this out, than pour over hundreds of log files!
Thanks,
Jim
You're in luck - You only require very simple regex for this. Assuming you want to capture the error code, this will work fine:
^.*Failed to install.*(exit code \d+)$
Try it online!
If you don't care about the error code, and just want to know if it failed or not, you can honestly get away with something as simple as:
^.*Failed to install.*$
Hope this helps.
EDIT: I am using Cygwin. I am unsure whether this is of relevance and it was a detail I missed during writing this question.
EDIT2: Have tried replacing the "TAB" char people pointed out with the RegEx \s which covers spacing chars (spaces and tabs primarily) and this did not affect the expression at all, meaning that it is not the tabs causing the issue, especially since the expression runs once without errors anyway.
So far this script has been causing me a ton of trouble.
I DID have an issue before but I resolved that while I was writing a question here (lucky imo) but this one I've been stuck on for at least an hour now and I've tried varying solutions, none of which actually work or told me something I didn't already try.
I have a rather cool seeming FTP log fetcher script and part of this script replaces the 600MB of errors in this logfile to nothing, essentially removing them. Unfortunately this script also gets rid of parts of other errors too, so I've had to edit it. This is where I'm getting stuck.
Through base research I managed to find out that sed could do what I want, and through three hours of playing so far it does most of what I tell it to, minus one thing. One, and ONLY one, of the sed statements I have built only replaces the first instance of the string I've given it despite having the g modifier attached to the end.
I am working with a test script right now as to avoid potential permanent damage to my original FTP script, and the test script copies over an example file with a few of the errors I need replacing.
Walkthrough of the scripts INTENDED behaviour before showing:
1. Sets a prefix which happens on ALL lines in the file, pretty important part of the script.
2. Copies the example file to a file named test2.log
3. Replace all instances of the UNIX newline char \n with [loll] (first thing that came to my mind)
4. Remove all instances of battle error type 1 and 2.
5. Return all [loll] strings with the UNIX \n for newlines, therefore returning the logfile to its original state minus the errors.
Script:
#DTP="\[([0-9]+-[0-9]+-[0-9]+-[0-9]+|latest)\.log\] \[[0-9]+:[0-9]+:[0-9]+\] \[Server thread/(INFO|WARN)\]: "
echo "${DTP}"
DTP1="\[[0-9]*:[0-9]*:[0-9]*\]\s\[Server\sThread\/\(WARN\|INFO\)\]:\s"
DTP="\[loll\]\[[0-9]*:[0-9]*:[0-9]*\]\s\[Server\sThread\/\(WARN\|INFO\)\]:\s"
echo "${DTP}"
echo "1"
cp test.log test2.log
#cat test.log >test2.log
sed -i ':a;N;$!ba;s/\n/\[loll\]/g' test2.log #| egrep -i "" >test2.log
sed -i 's/'${DTP1}'Caught error in battle. Continuing...'${DTP}'java.lang.NullPointerException'${DTP}' at com.pixelmonmod.pixelmon.battles.controller.participants.PixelmonWrapper.useAttack(PixelmonWrapper.java:173)'${DTP}' at com.pixelmonmod.pixelmon.battles.controller.participants.PixelmonWrapper.takeTurn(PixelmonWrapper.java:330)'${DTP}' at com.pixelmonmod.pixelmon.battles.controller.BattleControllerBase.takeTurn(BattleControllerBase.java:276)'${DTP}' at com.pixelmonmod.pixelmon.battles.controller.BattleControllerBase.update(BattleControllerBase.java:157)'${DTP}' at com.pixelmonmod.pixelmon.battles.BattleRegistry.updateBattles(BattleRegistry.java:63)'${DTP}' at com.pixelmonmod.pixelmon.battles.BattleTickHandler.tickStart(BattleTickHandler.java:12)'${DTP}' at cpw.mods.fml.common.eventhandler.ASMEventHandler_20_BattleTickHandler_tickStart_WorldTickEvent.invoke(.dynamic)'${DTP}' at cpw.mods.fml.common.eventhandler.ASMEventHandler.invoke(ASMEventHandler.java:51)'${DTP}' at cpw.mods.fml.common.eventhandler.EventBus.post(EventBus.java:122)'${DTP}' at cpw.mods.fml.common.FMLCommonHandler.onPostWorldTick(FMLCommonHandler.java:255)'${DTP}' at net.minecraft.server.MinecraftServer.func_71190_q(MinecraftServer.java:929)'${DTP}' at net.minecraft.server.dedicated.DedicatedServer.func_71190_q(DedicatedServer.java:429)'${DTP}' at net.minecraft.server.MinecraftServer.func_71217_p(MinecraftServer.java:776)'${DTP}' at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:639)'${DTP}' at java.lang.Thread.run(Thread.java:745)//gI' test2.log
echo "2"
sed -i 's/'${DTP1}'Caught error in battle. Continuing...'${DTP}'java.lang.NullPointerException\[loll\]//gI' test2.log
echo "3"
sed -i 's/\[loll\]/\n/g' test2.log
I've set them to also run case insensitive checks on the provided strings as sometimes I write with all lower case, however for most of this I copied and pasted it directly.
Sample input:
http://pastebin.com/3KPB33X2
Outputs:
Expected:
meow
Test message
WOOF MEOWLOL
Actual: http://pastebin.com/pnvDwkxz
It's been killing my mind for a while now because I had this issue even before the other one, except I barely noticed it. I can't find any predictable behaviour in the script, and as far as I am aware it SHOULD be working perfectly fine and giving me the output I expect.
Any help would be appreciated, because as soon as I can get this bug sorted out I'll be able to enter in the rest of the script and replace this with the existing battle-error replacement script in my log-fetcher.
Knowing me it's something small and stupid but I've tried literally everything I came across, including adding the :a;N;$!ba; to the start of the bit which isn't working properly (and realising that failed horribly).
Thanks.
~BAI1
Are you looking for something like this:
sed -n ':a;s/\[.*Server thread\/\(INFO\|WARN\).*//i;/^$/!p;n;b a' battle.log
I live off the regex search/replace in BBEdit.
At times I cycle through a history of 8-9 search/replaces to convert a file.
Is there anyway to extract the BBEdit search/replace history?
Best would be to just have the history auto generate a shell script.
I realise I can copy them by hand, but by the time I realise I need it; I'm up to 7-9 rather complex regex blots that would just be annoying to hand copy and paste.
Any ideas warmly welcomed.
Found what I should have looked for from the beginning.
com.barebones.bbedit.plist has an array entry
FindDialog:SearchReplaceHistory
This entry is an array of dicts that includes all settings for the search/replace.
A simple tool can be spun to pull the data and convert in on the fly to a shell script.
Is there any way to write a RegEx which can be used to find files with different Extensions.
This works in Bash:
find . -regex '.*\\.\\(pdf\|chm\|doc\\)'
Assuming you have a list of files and you are looking for .pdf, .chm and .doc, you can check it with:
\.pdf$|\.chm$|\.doc$
Regex above should work if you will check it against single filenames.
I'm sure there is, but the question you should be asking is "What's the best way to find files which have specific extensions?".
Regular expressions are not the best answer to every question.
I would suggest just getting a list of all files and passing them into a function like IsThisFileOneIWant(fileName,extensionList). That's far easier than trying to shoehorn the use of regular expressions into your problem.
Something like this should do it:
function IsThisFileOneIWant(fileName,extensionList):
for each extension in extensionList:
if fileName.endsWith (extension):
return true
return false
Done in pseudo-code since it should be simple enough to turn into any other language.
If you must have a regex, it's going to look something like (based on the values in your question):
"ASPX$|ASCX$|\.js$|\.rpt$|\.xml$"
but it depends entirely on the RE engine that you want to use. For example, here's the output from an egrep command in my work directory:
pax#paxbox1:~/work$ ls -1 | egrep '\.sh$|\.c$'
backup0.sh
backup1.sh
eclipse.sh
monbt.sh
qq.c
qq.sh
xx yy.sh