I would like to remove various ligands from PDB records.
Is it just sufficient to remove HET, HETNAM,HETATM...., ie. those, where is compound identified with its 3letter code, or is it necessary to clean some other fields?
Is there any python|perl script already written for this purpose?
open(FILE,"file.pdb");
#file=<FILE>;
foreach (#file){
if (/^HETATM/){
print $_,"\n";
}}
this seperates out the ligand. to delet the ligand, keep not equal to infront of regex.
Related
I'm trying to write a perl script to process a log4net log file. The fields in the log file are separated by a semi-colon. My end goal is to capture each field and populate a mysql table.
Usually I have lines that look a little like this (all on a single line)
DEBUG;2017-06-13T03:56:38,316-05:00;2017-06-13 08:56:38,316;79ab0b95-7f58-
44a8-a2c6-1f8feba1d72d;(null);WorkerStartup 1;"Starting services."
These are easy to process. I can simply split by semicolon to get the information I need.
However occassionally the "message" field at the end may span several lines, especially if there is a stack trace. I would want to capture the entire message as a single column. I cannot use split by semicolon, because the next lines would typically look like:
at some.random.classname
at another.classname
...
Can someone give some tips how to solve this problem?
The following solution uses that the number of " in a field is even ($p=~y/"//%2), this condition number of " odd may be changed by other that can indicate the field is not complete.
The number of columns splitted is fixed to 7 (to allow ; in last field) and may be changed for example #array = map {s/;$//} $p=~/\G(?:"[^"]*"|[^;])*;/g;.
The file is read line by line but a line is processed sub process when it's complete $p variable to store the previous line the last line is processed in END block.
perl -ne '
sub process {
#array = split /;/,$p,7;
# do something with array
print ((join "\n---\n", #array),"\n");
}
if ($p=~y/"//%2) {
$p.=$_;
next;
}
process;
$p=$_;
END{process}
' < logfile.txt
I have this path ../../Capture.jpg. So far I've figured out this incomplete regex: '[../]+'. I want to check if user puts in the right path like ../../image file name. The file extensions can be jpg, png, ..
your [../]+ is not sufficient or correct for the job at hand, if you REALLY want to match a bunch of ../ at the start of a filename.
It's not completely clear what you want to do exactly, but the following will match one or more ../ at the start of a string:
/^((?:\.\.\/)+)/
basically:
^ to anchor to the start of the string being tested - will not match any ../ INSIDE the string
( and the balancing ) at the end: capture the contents within. All your ../../ will be available in a variable called $1
then I'm using (?: ) to wrap the next content. This groups the bit inside, but does NOT save the value inside a $1, $2, etc. More information soon...
The REAL pattern of interest is
\.\.\/
Since . and / are magic characters, they need 'escaping' with backslash. This tells Perl that the . and / do NOT have a special meaning at this point.
I've used the (?: ) wrapper to group them together, so that the + operates on all 3 characters of interest. The + operator means "one or more repetitions".
So, my pattern will match one or more repetitions of ../ which are anchored to the start of the string. Furthermore, the exact contents matched will be available in $1 if you are interested in doing something with that (eg count how many ../ you have)
Please ask if you have further questions, or I have misunderstood your goals.
EDIT: to suit your new requirements, and add a bit of bonus:
m!^\.\./\.\./(([^/]+)\.([^.]+))$!
Note first that I've used m!pattern! instead of /pattern/. Firstly, if Perl sees /pattern/ it assumes it's m/pattern/ but you can use an alternative character to wrap the patterns. This is useful if you actually want to use / in your pattern without having to go nuts with backslashes.
so:
^ exactly match only from the start
followed by exactly ../../
next I've used ( ) wrappers to capture the bits following. Explanation after...
ignoring the ( and ) now:
[^/]+ one or more repetitions (+) of any character that isn't /
. literally a dot - the one before the extension
[^./]+ one or more repetitions of any character that isn't . or /
Notice how the [^/]+ allows for any character including . but prevents another directory part from sneaking in. Thus, the filename could be foo.bar.jpg and it will be collected properly.
Notice how [^./]+ allows for any character in the extension except a dot - and also excluding / to prevent another directory segment from sneaking in.
Finally, $ is used to ensure we've reached the end of the pattern.
as for the captures:
$1 will contain all of foo.bar.jpg
$2 will contain foo.bar
$3 will contain jpg (not .jpg) but I'll leave it up to you to figure out what to change if you wish to capture the dot as well.
FINALLY - in a typical script, you might do something like:
if($filename =~ m!^\.\./\.\./(([^/]+)\.([^./]+))$!) {
print "You correctly entered ../../$1 giving basename=$2 and extension=$3 - Bravo!\n";
}
else {
print "you've failed to read the instructions properly\n";
}
As a bonus, I even tested that, and found 2 spolling mistaiks you'll never have to see
cheers.
# convert relative file paths to md links ...
# file paths and names with letters , nums - and _ s supported
$str =~ s! (\.\.\/([a-zA-Z0-9_\-\/\\]*)[\/\\]([a-zA-Z0-9_\-]*)\.([a-zA-Z0-9]*)) ! [$3]($1) !gm
If you don't care the path prefix, use:
$path =~ /\.(jpg|png)$/
or
substr($path, -4) ~~ ['.jpg', '.png']
With exactly '../../', use:
$path =~ m!^\.\./\.\./[^/]*\.(jpg|png)$!
With any number of '../'s, use:
$path =~ m!^(\.\./)*[^/]*\.(jpg|png)$!
I have a file that I am reading in. I'm using perl to reformat the date. It is a comma seperated file. In one of the files, I know that element.0 is a zipcode and element.1 is a counter. Each row can have 1-n number of cities. I need to know the number of elements from element.3 to the end of the line so that I can reformat them properly. I was wanting to use a foreach loop starting at element.3 to format the other elements into a single string.
Any help would be appreciated. Basically I am trying to read in a csv file and create a cpp file that can then be compiled on another platform as a plug-in for that platform.
Best Regards
Michael Gould
you can do something like this to get the fields from a line:
my #fields = split /,/, $line;
To access all elements from 3 to the end, do this:
foreach my $city (#fields[3..$#fields])
{
#do stuff
}
(Note, based on your question I assume you are using zero-based indexing. Thus "element 3" is the 4th element).
Alternatively, consider Text::CSV to read your CSV file, especially if you have things like escaped delimiters.
Well if your line is being read into an array, you can get the number of elements in the array by evaluating it in scalar context, for example
my $elems = #line;
or to be really sure
my $elems = scalar(#line);
Although in that case the scalar is redundant, it's handy for forcing scalar context where it would otherwise be list context. You can also find the index of the last element of the array with $#line.
After that, if you want to get everything from element 3 onwards you can use an array slice:
my #threeonwards = #line[3 .. $#line];
I am using Net::Whois::Raw to query a list of domains from a text file and then parse through this to output relevant information for each domain.
It was all going well until I hit Nominet results as the information I require is never on the same line as that which I am pattern matching.
For instance:
Name servers:
ns.mistral.co.uk 195.184.229.229
So what I need to do is pattern match for "Name servers:" and then display the next line or lines but I just can't manage it.
I have read through all of the answers on here but they either don't seem to work in my case or confuse me even further as I am a simple bear.
The code I am using is as follows:
while ($record = <DOMAINS>) {
$domaininfo = whois($record);
if ($domaininfo=~ m/Name servers:(.*?)\n/){
print "Nameserver: $1\n";
}
}
I have tried an example of Stackoverflow where
<DOMAINS>;
will take the next line but this didn't work for me and I assume it is because we have already read the contents of this into $domaininfo.
EDIT: Forgot to say thanks!
how rude.
So, the $domaininfo string contains your domain?
What you probably need is the m parameter at the end of your regular expression. This treats your string as a multilined string (which is what it is). Then, you can match on the \n character. This works for me:
my $domaininfo =<<DATA;
Name servers:
ns.mistral.co.uk 195.184.229.229
DATA
$domaininfo =~ m/Name servers:\n(\S+)\s+(\S+)/m;
print "Server name = $1\n";
print "IP Address = $2\n";
Now, I can match the \n at the end of the Name servers: line and capture the name and IP address which is on the next line.
This might have to be munged a bit to get it to work in your situation.
This is half a question and perhaps half an answer (the question's in here as I am not yet allowed to write comments...). Okay, here we go:
Name servers:
ns.mistral.co.uk 195.184.229.229
Is this what an entry in the file you're parsing looks like? What will follow immediately afterwards - more domain names and IP addresses? And will there be blank lines in between?
Anyway, I think your problem may (in part?) be related to your reading the file line by line. Once you get to the IP address line, the info about 'Name servers:' having been present will be gone. Multiline matching will not help if you're looking at your file line by line. Thus I'd recommend switching to paragraph mode:
{
local $/ = ''; # one paragraph instead of one line constitutes a record
while ($record = <DOMAINS>) {
# $record will now contain all consecutive lines that were NOT separated
# by blank lines; once there are >= 1 blank lines $record will have a
# new value
# do stuff, e.g. pattern matching
}
}
But then you said
I have tried an example of Stackoverflow where
<DOMAINS>;
will take the next line but this didn't work for me and I assume it is because we have already read the contents of this into $domaininfo.
so maybe you've already tried what I have just suggested? An alternative would be to just add another variable ($indicator or whatever) which you'll set to 1 once 'Name servers:' has been read, and as long as it's equal to 1 all following lines will be treated as containing the data you need. Whether this is feasible, however, depends on you always knowing what else your data file contains.
I hope something in here has been helpful to you. If there are any questions, please ask :)
I have to parse a file and store it in a table. I was asked to use a hash to implement this. Give me simple means to do that, only in Perl.
-----------------------------------------------------------------------
L1234| Archana20 | 2010-02-12 17:41:01 -0700 (Mon, 19 Apr 2010) | 1 line
PD:21534 / lserve<->Progress good
------------------------------------------------------------------------
L1235 | Archana20 | 2010-04-12 12:54:41 -0700 (Fri, 16 Apr 2010) | 1 line
PD:21534 / Module<->Dir,requires completion
------------------------------------------------------------------------
L1236 | Archana20 | 2010-02-12 17:39:43 -0700 (Wed, 14 Apr 2010) | 1 line
PD:21534 / General Page problem fixed
------------------------------------------------------------------------
L1237 | Archana20 | 2010-03-13 07:29:53 -0700 (Tue, 13 Apr 2010) | 1 line
gTr:SLC-163 / immediate fix required
------------------------------------------------------------------------
L1238 | Archana20 | 2010-02-12 13:00:44 -0700 (Mon, 12 Apr 2010) | 1 line
PD:21534 / Loc Information Page
------------------------------------------------------------------------
I want to read this file and I want to perform a split or whatever to extract the following fields in a table:
the id that starts with L should be the first field in a table
Archana20 must be in the second field
timestamp must be in the third field
PD must be in the fourth field
Type (content preceding / must be in the last field)
My questions are:
How to ignore the --------… (separator line) in this file?
How to extract the above?
How to split since the file has two delimiters (|, /)?
How to implement it using a hash and what is the need for this?
Please provide some simple means so that I can understand since I am a beginner to Perl.
My questions are:
How to ignore the --------… (separator line) in this file?
How to extract the above?
How to split since the file has two delimiters (|, /)?
How to implement it using a hash and what is the need for this?
You will probably be working through the file line by line in a loop. Take a look at perldoc -f next. You can use regular expressions or a simpler match in this case, to make sure that you only skip appropriate lines.
You need to split first and then handle each field as needed after, I would guess.
Split on the primary delimiter (which appears to be ' | ' - more on that in a minute), then split the final field on its secondary delimiter afterwards.
I'm not sure if you are asking whether you need a hash or not. If so, you need to pick which item will provide the best set of (unique) keys. We can't do that for you since we don't know your data, but the first field (at a glance) looks about right. As for how to get something like this into a more complex data structure, you will want to look at perldoc perldsc eventually, though it might only confuse you right now.
One other thing, your data above looks like it has a semi-important typo in the first line. In that line only, there is no space between the first field and its delimiter. Everywhere else it's ' | '. I mention this only because it can matter for split. I nearly edited this, but maybe the data itself is irregular, though I doubt it.
I don't know how much of a beginner you are to Perl, but if you are completely new to it, you should think about a book (online tutorials vary widely and many are terribly out of date). A reasonably good introductory book is freely available online: Beginning Perl. Another good option is Learning Perl and Intermediate Perl (they really go together).
When you say This is not a homework...to mean this will be a start to assess me in perl I assume you mean that this is perhaps the first assignment you have at a new job or something, in which case It seems that if we just give you the answer it will actually harm you later since they will assume you know more about Perl than you do.
However, I will point you in the right direction.
A. Don't use split, use regular expressions. You can learn about them by googling "perl regex"
B. Google "perl hash" to learn about perl hashes. The first result is very good.
Now to your questions:
regular expressions will help you ignore lines you don't want
regular expressions with extract items. Look up "capture variables"
Don't split, use regex
See point B above.
If this file is line based then you can do a line by line based read in a while loop. Then skip those lines that aren't formatted how you wish.
After that, you can either use regex as indicated in the other answer. I'd use that to split it up and get an array and build a hash of lists for the record. Either after that (or before) clean up each record by trimming whitespace etc. If you use regex, then use the capture expressions to add to your list in that fashion. Its up to you.
The hash key is the first column, the list contains everything else. If you are just doing a direct insert, you can get away with a list of lists and just put everything in that instead.
The key for the hash would allow you to look at particular records for fast lookup. But if you don't need that, then an array would be fine.
You can try this one,
Points need to know:
read the file line by line
By using regular expression, removing '----' lines.
after that use split function to populate Hashes of array .
#!/usr/bin/perl
use strict;
use warning;
my $test_file = 'test.txt';
open(IN, '<' ,"$test_file") or die $!;
my (%seen, $id, $name, $timestamp, $PD, $type);
while(<IN>){
chomp;
my $line = $_;
if($line =~ m/^-/){ #removing '---' lines
# print "$line:hello\n";
}else{
if ($line =~ /\|/){
($id , $name, $timestamp) = split /\|/, $line, 4;
} else{
($PD, $type) = split /\//, $line , 3;
}
$seen{$id}= [$name, $timestamp, $PD, $type]; //use Hashes of array
}
}
for my $test(sort keys %seen){
my $test1 = $seen{$test};
print "$test:#{$test1}\n";
}
close(IN);