I have numerous sequences in one fasta file like the one below (downloaded from UniProtKB):
>sp|P00045|CYC7_YEAST Cytochrome c iso-2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CYC7 PE=1 SV=1
MAKESTGFKPGSAKKGATLFKTRCQQCHTIEEGGPNKVGPNLHGIFGRHSGQVKGYSYTD
ANINKNVKWDEDSMSEYLTNPKKYIPGTKMAFAGLKKEKDRNDLITYMTKAAK
Since they are all amino acid sequences for cytochrome c, I care only about the organism (i.e. Saccharomyces cerevisiae for the above entry). So I wish to modify headers of these sequences as below:
>Saccharomyces cerevisiae
MAKESTGFKPGSAKKGATLFKTRCQQCHTIEEGGPNKVGPNLHGIFGRHSGQVKGYSYTD
ANINKNVKWDEDSMSEYLTNPKKYIPGTKMAFAGLKKEKDRNDLITYMTKAAK
Organism names always come after "OS=" and stop when either one of:
space(.*) # strain information
space..=
is met.
So could anybody give me some clues on how to make it? Thx!
You can use this:
sed 's/.*OS=\([^(]*\).*/>\1/' input
Related
I am busy implementing a lab for pen testers to create MD5 hashes from 4 letter words. I need the words to have a combination of lower and uppercase letters as well as numeric and special characters, but I just do not seem to find out how to combine any given characters in all orders. So currently I have this:
my $str = 'aaaa';
print $str++, $/ while $str le 'dddd';
Which will do:
aaaa
aaab
aaac
aaad
...
...
dddd
There is no way however how I can make it do:
Aaaa
AAaa
aAaa
...
dddD
Not even to mention adding numbers and special characters. What I really wanted to do was to make the characters to create words based on a given list. So if I feel I want to use abeDod## it should create all combinations from those characters.
Edit to clarify.
Let's say I give the characters aBc# I need it to give it a a count to say it must have maximum of 4 letters per word and with combination of all the given characters, like:
aBc#
Bac#
caB#
#Bca
...
I hope that clarifies the question.
Use a list of integers that are ASCII codes for the characters you accept, to sample from it using your favorite (pseudo-)random number generator. Then convert each to its character using chr and concatenate them.
Like
perl -wE'$rw .= chr( 32+(int rand 126-32) ) for 1..4; say $rw'
Notes
I use a one-liner merely for easy copy-paste testing. Write this nicely in a script, please
I use the sketchy rand, good for shuffling things a bit. Replace with a better one if needed
Glueing four (pseudo-)random numbers does not build a good distribution; even as each letter on its own does, the whole thing does not. But the four should satisfy most needs.
If not, I think that you'd need to produce a far longer list (range of allowed chars repeated four times perhaps) and randomize it, then draw four-letter subsequences. A lot more work
I need to tap dance a little to produce (random-ish) integers from 32 to 126 using rand, since it takes only the end of range. Also, this takes all of them from that range, likely not what you want; so specify subranges, or specific lists that you want to draw from
I need to use Perl-compatible regex to match several strings which appear over multiple lines in a file.
The matches need to appear in any order (server servernameA.company.com followed by servernameZ.company.com followed by servernameD.company.com or any order combination of the three). Note: All matches will appear at the beginning of each line.
In my testing with grep -P, I haven't even been able to produce a match on simple string terms that appear in any order over new lines (even when using the /s and /m modifiers). I am pretty sure from reading I need a look-ahead assertion but the samples I used didn't produce a match for me even after analyzing each bit of the regex to make sure it was relevant to my scenario.
Since I need to support this in Production, I would like an answer that is simple and relatively straight-forward to interpret.
Sample Input
irrelevant_directive = 0
# Comment
server servernameA.company.com iburst
additional_directive = yes
server servernameZ.company.com iburst
server servernameD.company.com iburst
# Additional Comment
final_directive = true
Expectation
The regex should match and return the 3 lines beginning with server (that appear in any order) if and only if there is a perfect match for strings'serverA.company.com', 'serverZ.company.com', and 'serverD.company.com' followed by iburst. All 3 strings must be included.
Finally, if the answer (or a very similar form of the answer) can address checking for strings in any order on a single line, that would be very helpful. For example, if I have a single-line string of: preauth param audit=true silent deny=5 severe=false unlock_time=1000 time=20ms and I want to ensure the terms deny=5 and time=20ms appear in any order and if so match.
Thank you in advance for your assistance.
Regarding the main issue [for the secondary question see Casimir et Hippolyte answer] (using x modifier): https://regex101.com/r/mkxcap/5
(?:
(?<a>.*serverA\.company\.com\s+iburst.*)
|(?<z>.*serverZ\.company\.com\s+iburst.*)
|(?<d>.*serverD\.company\.com\s+iburst.*)
|[^\n]*(?:\n|$)
)++
(?(a)(?(z)(?(d)(*ACCEPT))))(*SKIP)(*F)
The matches are now all in the a, z and d capturing groups.
It's not the most efficient (it goes three times over each line with backtracking...), but the main takeaway is to register the matches with capturing groups and then checking for them being defined.
You don't need to use the PCRE features, you can simply write in ERE:
grep -E '.*(\bdeny=5\b.*\btime=20ms\b|\btime=20ms\b.*\bdeny=5\b).*' file
The PCRE approach will be different: (however you can also use the previous pattern)
grep -P '^(?=.*\bdeny=5\b).*\btime=20ms\b.*' file
I'm endeavoring to create a system to generalize rules from input text. I'm using reVerb to create my initial set of rules. Using the following command[*], for instance:
$ echo "Bananas are an excellent source of potassium." | ./reverb -q | tr '\t' '\n' | cat -n
To generate output of the form:
1 stdin
2 1
3 Bananas
4 are an excellent source of
5 potassium
6 0
7 1
8 1
9 6
10 6
11 7
12 0.9999999997341693
13 Bananas are an excellent source of potassium .
14 NNS VBP DT JJ NN IN NN .
15 B-NP B-VP B-NP I-NP I-NP I-NP I-NP O
16 bananas
17 be source of
18 potassium
I'm currently piping the output to a file, which includes the preceding white space and numbers as depicted above.
What I'm really after is just the simple rule at the end, i.e. lines 16, 17 & 18. I've been trying to create a script to extract just that component and put it to a new file in the form of a Prolog clause, i.e. be source of(banans, potassium).
Is that feasible? Can Prolog rules contain white space like that?
I think I'm locked into getting all that output from reVerb so, what would be the best way to extract the desirable component? With a Perl script? Or maybe sed?
*Later I plan to replace this with a larger input file as opposed to just single sentences.
This seems wasteful. Why not leave the tabs as they are, and use:
$ echo "Bananas are an excellent source of potassium." \
| ./reverb -q | cut --fields=16,17,18
And yes, you can have rules like this in Prolog. See the answer by #mat. You need to know a bit of Prolog before you move on, I guess.
It is easier, however, to just make the string a a valid name for a predicate:
be_source_of with underscores instead of spaces
or 'be source of' with spaces, and enclosed in single quotes.
You can use probably awk to do what you want with the three fields. See for example the printf command in awk. Or, you can parse it again from Prolog directly. Both are beyond the scope of your current question, I feel.
sed -n 'N;N
:cycle
$!{N
D
b cycle
}
s/\(.*\)\n\(.*\)\n\(.*\)/\2 (\1,\3)/p' YourFile
if number are in output and not jsut for the reference, change last sed action by
s/\^ *[0-9]\{1,\} \{1,\}\(.*\)\n *[0-9]\{1,\} \{1,\}\(.*\)\n *[0-9]\{1,\} \{1,\}\(.*\)/\2 (\1,\3)/p
assuming the last 3 lines are the source of your "rules"
Regarding the Prolog part of the question:
Yes, Prolog facts can contain whitespace like this, with suitable operator declarations present.
For example:
:- op(700, fx, be).
:- op(650, fx, source).
:- op(600, fx, of).
Example query and its result, to let you see the shape of terms that are created with this syntax:
?- write_canonical(be source of(a, b)).
be(source(of(a,b))).
Therefore, with these operator declarations, a fact like:
be source of(a, b).
is exactly the same as stating:
be(source(of(a,b)).
Depending on use cases and other definitions, it may even be an advantage to create this kind of facts (i.e., facts of the form be/1 instead of source_of/2). If this is the only kind of facts you need, you can simply write:
source_of(a, b).
This creates no redundant wrappers and is easier to use.
Or, as Boris suggested, you can use single quotes as in 'be source of'/2.
Qu.17 Write down the program to output the pattern given below using appropriate control structures. Use of control structures is compulsory in this program.
(*****)
(****)
(***)
(**)
(*)
(**)
(***)
(****)
(*****)
edit: have removed probable extra (**)
sounds like a college assignment to me :)
break down the problem into its simplest form and write a test to check your program.
your first test could be something really simple:
can print out single asterisk: (*)
then build it up from there:
given starting number of 2, prints 3 lines of two asterisks (**), (**), (**)
second line should only have one asterisk (**), (*), (**)
...
given starting number x, prints 2x - 1 lines
So me being the 'noob' that I am, being introduced to programming via Perl just recently, I'm still getting used to all of this. I have a .fasta file which I have to use, although I'm unsure if I'm able to open it, or if I have to work with it 'blindly', so to speak.
Anyway, the file that I have contains DNA sequences for three genes, written in this .fasta format.
Apparently it's something like this:
>label
sequence
>label
sequence
>label
sequence
My goal is to write a script to open and read the file, which I have gotten the hang of now, but I have to read each sequence, compute relative amounts of 'G' and 'C' within each sequence, and then I'm to write it to a TAB-delimited file the names of the genes, and their respective 'G' and 'C' content.
Would anyone be able to provide some guidance? I'm unsure what a TAB-delimited file is, and I'm still trying to figure out how to open a .fasta file to actually see the content. So far I've worked with .txt files which I can easily open, but not .fasta.
I apologise for sounding completely bewildered. I'd appreciate your patience. I'm not like you pros out there!!
I get that it's confusing, but you really should try to limit your question to one concrete problem, see https://stackoverflow.com/faq#questions
I have no idea what a ".fasta" file or 'G' and 'C' is.. but it probably doesn't matter.
Generally:
Open input file
Read and parse data. If it's in some strange format that you can't parse, go hunting on http://metacpan.org for a module to read it. If you're lucky someone has already done the hard part for you.
Compute whatever you're trying to compute
Print to screen (standard out) or another file.
A "TAB-delimite" file is a file with columns (think Excel) where each column is separated by the tab ("\t") character. As quick google or stackoverflow search would tell you..
Here is an approach using 'awk' utility which can be used from the command line. The following program is executed by specifying its path and using awk -f <path> <sequence file>
#NR>1 means only look at lines above 1 because you said the sequence starts on line 2
NR>1{
#this for-loop goes through all bases in the line and then performs operations below:
for (i=1;i<=length;i++)
#for each position encountered, the variable "total" is increased by 1 for total bases
total++
}
{
for (i=1;i<=length;i++)
#if the "substring" i.e. position in a line == c or g upper or lower (some bases are
#lowercase in some fasta files), it will carry out the following instructions:
if(substr($0,i,1)=="c" || substr($0,i,1)=="C")
#this increments the c count by one for every c or C encountered, the next if statement does
#the same thing for g and G:
c++; else
if(substr($0,i,1)=="g" || substr($0,i,1)=="G")
g++
}
END{
#this "END-block" prints the gene name and C, G content in percentage, separated by tabs
print "Gene name\tG content:\t"(100*g/total)"%\tC content:\t"(100*c/total)"%"
}