How to change many .sra documents into one fastq document? - linux

I download a series of .sra which belong to one sample from NCBI. I tried to change one sra into fastq, but it is error.
My code:
$fastq-dump I --split-files ERRXXXXX.sra.
And My .sra document is paired.
I used $fastq-dump SRR5XXXXX.sra to change another process, and it worked well.
Therefore I would like to know how to make many .sra into one .fastq document? Thank you for your kindness.


I don't really understand the whole message, but regarding your specific question "how to make many .sra into one .fastq document", the answer is pretty simple:
Generate multiple fastq files from all the sra files you are interested in in the usual way.
Concatenate all those fastq files in a single one: cat fastq1.fq fastq2.fq ... fastqN.fq > new_fastq.fq
Remove intermediate files if no longer needed
The new_fastq.fq file contains all the information from the original sra files.
Take care and don't mix first and second ends in the same fastq (unless you know what you are doing, of course).

Related

Adding multiple keywords with Exiftool, but only if they're not already present

I'm running the following command to add multiple keywords to an image:
exiftool -keywords+="Flowering" -keywords+="In Flower" -keywords+="Primula vulgaris" -overwrite_original "/pictures/Some Folder/P4130073.JPG"
However, I've noticed that if I do this for an image which already contains a particular keyword, then it'll get added a second time.
How can I ensure that keywords are added only if they're already missing, and that if they exist, it'll do a no-op (and ideally leave the file untouched). I've read a few questions on the forum and the docs, but NoDups docs isn't clear to me (I'm an exiftool n00b) and all the answers I've found only process a single keyword addition.
For an added bonus, if the 'exists' check could be case-insensitive, so much the better (e.g., so that if I'm doing keywords+="Flowering" and the image already has the keyword "flowering", nothing will be done.
I also need this to work on Linux, MacOS and Windows (I know the quotes can complicate things!).

See Exiftool FAQ #17
To prevent duplication when adding new items, specific items can be
deleted then added back again in the same command. For example, the
following command adds the keywords "one" and "two", ensuring that
they are not duplicated if they already existed in the keywords of an
image:
exiftool -keywords-=one -keywords+=one -keywords-=two -keywords+=two DIR
The NoDups helper function is used to remove duplicates when they already exist in the file. It isn't used to prevent duplicates from being added in the first place.

Compare two text columns to find partial match and new rows

I have two lists of messages. The first one is short messages and the second one is a master file which has longer texts which includes the short messages in the first list but also has many new messages. I want to find the new ones in master file (second list) which has no partial matches.
something like above. then NO means they are new errors
I tried =IF(ISERROR(VLOOKUP(""&A2&"",C:C,1,0)),"No","Yes") but it is other way around. it will find short messages within master file with big messages. I want to check big messages which have the short messages inside compare with the list with short messages and if there is no (partial) match label it as new.

This should work, currently can't test it though
=if(sumproduct(--isnumber(search($a$2:$a$8,b2)))>0,"YES","NO")

Try:
=IF(OR(ISNUMBER(FIND(" "&$A$2:$A$8&" "," "&B2& " "))),"YES","NO")
Note the use of spaces otherwise aaa would be found in kkaaa

batch file extract numbers from text file with little information

So This is related to my other two posts. Im dealing with extracting text from a text file and analyzing it and I've run into some problems. For A while I've been using a method that sets all the text between two other strings as a variable, but here is the situation I have. I need to extract the speed (numbers) from the below string: "etc...,query":{"ping":47855},"cmts":...etc. The problem is that the text cmts sometimes changes to something else so really I need to extract all the numbers from this:
,query":{"ping":47855},"
One more thing that makes this difficult is that the characters }," Are all over the file. Thank you for helping me! -Lucas EDG Programmer.
Here's the full file:
{"_id":53291,"ip":"158.69.22.95","domain":"jectile.com","port":25565,"url":"","date_add":1453897770,"status":1,"scan":1,"uptime":99.53,"last_update":1485436105,"geo":{"country":"US","country_name":"United States","city":"Lake Forest"},"info":{"name":" Jectile | jectile.com [1.8-1.11]\n Shoota (Call of Duty) \/ Zambies (Zombie Survival)","type":"FML","version":"1.10","plugins":[],"players":18,"max_players":420,"players_list":[],"map":"world","software":"BungeeCord 1.8.x, 1.9.x, 1.10.x, 1.11.x","avg_player_day":24.458333,"avg_load_day":5.8234,"platform":"MINECRAFT","icon":true},"counter":{"online":47871,"offline":228,"players":{"date":"2017-01-26","total":0},"last_offline":0,"query":{"ping":47855},"cmts":1},"rating":{"main":19.24,"difference":-0.64,"content_up":0.15,"K":0},"last":{"offline":1485415702,"online":1485436105},"chart":{"14:30":14,"14:40":16,"14:50":15,"15:00":18,"15:10":12,"15:20":13,"15:30":9,"15:40":9,"15:50":11,"16:00":12,"16:10":11,"16:20":11,"16:30":18,"16:40":25,"16:50":23,"17:00":27,"17:10":27,"17:20":23,"17:30":24,"17:40":26,"17:50":33,"18:00":31,"18:10":31,"18:20":32,"18:30":37,"18:40":38,"18:50":39,"19:00":38,"19:10":34,"19:20":33,"19:30":40,"19:40":36,"19:50":37,"20:00":38,"20:10":36,"20:20":38,"20:30":37,"20:40":37,"20:50":37,"21:00":34,"21:10":32,"21:20":33,"21:30":33,"21:40":29,"21:50":28,"22:00":26,"22:10":21,"22:20":24,"22:30":29,"22:40":22,"22:50":23,"23:00":27,"23:10":24,"23:20":26,"23:30":25,"23:40":28,"23:50":27,"00:00":32,"00:10":29,"00:20":33,"00:30":32,"00:40":31,"00:50":33,"01:00":40,"01:10":40,"01:20":40,"01:30":41,"01:40":45,"01:50":48,"02:00":43,"02:10":45,"02:20":46,"02:30":46,"02:40":43,"02:50":42,"03:00":39,"03:10":36,"03:20":44,"03:30":34,"03:40":0,"03:50":32,"04:00":35,"04:10":35,"04:20":33,"04:30":43,"04:40":37,"04:50":26,"05:00":31,"05:10":31,"05:20":27,"05:30":25,"05:40":26,"05:50":18,"06:00":13,"06:10":15,"06:20":17,"06:30":18,"06:40":17,"06:50":15,"07:00":16,"07:10":17,"07:20":16,"07:30":16,"07:40":18,"07:50":19,"08:00":14,"08:10":12,"08:20":12,"08:30":13,"08:40":17,"08:50":20,"09:00":18,"09:10":0,"09:20":0,"09:30":27,"09:40":18,"09:50":20,"10:00":15,"10:10":13,"10:20":12,"10:30":10,"10:40":10,"10:50":11,"11:00":13,"11:10":13,"11:20":16,"11:30":19,"11:40":17,"11:50":13,"12:00":10,"12:10":11,"12:20":12,"12:30":16,"12:40":15,"12:50":16,"13:00":14,"13:10":10,"13:20":13,"13:30":16,"13:40":16,"13:50":17,"14:00":20,"14:10":16,"14:20":16},"query":"ping","max_stat":{"max_online":{"date":1470764061,"players":129}},"status_query":"ok"}
By the way, the reason things change is because it looks at info from different servers

Very similar to ther answer I gave you to your first question:
#Echo Off
Set/P var=<some.json
Set var=%var:*:{"ping":=%
Set var=%var:},=&:%
Echo=%var%
Timeout -1

Perl: Find duplicate in excel/csv file and write an output file with them

First of all I am a completely newbie (for now) with Perl, and I would like to ask you a quick advice.
I have to deal with a some lists of journals and publishers in different Excel/CSV files. I would like to find a way to cross the data in order to have the list of the titles & publishers in common between two files, and a list with the publisher and the number of journal published.
I would like to ask you if it is possible to do it with Perl (it should be the best method for what I understood, but I would like a confirmation!), and how advance it is.
Sorry for the strange request but I am writing my thesis and I would not like to spend time on something and discover that is not possible!
Thanks!

Yes.
To parse a CSV file:
Text::CSV_XS
To parse an Excel file:
Spreadsheet::ParseExcel
To find the common elements of two lists:
my %list1 = map { $_ => 1 } #list1;
my #common = grep $list1{$_}, #list2;

three pdf-documents in one appendix

Hallo,
I wanted to ask how I can join three different pdf documents so that it appears in one single appendix. The command I gave was:
See Appendix~\ref{sec:corr-1}~\ref{sec:corr-2}~\ref{sec:corr-3}
and I have the following on my appendixes list:
\subsubsection{Writing}
\label{sec:writing}
\input{corr-1.tex}
\input{corr-2.tex}
\input{corr-3.tex}
Unforunately I cannot compile the final document.
Thanks a lot in advance.
Have a nice day.
Marie

In your example you just include tex files.
Have a look at the package pdfpages: http://mirror.ox.ac.uk/sites/ctan.org/macros/latex/contrib/pdfpages/pdfpages.pdf
Add to the top of your document:
\usepackage{pdfpages}
You should call this in the text where you want the PDF to appear:
\includepdf{test.pdf}

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