Notepad++ Bookmark Lines, Advanced Search and Replace, Alternative Native to Ubuntu 19.04

I am in the process of moving completely from Windows to Ubuntu. One of my favourite Software in Notepad++. I know it is possible to install it in Ubuntu with wine but I would like something native to Linux if possible.

One of the things that I use the most is Search for a term and bookmark the lines where this term is located. Then I use the “Paste to replace bookmarked Lines” function to get rid of this lines with a new text.

Is there a software capable to bookmark lines with the search function as Notepad++ does. Maybe notepadqq can but I dont know how…

Thank you!

Notepad++ RegEx Only change last line in specific file

The problem is i want to comment out a specific string in some files. Also i am not very found of RegEx.

In most of them it looks like this

countries = {"GER","NZG",} 

Replacing this is trivial. However there are some exception in which the string looks like this:

    countries = {          "GER","NZG",     } 

I replaced the first line in the first run through by replacing “countries” with “–countries”.

Now i found the next row with

^([\s][\"][A-Z]{3}[\"]) 

and Replaced it by

--  

Now my files look like this

 --countries = {  --      "GER","NZG",    } 

I know this is not very efficent but like i said, i’n not very found with RegEx As you can see i need to comment out the last “}”. It is the last “}” in every file. But there are other single “}” in one rows.

Would be nice if someone could help me with that.

regards

Notepad++ space within a keyword in Autocomplete

I created my autocomplete file after reading some documents. The problem is i cant add space within a keyword. My keyword is “define method .xx” But notepad++ recognise all of the worda separately. Is there any way to do it. I read somewhere that i will have to edit some notepad files in c. I am pretty new, so please can anyone guide me. Any help would really be appreciated.

Notepad++ REGEX 3 or 4 digits at the end of string

Why is my pattern only matching the thousands matching and not the hundreds? Thanks.

Here’s my pattern:

(.*)(\d{1}?\,?\d{3}\.\d{2}) 

Here’s my sample

abc-anything320.00 abc-anything400.00 abc-anything577.32 abc-anything290.00 abc-anything204.00 abc-anything205.00 abc-anything214.00 abc-anything365.00 abc-anything365.00 abc-anything400.00 abc-anything299.00 abc-anything235.50 abc-anything213.00 abc-anything319.00 abc-anything272.00 abc-anything109.00 abc-anything239.00 abc-anything400.00 abc-anything600.00 abc-anything2,199.75 abc-anything289.00 abc-anything640.00 abc-anything157.00 abc-anything202.00 abc-anything125.00 abc-anything1,550.00 abc-anything194.00 

Replace by: $ 2

Can I make an auto-increment thingie in Notepad++?

I’m trying to do this DAISY talking book thing, and instead of using Dolphin Publisher’s HTML thingie (which is hideous), I thought I’d play with doing it without the GUI, in notepad++, since I know basic HTML.

So I need to surround each sentence with

<span class="sentence" id="aiw_0002"> text of sentence </span> 

And of course that ID number needs to increment. Is there a magic way I can make a keystroke/macro that would do that? Basically paste </span><span class="sentence" id="something_xxxx"> where X goes up 1 each time?

My non-fancy way of doing it to copy the span statement (stopping before final-quote-mark-and-greater-than-sign), into Excel2016, doing a second one (0003) to establish the pattern, and do the click-drag thing to autopopulate. I just have to add in the last tip of the tag (if I don’t end with a numeral, there’s no auto-increment thingie).

I can’t install anything – government computer, things are pretty locked. And no one else in my area uses Dolphin or knows web stuff at all.

Script problem using Notepad ++.exe

Hi I prepared script copied from biostar handbook. The file is saved in Unix mode LF and saved as sh file. Here it is

Accession number for the reference genome

ACC=AF086833

SRA run number.

SRR=SRR1972739

How many reads to extract from the dataset.

N=10000

The reference genome in three different formats: GenBank, FASTA and GFF

GB=refs/$ ACC.gb FA=refs/$ ACC.fa GFF=refs/$ ACC.gff

Make the reference directory.

mkdir -p refs

Get a genbank file.

efetch -db nucleotide -format=gb -id=$ ACC > $ GB

Convert the GenBank file into GFF3.

cat $ GB | seqret -filter -feature -osformat gff3 > $ GFF

Convert the GenBank file into FASTA.

cat $ GB | seqret -filter -feature -osformat fasta > $ FA

Create an index of the FASTA file

samtools faidx $ FA

Obtain the dataset.

fastq-dump -X $ N –split-files $ SRR

Index reference with bwa.

bwa index $ FA

Index the reference with samtools.

samtools faidx $ FA

Shortcuts to read names

R1=$ {SRR}_1.fastq R2=$ {SRR}_2.fastq

Align with bwa mem.

bwa mem $ FA $ R1 $ R2 | samtools sort > $ SRR.bwa.bam

Index the BAM file generated with bwa.

samtools index $ SRR.bwa.bam

Index reference with bowtie2.

bowtie2-build $ FA $ FA

Align the same data with bowtie2.

bowtie2 -x $ FA -1 $ R1 -2 $ R2 | samtools sort > $ SRR.bowtie.bam

Index the BAM file produced with bowtie2.

samtools index $ SRR.bowtie.bam

These all commands work in ubuntu with copy and paste but when I tried to open the myscript.sh file through ubuntu using command cat myscript.sh I got error permission denied Then I used command line se) asifa86@DESKTOP-012ORAQ ~ $ conda activate bioinfo (bioinfo) asifa86@DESKTOP-012ORAQ ~ $ cat myscript.sh cat: myscript.sh: Permission denied (bioinfo) asifa86@DESKTOP-012ORAQ ~ $ sudo cat myscript.sh [sudo] password for asifa86:

Accession number for the reference genome

ACC=AF086833

SRA run number.

SRR=SRR1972739

How many reads to extract from the dataset.

N=10000

The reference genome in three different formats: GenBank, FASTA and GFF

GB=refs/$ ACC.gb FA=refs/$ ACC.fa GFF=refs/$ ACC.gff

Make the reference directory.

mkdir -p refs

Get a genbank file.

efetch -db nucleotide -format=gb -id=$ ACC > $ GB

Convert the GenBank file into GFF3.

cat $ GB | seqret -filter -feature -osformat gff3 > $ GFF

Convert the GenBank file into FASTA.

cat $ GB | seqret -filter -feature -osformat fasta > $ FA

Create an index of the FASTA file

samtools faidx $ FA

Obtain the dataset.

fastq-dump -X $ N –split-files $ SRR

Index reference with bwa.

bwa index $ FA

Index the reference with samtools.

samtools faidx $ FA

Shortcuts to read names

R1=$ {SRR}_1.fastq R2=$ {SRR}_2.fastq

Align with bwa mem.

bwa mem $ FA $ R1 $ R2 | samtools sort > $ SRR.bwa.bam

Index the BAM file generated with bwa.

samtools index $ SRR.bwa.bam

Index reference with bowtie2.

bowtie2-build $ FA $ FA

Align the same data with bowtie2.

bowtie2 -x $ FA -1 $ R1 -2 $ R2 | samtools sort > $ SRR.bowtie.bam

Index the BAM file produced with bowtie2.

samtools index $ SRR.bowtie.bam(bioinfo) asifa86@DESKTOP-012ORAQ ~ $ sudo bash myscript.sh myscript.sh: line 14: efetch: command not found myscript.sh: line 16: seqret: command not found myscript.sh: line 18: seqret: command not found myscript.sh: line 20: samtools: command not found myscript.sh: line 22: fastq-dump: command not found myscript.sh: line 24: bwa: command not found myscript.sh: line 26: samtools: command not found myscript.sh: line 31: bwa: command not found myscript.sh: line 31: samtools: command not found myscript.sh: line 33: samtools: command not found myscript.sh: line 35: bowtie2-build: command not found myscript.sh: line 37: bowtie2: command not found myscript.sh: line 37: samtools: command not found myscript.sh: line 39: samtools: command not found (bioinfo)

These commands work individually but with bash ubuntu script is not working. The problem is I have to complete the work if any body can guide me how to solve this situation I shall be thankful to you