'How to make a csv row for each 2 lines in a txt file

I have a text file like this:

Viruses/GCF_000820355.1_ViralMultiSegProj14361_genomic.fna.gz
Sclerophthora macrospora virus A
Viruses/GCF_000820495.2_ViralMultiSegProj14656_genomic.fna.gz
Influenza B virus RNA
Viruses/GCF_000837105.1_ViralMultiSegProj14079_genomic.fna.gz
Tomato mottle virus

And I need to get a csv file like this:

Viruses/GCF_000820355.1_ViralMultiSegProj14361_genomic.fna.gz,Sclerophthora macrospora virus A
Viruses/GCF_000820495.2_ViralMultiSegProj14656_genomic.fna.gz,Influenza B virus RNA
Viruses/GCF_000837105.1_ViralMultiSegProj14079_genomic.fna.gz,Tomato mottle virus

Because later I want to use this like a tuple to find the compressed file, read it and get a final file with names like:

Viruses/GCF_000837105.1/Tomato mottle virus.fna

I just need to learn how to do the first part of the problem. It could by with:

  • sed
  • awk
  • R
  • Python

Any help would be very appreciated. This is hard for me to accomplish because the original filenames are very messed up.

I have tried this:

sed -z 's/\n/,/g;s/,$/\n/' multi_headers

However it put comma in all \n.

pythonrbashawksedjavascriptreactjs


Solution 1:[1]

Bash

You can do a paste (thanks @glenn jackman for pointing out my previous useless use of cat).

# or cat mytext.txt | paste -d "," - -
paste -d "," - - < mytext.txt 

Viruses/GCF_000820355.1_ViralMultiSegProj14361_genomic.fna.gz,Sclerophthora macrospora virus A
Viruses/GCF_000820495.2_ViralMultiSegProj14656_genomic.fna.gz,Influenza B virus RNA
Viruses/GCF_000837105.1_ViralMultiSegProj14079_genomic.fna.gz,Tomato mottle virus

R

The R function is also paste, together with sapply:

mytext <- scan("mytext.txt", character(), sep = "\n")

sapply(seq(1, length(mytext), 2), function(x) paste(mytext[x], mytext[x + 1], sep = ","))
[1] "Viruses/GCF_000820355.1_ViralMultiSegProj14361_genomic.fna.gz,Sclerophthora macrospora virus A"
[2] "Viruses/GCF_000820495.2_ViralMultiSegProj14656_genomic.fna.gz,Influenza B virus RNA"           
[3] "Viruses/GCF_000837105.1_ViralMultiSegProj14079_genomic.fna.gz,Tomato mottle virus"

Solution 2:[2]

Using sed

$ sed '/^Viruses/{N;s/\n\(.*\)/,\1/}' multi_headers
Viruses/GCF_000820355.1_ViralMultiSegProj14361_genomic.fna.gz,Sclerophthora macrospora virus A
Viruses/GCF_000820495.2_ViralMultiSegProj14656_genomic.fna.gz,Influenza B virus RNA
Viruses/GCF_000837105.1_ViralMultiSegProj14079_genomic.fna.gz,Tomato mottle virus

  • /^Viruses/ - Match lines starting with the string Viruses

  • {N; - Read/append the next line of input into the pattern space.

  • s/\n\(.*\)/,\1/ - Remove the \n from the pattern space and replace it with a comma ,

Solution 3:[3]

This might work for you (GNU sed and paste):

sed 'N;s/\n/,/' file

Append the next line to the current line and replace the newline between then with a comma.

or:

paste -sd',\n' file

Paste the file as one long string, replacing every other newline with a comma.

Solution 4:[4]

A simple writerows():

import csv

with open("text.txt", "r") as f:
    with open("data.csv", "w", newline="") as w:
        writer = csv.writer(w)
        # May want to add headers
        writer.writerow(["Heading1", "Heading2"])
        x = f.readlines()
        writer.writerows([x[i:i+2] for i in range(0, len(x), 2)])

Which yields:

Heading1,Heading2
Viruses/GCF_000820355.1_ViralMultiSegProj14361_genomic.fna.gz,Sclerophthora macrospora virus A
Viruses/GCF_000820495.2_ViralMultiSegProj14656_genomic.fna.gz,Influenza B virus RNA
Viruses/GCF_000837105.1_ViralMultiSegProj14079_genomic.fna.gz,Tomato mottle virus

Solution 5:[5]

What about this.

with open('test.txt') as f:
    data = f.read().split('\n')
new_data = []

for a in range(0,len(data),2):
    new_data.append(data[a]+','+data[a+1]+'\n')
    
with open('result.txt','w') as f:
    f.writelines(new_data)

or

with open('test.txt') as f_read, open('result.txt','w') as f_write:
    data = f_read.read().split('\n')
    new_data = []

    for a in range(0,len(data),2):
        new_data.append(data[a]+','+data[a+1]+'\n')

    f_write.writelines(new_data)

Solution 6:[6]

Another R approach, relying on vector recycling.

t = readLines("txt.txt")
paste0(t[c(T, F)], ",", t[c(F, T)]) |> writeLines("txt.csv")

or for final file names

t = readLines("R/txt.txt")
sub("(?<=\\.\\d).*", "", t, perl = T) |>
  (\(.) paste0(.[c(T, F)], "/", .[c(F, T)], ".fna"))()

#> [1] "Viruses/GCF_000820355.1/Sclerophthora macrospora virus A.fna"
#> [2] "Viruses/GCF_000820495.2/Influenza B virus RNA.fna"           
#> [3] "Viruses/GCF_000837105.1/Tomato mottle virus.fna"

Solution 7:[7]

Simple python3 solution, let file.txt content be

Viruses/GCF_000820355.1_ViralMultiSegProj14361_genomic.fna.gz
Sclerophthora macrospora virus A
Viruses/GCF_000820495.2_ViralMultiSegProj14656_genomic.fna.gz
Influenza B virus RNA
Viruses/GCF_000837105.1_ViralMultiSegProj14079_genomic.fna.gz
Tomato mottle virus

and script.py

with open("file.txt","r") as f:
    for inx, line in enumerate(f):
        print(line.rstrip(), end='\n' if inx%2 else ',')

then

python script.py

output

Viruses/GCF_000820355.1_ViralMultiSegProj14361_genomic.fna.gz,Sclerophthora macrospora virus A
Viruses/GCF_000820495.2_ViralMultiSegProj14656_genomic.fna.gz,Influenza B virus RNA
Viruses/GCF_000837105.1_ViralMultiSegProj14079_genomic.fna.gz,Tomato mottle virus

Explanation: I use .rstrip to jettison trailing newline, then depending on whatever line is odd or even I apply \n or , respectively as line end. Note that enumerate default is starting at 0 as opposed to GNU AWK starting at 1. Note that using for ... in filehandle does prevent loading whole file as once, so this solution could be used also for files bigger than available RAM space.

Solution 8:[8]

To add yet another solution into the mix, you can also use xargs and group input lines by 2, then replace first space with ',' in each output line.

xargs -n2 -d'\n' -a input.txt | sed 's/ /,/'

Solution 9:[9]

Make sure that when you call changeTitle the variable form.name is not undefined. If you are using react hooks and the variable form is a state or prop you can use a useEffect and change the state of title only when the variable form.name is defined

useEffect(() => {
 if(form.name){
  changeTitle(form.name);
 }
},[form.name]);

Sources

This article follows the attribution requirements of Stack Overflow and is licensed under CC BY-SA 3.0.

Source: Stack Overflow

Solution Source
Solution 1
Solution 2
Solution 3 potong
Solution 4
Solution 5 Sharim Iqbal
Solution 6
Solution 7
Solution 8 Michail Alexakis
Solution 9

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