I there, 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 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 latter 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.
Thank you all for your time.
Paulo
PS- I have tried this:
sed -z 's/\n/,/g;s/,$/\n/' multi_headers
However it put comma in all \n.
CodePudding user response:
Bash
You can do a paste
.
cat mytext.txt | paste -d "," - -
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 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"
CodePudding user response:
Using any awk in any shell on every Unix box and only storing 1 line at a time in memory so it'll work no matter how large your input file is:
$ awk '{ORS=(NR%2 ? "," : RS)} 1' file
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
There's a lot happening in a small amount of code above so here's an explanation:
ORS
is the builtin variable containing the string to be printed at the end of each output record (record = line in this case), a newline by default.RS
is the builtin variable containing the string (or regexp) that separates each input record, a newline by default.NR
is the builtin variable containing the current record/line number soNR%2
is1
for odd numbered records and 0 for even numbered.NR%2 ? "," : RS
is a ternary expression resulting in,
for odd numbered lines,\n
(or whatever else you have setRS
to, e.g.\r\n
) for even numbered.1
is a true condition which causes the default action of printing the current record to be executed.
So the above script says "if the current line number is odd print it with a ,
at the end, otherwise print it with a newline at the end", hence it's joining every pair of lines with a ,
between.
CodePudding user response:
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 stringViruses
{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,
CodePudding user response:
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)
CodePudding user response:
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.read().split("\n")
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
CodePudding user response:
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"
CodePudding user response:
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.
CodePudding user response:
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.