Hi
It's been helpful, it does work for one file at the time, but I need to do this for several files at the time (415), if you could help me out a little bit further I would appreciate it.
Hi
Its for my investigation project, not a homework, I need to reedit files in order it works and pass filters in a software I'm trying to use (syntenet). Im a bioinformatician with not much programming expertise
Hi
I was wondering if you could help me out to propose a command for the issue I need to resolve. I basically need to erase all characters following the first word, including white space, in multiple lines containing as first character the symbol ">" inside a plain text file (extension .fa), for...
Hi
I was wondering if you could help me out a little bit more
after first line is edited
file 1: >strain_1Mo
file 2: >2012EL-1097_89x
file 3: >strain_4536
I need to add after the last character ".chr1"
for instance
file 1: >strain_1Mo.chr1
file 2: >2012EL-1097_89x.chr1
file 3...
Hi
Thanks for the short time response, but I tried both commands and it eliminates eveything after "Vibrio_cholerae_" I need to preserve whats next to it, for instance
file 1: >strain_1Mo
file 2: >2012EL-1097_89x
file 3: >strain_4536
Thanks in advance, really grateful
Hi
I have a series of .fasta files which first line looks like this
file 1: >Vibrio_cholerae_strain_1Mo
file 2: >Vibrio_cholerae_2012EL-1097_89x
file 3: >Vibrio_cholerae_strain_4536
I would like to remove from the first line all the "Vibrio_cholerae_" characters from this line, leaving the...
Hi
I removed the sed part, nevertheless this is what i got
sed -n '1p' *.fasta |wc -m |awk '{print($1-1)}'
32
I need to do it for several files, thats why I use *.fasta, but it seems it only counted one file and didn´t display which one
Hi
Indeed, theres no spaces in the characters from the first line
all lines go like this
file 1: >Vibrio_cholerae_strain_1Mo
file 2: >Vibrio_cholerae_strain_39Ki
file 3: >Vibrio_cholerae_strain_107V1216
and so on....
I need to determine which files contains in the first line > 38 characters...
Hi
The command line doesn't work
it returns -1 for several files at the time ans a single file
sed -n '1p' *.fasta |sed -n 's/ //gp' |wc -m |awk '{print($1-1)}'
-1
sed -n '1p' 1Mo_UM.fasta |sed -n 's/ //gp' |wc -m |awk '{print($1-1)}'
-1
Beg your pardon
and print it out per file
The reason I ask this newbie question is because I'm using a tool that throws an error when the first line of the file has more than (> 38 characters). It would be awesome if the pipeline you help me out with could include in the print just those files...
Hi
I was wondering if you could help me out to figure out how to count the characters from the first line in several text files contained in a directory