I put my answer back as I met the scenarios:
1) when file2.fasta contains more entries than in file1.fasta and vice versa. and
2) when the sequence part can have more than one row;
This only works for 2-line fasta sequence files (i.e. each entry has two lines, One starts with ">" as the header, the other is the DNA sequence. @vgersh99, could you please elaborate your code for scenario 2)? Thanks!
My previously posted attempt was for the provided sample files ONLY - 2 lines for each sequence: 1 header and 1 "data" lines.
Had the OP elaborated on the possible other sample data files, an alternate solution would have been provided.
Hi, I have two files where 1 contains data and the other contains strings eg
file 1
-0.00000 0.00000 0.00000
0.00000 0.00000 0.80000
0.50000 0.50000 0.60000
0.50000 0.50000 0.20000
-0.00000 0.00000 0.40000
file 2
F F F
F F F
T T T
T T T
T T T
How to I append file2 to file 1 to... (1 Reply)
I would like to extract the sequences larger than 10 bases but shorter than 18 along with the identifier from a FASTA file that looks like this:
> Seq I
ACGACTAGACGATAGACGATAGA
> Seq 2
ACGATGACGTAGCAGT
> Seq 3
ACGATACGAT
I know I can extract the IDs alone with the following code
grep... (3 Replies)
I have a fasta file that looks like this:
>Noname
ACCAAAATAATTCATGATATACTCAGATCCATCTGAGGGTTTCACCACTTGTAGAGCTAT
CAGAAGAATGTCAATCAACTGTCCGAGAAAAAAGAATCCCAGG
>Noname
ACTATAAACCCTATTTCTCTTTCTAAAAATTGAAATATTAAAGAAACTAGCACTAGCCTG
ACCTTTAGCCAGACTTCTCACTCTTAATGCTGCGGACAAACAGA
...
I want to... (2 Replies)
I tried to write a script ( not working) to append first value from mylist to a file called my myfirstResult and to another called mysecondResult
awk ' {print $1} >> myfirsResult ' < mylist
awk ' {print $1} >> mysecondResult ' < mylist
$ cat mylist
A 02/16/2012
B 02/19/2012
C... (3 Replies)
Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
for i in *.rtf.out
do
awk '/^>/{f=++d".fasta"} {print > $i.out}' $i
done (1 Reply)
Hi All,
I have to append 2 lines at the end of a text file. If those 2 lines are already there then do not append else append the 2 lines to the text file.
Eg: I have a text file, file.txt
This text file might look like this,
/home/kp/make.jsp
/home/pk/model.jsp
I have to append... (1 Reply)
Hi frnds,
My requirement is I have a zip file with name say eg: test_ABC_UH_ccde2a_awdeaea_20150422.zip
within that there are subdirectories on each directory we again have .zip files and in that we have files like mama20150422.gz and so on.
Iam in need of a bash script so that it unzips... (0 Replies)
Hii,
Could someone help me to append string to the starting of all the filenames inside a directory but it should exclude .zip files and subdirectories.
Eg.
file1: test1.log
file2: test2.log
file3 test.zip
After running the script
file1: string_test1.log
file2: string_test2.log
file3:... (4 Replies)
set_color(1) fish set_color(1)NAME
set_color - set_color - set the terminal color
set_color - set the terminal color
Synopsis
set_color [-v --version] [-h --help] [-b --background COLOR] [COLOR]
Description
Change the foreground and/or background color of the terminal. COLOR is one of black, red, green, brown, yellow, blue, magenta, purple,
cyan, white and normal.
o -b, --background Set the background color
o -c, --print-colors Prints a list of all valid color names
o -h, --help Display help message and exit
o -o, --bold Set bold or extra bright mode
o -u, --underline Set underlined mode
o -v, --version Display version and exit
Calling set_color normal will set the terminal color to whatever is the default color of the terminal.
Some terminals use the --bold escape sequence to switch to a brighter color set. On such terminals, set_color white will result in a grey
font color, while set_color --bold white will result in a white font color.
Not all terminal emulators support all these features. This is not a bug in set_color but a missing feature in the terminal emulator.
set_color uses the terminfo database to look up how to change terminal colors on whatever terminal is in use. Some systems have old and
incomplete terminfo databases, and may lack color information for terminals that support it. Download and install the latest version of
ncurses and recompile fish against it in order to fix this issue.
Version 1.23.1 Sun Jan 8 2012 set_color(1)