May I paraphrase your request: You want file2's sequences to prevail and file1's sequences inserted only if there's no equivalent in file2. If so, try
with any length fasta sequences. The traiing ">" can be taken care of piping through | sed '$d' if need be. Please be aware that your desired output's "Contig_98" line is missing an "AG" at the end.
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)
DIFF(1) General Commands Manual DIFF(1)NAME
diff - print differences between two files
SYNOPSIS
diff [-c | -e | -C n] [-br]file1 file2
OPTIONS -C n Produce output that contains n lines of context
-b Ignore white space when comparing
-c Produce output that contains three lines of context
-e Produce an ed-script to convert file1 into file2
-r Apply diff recursively to files and directories of
EXAMPLES
diff file1 file2 # Print differences between 2 files
diff -C 0 file1 file2
# Same as above
diff -C 3 file1 file2
# Output three lines of context with every
diff -c file1 file2 # Same
diff /etc /dev # Compares recursively the directories /etc and /dev
diff passwd /etc # Compares ./passwd to /etc/passwd
DESCRIPTION
the same name, when file1 and file2 are both directories" difference encountered"
Diff compares two files and generates a list of lines telling how the two files differ. Lines may not be longer than 128 characters. If
the two arguments on the command line are both directories, diff recursively steps through all subdirectories comparing files of the same
name. If a file name is found only in one directory, a diagnostic message is written to stdout. A file that is of either block special,
character special or FIFO special type, cannot be compared to any other file. On the other hand, if there is one directory and one file
given on the command line, diff tries to compare the file with the same name as file in the directory directory.
SEE ALSO cdiff(1), cmp(1), comm(1), patch(1).
DIFF(1)