I'm trying to match the end of line character in a shell script under bash. What I have done it got is a loop that reads each line of a file into a temp variable and then I get each letter of that variable and do some work on it. One think I want to do it check if the character I checking if the... (1 Reply)
How do i determine what the end of the line character is in a text file. for eg. is it \n or \f or \t etc..
Is there a unix command for this? (5 Replies)
Hi, I've got a file where in the middle of the record is a $ end of line character, visible only when I open the file in vi and do :set list. How to I get rid of the character in the middle and keep it at the end. The middle $ character always appears after SW, so that can be used to tag it.... (3 Replies)
hi all, i have this question: How to add new line character at the end of a file????
i need this because i am loading a file to sybase and i have problems with the last record
thanks for your help (5 Replies)
Hi,
i want to append a character '|' at end of each line of a file abc.txt.
for example if the file abc.txt conatins:
a|b|c
1|2|33
w|2|11
i want result file xyz.txt
a|b|c|
1|2|33|
w|2|11|
I know this is simple but sumhow i am not able to reach end of line.
its urgent, thanks for... (4 Replies)
Hi All
I have a rather unusual problem, which i have not faced till now. I have a script which exports some paths to a text file. The script runs fine but when i check the output file i can see some junk characters ^M appended at end of lines and random places. I am not able to figure... (4 Replies)
I need to remove new line character from end of file.
Suppose here are content.
a|b|c|d|r
a|b|c|d|r
a|b|c|d|r
<new line>
that means file contains 4 lines but data is there in 3 lines.
so I want that only 3 lines should be there in file.
Please help (20 Replies)
I have a file and some records may contain double quotes at beginning and at end of line. So how do I strip them?
For Example, file is somethings like this
Field1;Field2;Field3
01;'Test';'Test Field3'
"01;'This is 2nd field';This is 3rd field' "
Desired Output is:
... (6 Replies)
Need to add end of line character to last record in a fixed width file.
When i take the record length of each line, for all the records it gives example like 200 except the last line as 199.
Due to this my other script fails.
Please help me on this. (4 Replies)
Hai,
I have got a small requirement in my script. and i am using bash shell. I need to add a dot (.) for some particular line in a file. Say for example,
$Cat rmfile
1 This is line1
2 This is line2
3 This is line3
O/p should be :
$Cat rmfile
1 This is line1
2 This is line2. #... (2 Replies)
Discussion started by: Sivajee
2 Replies
LEARN ABOUT DEBIAN
blastclust
BLASTCLUST(1) NCBI Tools User's Manual BLASTCLUST(1)NAME
blastclust - BLAST score-based single-linkage clustering
SYNOPSIS
blastclust [-] [-C] [-L X] [-S X] [-W N] [-a N] [-b F] [-c filename] [-d filename] [-e F] [-i filename] [-l filename] [-o filename] [-p F]
[-r filename] [-s filename] [-v [filename]]
DESCRIPTION
blastclust automatically and systematically clusters protein or DNA sequences based on pairwise matches found using the BLAST algorithm in
case of proteins or Mega BLAST algorithm for DNA. In the latter case a single Mega BLAST search is performed for all the sequences combined
against a database created from the same sequences. blastclust finds pairs of sequences that have statistically significant matches and
clusters them using single-linkage clustering.
OPTIONS
A summary of options is included below.
- Print usage message
-C Complete unfinished clustering
-L X Length coverage threshold (default = 0.9)
-S X Score coverage threshold (bit score / length if < 3.0, percentage of identities otherwise; default = 1.75)
-W N Use words of size N (length of best perfect match; zero invokes default behavior: 3 for proteins, 32 for nucleotides)
-a N Number of CPU's to use (default = 1)
-b F Do not require coverage on both neighbours
-c filename
Read advanced options from configuration file filename
-d filename
Input as a database
-e F Disable id parsing in database formatting
-i filename
FASTA input file (program will format the database and remove files in the end; default = stdin)
-l filename
Restrict reclustering to id list in filename
-o filename
Output file for list of clusters (default = stdout)
-p F Input is nucleotides, not proteins.
-r filename
Restore neighbors for reclustering from filename
-s filename
Save all neighbours to filename
-v [filename]
Print verbose progress messages (to filename)
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO blast(1), formatdb(1), /usr/share/doc/blast2/blastclust.html, <http://www.ncbi.nlm.nih.gov/BLAST/>
NCBI 2004-06-25 BLASTCLUST(1)