I have two input files (given below) and to compare each line of the File1 with each line of File2 starts with '>sample1'. If a match occurs and that matched line in the File2 contains another line or sequence of lines starting with "Chr" they have to be displayed in output file with that sample. If a match occurs and the matched line in File2 does not contain a 'Chr' line(s) it has be omitted or not taken into consideration for output file. For easy understanding, I marked the matched lines in file1 and file2 with blue color which are taken into consideration for final output. I maked the matched lines in file1 with file2 (which doesnt contain 'Chr' lines) in red color which are not taken into account for output. The final output to be selected also given below. [COLOR="Blue"]PLS. KINDLY HELP ME FOR THE SHELL SCRIPTING OF THIS. [/COLOR
My input file (data1) is like this
I written a shell program like this.
It has to read a line like Chr8:4000-4500 from input file and that line has to be executed in a command like 'samtools faidx Bos_taurusUMD3.fa
but when I execute the shell it is displaying the output like this
but not displaying the sequence.but I execute the command at $ prompt like
$samtools faidx Bos_taurusUMD3.fa Chr8:4000-4500
it is running and displaying the sequence.
How to execute it in my shell by reading each line from input line, execute it in command and display the sequences.
KINDLY HELP ME
This User Gave Thanks to hravisankar For This Post:
I have an input file in this format (shown below). I have to select the lines which doesnt followed by 'miR-" and to save such lines into an output file. For easy identification they are shown here in blue color. They have to be selected. Pls. help me to write a shell script to select those lines which doesnt followed by miR- and have to write them in a file.
KINDLY DO THE HELP
Hi i have a file like this as shown below:
DA PROCESS_ID IDENTIFIER DA_FILE STATUS WAITING_FOR SCOPED_DEPENDENT
1836 21000 01052019 BH90P.TEMP.DA1836.FTP W NULL ... (6 Replies)
I have a shell script scheduled in cron job to run at every 1 minute which transfers files to remote machine and then move the files to backup folder.
cd /u01/app/ftp_tmp
sftp user@hostname <<-EOF
cd /home/user/ftp
mput *
bye
EOF
mv /u01/app/ftp_tmp/* /u01/app/ftp_bkp
Now the problem is... (6 Replies)
Hey guys,
I want the below files to be processed with the help of BASH so that i will be able to find the missing file names :
PP01674520141228X.gz
PP01674620141228X.gz
PP01674820141228X.gz
PP01674920141228X.gz
PP01675420141228X.gz
PP01675520141228X.gz
PP01676020141228X.gz
.
.
.
.... (4 Replies)
Hi,
I am using the nested for loops to generate the sequence ,
taking start and end sequence number input from test.txt
(sample content mentioned below).
Also , can I print the rest of columns as well with sequence number into the same file.
for i in `cat test.txt|cut -d"," -f7`
do ... (8 Replies)
Hi all,
I have a file like this
ID 3BP5L_HUMAN Reviewed; 393 AA.
AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 05-SEP-2012, entry version 71.
FT COILED 59 140 ... (1 Reply)
Hello Folks,
i have to write shell scripting for given expected output manner.
in given input we have to write shell script in such a way that sequence no can b merged/link between start and end digit with hyphen "-" symbol and rest of digit separated by ","
Eg :
For Input "2 6 7 8 11 12... (9 Replies)
Hi All,
I need a shell script which could insert a sequence number column inside a dat file(pipe delimited).
I have the dat file similar to the one as shown below..
|A|B|C||D|E
|F|G|H||I|J
|K|L|M||N|O
|P|Q|R||S|T
As shown above, the column 4 is currently blank and i need to insert sequence... (5 Replies)
KINDLY HELP ME FOR SHELL SCRIPTING FOR THIS TASK.
My input file consists of thousands of sequence in this format. The given input file consists of four sequences which are starting with ‘>’ symbol (each sequence shown in different colour for easy understanding). I have to use a command at $... (3 Replies)
I have two input files (given below) and to compare each line of the File1 with each line of File2 starts with '>sample1'. If a match occurs and that matched line in the File2 contains another line or sequence of lines starting with "Chr" they have to be displayed in output file with that sample.... (4 Replies)