The below bash (though not optimized), yields the desired result for one entry. That is depending on the digits in the file manually selected in the first process, the second file used is automatically selected using the matching digits along with the full path. The problem is this seems to work for the first file but not for others. Thank you .
file manually selected: 123_base_counts.txt
Code:
123_base_counts.txt
456_base_counts.txt
file selected automatically using the matching digits in (/home/user)
# manual selection of file
FILESDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools
ANNOVARDIR=/home/user
PS3="please select a file to analyze with a panel: " # specify file1
select file1 in $(cd ${FILESDIR};ls);do break;done
file1=`basename ${FILESDIR}/${file1}`
printf "FILE is: ${file1} and will be used
# automatic file based on match
FILESDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools # match directory
ANNOVARDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/vcf/overall/annovar # search directory
printf "\n\n"
printf "These are all vcf files in the directory: \n"
ls ${ANNOVARDIR}
file1=`basename ${FILESSDIR}/${file1}` # file matched
file2=(${ANNOVARDIR}/${file1%%_*}*)
printf "file2 is: ${file2} and will be used
output
Code:
1) 123_base_counts.txt
2) 456_base_counts.txt
please select a file to analyze with a panel: 1
FILE is: 123_base_counts.txt and will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for visualization, calculate 20x and 30x coverage, and filter the vcf for the 98 gene epilepsy panel
These are all files in the new directory:
123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
456_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
file2 is: /home/cmccabe/Desktop/NGS/API/5-14-2016/vcf/overall/annovar/123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt and will be used
second time results
1) 123_base_counts.txt
2) 456_base_counts.txt
please select a file to analyze with a panel: 2
FILE is: 456_base_counts.txt and will be used
These are all files in the new directory:
123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
456_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
file2 is: /home/user/123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt and will be used
Write a quick shell snippet to find all of the IPV4 IP addresses
in any and all of the files under /var/lib/output/*, ignoring
whatever else may be in those files. Perform a reverse lookup on
each, and format the output neatly, like "IP=192.168.0.1,
... (0 Replies)
I have a file with hundreds of records and I need to find those records that have three digits at the beginning and the same three digits at the end.
$GREP '\(\)\(\)\(\)\3\2\1'I
believe this is part of the script but I am not sure how to compare these 3 digits with the 3 digits at the end of... (2 Replies)
Hi there, im sure this is really simple but i have some strings like this
e1000g123001
e1000g0
nge11101
nge3and i want to create two variables ($DRIVER and $INSTANCE). the first one containing the alpha characters that make up the first part of the string, e.g. e1000g or nge and the... (9 Replies)
Hi. I need assistance with the replacing of text into a specific file via a bash script.
My bash script, once run, currently provides a menu of computer names to choose.The script copies onto my system various files, depending what computer was selected in the menu.This is working OK.
Now, I... (1 Reply)
Hi I have a problem, I am attempting to write a bash script that goes through a file and can determine how many characters are at a set point in a line starting with QTY+113:100:PCE, If it detects 3 digits (number in bold) then pad it out with 12 zero's
If there are only two digits then pad it... (8 Replies)
In the below portion of a bash script the user selects a file from a directory.
select file in $(cd /home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools;ls);do break;done
files in directory
123_base_counts.txt
456_base_counts.txt
789_base_counts.txt
second portion of bash currently (user... (4 Replies)
As part of a bash the below line strips off a numerical prefix from directory 1 to search for in directory 2.
for file in /home/cmccabe/Desktop/comparison/missing/*.txt
do
file1=${file##*/} # Strip off directory
getprefix=${file1%%_*.txt}
... (5 Replies)
The bash bash below extracts the oldest folder from a directory and stores it in filename
That result will match a line in bold in input. In the matching line there is an_xxx digit in italics that
(once the leading zero is removed) will match a line in link. That is the lint to print in output.... (2 Replies)
Hey everyone,
I am trying to extract column values from a column in a tab-delimited text file and overlay them in a 2nd tab-delimited text file using a V-lookup type script in Unix bash.
These are the 1st few rows of the 1st input file IN1:
rsid chromosome position allele1 ... (10 Replies)
Discussion started by: Geneanalyst
10 Replies
LEARN ABOUT REDHAT
dos2unix
dos2unix(1) General Commands Manual dos2unix(1)NAME
dos2unix - DOS/MAC to UNIX text file format converter
SYNOPSYS
dos2unix [options] [-c convmode] [-o file ...] [-n infile outfile ...]
Options:
[-hkqV] [--help] [--keepdate] [--quiet] [--version]
DESCRIPTION
This manual page documents dos2unix, the program that converts plain text files in DOS/MAC format to UNIX format.
OPTIONS
The following options are available:
-h --help
Print online help.
-k --keepdate
Keep the date stamp of output file same as input file.
-q --quiet
Quiet mode. Suppress all warning and messages.
-V --version
Prints version information.
-c --convmode convmode
Sets conversion mode. Simulates dos2unix under SunOS.
-o --oldfile file ...
Old file mode. Convert the file and write output to it. The program default to run in this mode. Wildcard names may be used.
-n --newfile infile outfile ...
New file mode. Convert the infile and write output to outfile. File names must be given in pairs and wildcard names should NOT be
used or you WILL lost your files.
EXAMPLES
Get input from stdin and write output to stdout.
dos2unix
Convert and replace a.txt. Convert and replace b.txt.
dos2unix a.txt b.txt
dos2unix -o a.txt b.txt
Convert and replace a.txt in ASCII conversion mode. Convert and replace b.txt in ISO conversion mode. Convert c.txt from Mac to Unix
ascii format.
dos2unix a.txt -c iso b.txt
dos2unix -c ascii a.txt -c iso b.txt
dos2unix -c mac a.txt b.txt
Convert and replace a.txt while keeping original date stamp.
dos2unix -k a.txt
dos2unix -k -o a.txt
Convert a.txt and write to e.txt.
dos2unix -n a.txt e.txt
Convert a.txt and write to e.txt, keep date stamp of e.txt same as a.txt.
dos2unix -k -n a.txt e.txt
Convert and replace a.txt. Convert b.txt and write to e.txt.
dos2unix a.txt -n b.txt e.txt
dos2unix -o a.txt -n b.txt e.txt
Convert c.txt and write to e.txt. Convert and replace a.txt. Convert and replace b.txt. Convert d.txt and write to f.txt.
dos2unix -n c.txt e.txt -o a.txt b.txt -n d.txt f.txt
DIAGNOSTICS BUGS
The program does not work properly under MSDOS in stdio processing mode. If you know why is that so, please tell me.
AUTHORS
Benjamin Lin - <blin@socs.uts.edu.au>
Bernd Johannes Wuebben (mac2unix mode) <wuebben@kde.org>
MISCELLANY
Tested environment:
Linux 1.2.0 with GNU C 2.5.8
SunOS 4.1.3 with GNU C 2.6.3
MS-DOS 6.20 with Borland C++ 4.02
Suggestions and bug reports are welcome.
SEE ALSO unix2dos(1)mac2unix(1)1995.03.31 dos2unix v3.0 dos2unix(1)
07-26-2016
.