In post #1, the labels in your sample input files were "train statistics" and "test statistics". In your latest code you have labels with underscores instead of spaces. You'll have to be sure your stats files and your labels match.
In post #3, you included a header line in your output; I don't see anything in your latest code that prints that header. And, unless each of your stats files contains all of the sets of statistics and includes them in the same order, what you have shown us will end up printing data for different sets of statistics under each other in the output with no indication of which set they came from. Do each of your stats files contain statistics from all of the possible sets of statistics and are each of those sets of statistics present in the same order in each stats file?
In your latest code you have:
which sets both your input file and your output file to be the same input parameter. I'm about 99% sure that isn't what you want.
The cat in your code isn't helping and seems to be working against you. I think you're going to want to end up with something more like:
Do you want your output fields to be tab separated, or do you want your output fields to be in aligned columns? Note that since your field headers vary in width from 6 characters (e.g., "test_n" to more than 9 characters (e.g. " train_MdAE" and your statistics data all fit in less than 8 characters, the two choices are mutually exclusive. (I.e., you can't have both.)
This User Gave Thanks to Don Cragun For This Post:
Hi
I need to pass an array to Awk script from Shell. Can you please tell how to do it? How to pass this array add_ct_arr to an awk script or access it in awk?
i=1
while ;
do
add_ct_arr=$(echo ${adda_count} | awk -v i=$i -F" " '{print $i;}')
echo ${add_ct_arr}
... (1 Reply)
Hi All :),
I am very new to unix. I am requiring ur help in developing shell script for below problem.
I have to replace the second field of file with values of array sequentially where first field is ValidateKeepVar
<File>
UT-ExtractField 1 | &LogEntry &Keep(DatatoValidate)... (3 Replies)
OS=HP-UX ksh
The following works, except I want to include the <start> and <end> in the output.
awk -F '<start>' 'BEGIN{RS="<end>"; OFS="\n"; ORS=""} {print $2} somefile.log'
The following work in bash but not in ksh
sed -n '/^<start>/,/^<end>/{/LABEL$/!p}' somefile.log (4 Replies)
Hi, all
suppose I have following myfile (delimited by tab)
aa bb
cc dd
ee ffand I have following awk command:
awk 'BEGIN{FS="\t"}{AwkArrayVar_1=$1;AwkArrayVar_2=$2};END{for(i=0; i<NR; i++) print i, AwkArrayVar_1, AwkArrayVar_2,}' myfileMy question is: how can I assign the awk array... (7 Replies)
hi,
i want to pass an array parameters to a sftp script so that i can transfer each file in the array to the remote server by connecting only once to the sftp remote server.
i thought of using a variable that contains list of file names separated by a space and pass the variable to the sftp... (3 Replies)
There are two parts to this. In the first part I need to read a list of files from a directory and split it into 4 arrays. I have done that with the following code,
# collect list of file names
STATS_INPUT_FILENAMES=($(ls './'$SET'/'$FOLD'/'*'in.txt'))
# get number of files... (8 Replies)
I need to create a shell script to delete multiple items (Strings) at a time from a file.
I need to iterate through a list of strings.
My plan is to create an array and then iterate through the array.
My code is not working
#!/bin/bash -x
declare -a array=(one, two, three, four)... (5 Replies)
Hello,
I have some tab delimited text data,
file: final_temp1
aname val
NAME;r'(1,) 3.28584
r'(2,)<tab>
NAME;r'(3,) 6.13003
NAME;r'(4,) 4.18037
r'(5,)<tab>
You can see that the data is incomplete in some cases. There is a trailing tab after the first column for each incomplete row. I... (2 Replies)
Hello,
I have a src code file where I need to uncomment many lines.
The lines I need to uncomment look like,
C CALL l_r(DESNAME,DESOUT, 'Gmax', ESH(10), NO_APP, JJ)
The comment is the "C" in the first column. This needs to be deleted so that there are 6 spaces preceding "CALL".... (7 Replies)
Discussion started by: LMHmedchem
7 Replies
LEARN ABOUT DEBIAN
vcf-isec
VCF-ISEC(1) User Commands VCF-ISEC(1)NAME
vcf-isec - create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files
SYNOPSIS
vcf-isec [OPTIONS] file1.vcf file2.vcf ...
DESCRIPTION
About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files.
Note that lines from all files can be intermixed together on the output, which can yield unexpected results.
OPTIONS -C, --chromosomes <list|file>
Process the given chromosomes (comma-separated list or one chromosome per line in a file).
-c, --complement
Output positions present in the first file but missing from the other files.
-d, --debug
Debugging information
-f, --force
Continue even if the script complains about differing columns.
-o, --one-file-only
Print only entries from the left-most file. Without -o, all unique positions will be printed.
-n, --nfiles [+-=]<int>
Output positions present in this many (=), this many or more (+), or this many or fewer (-) files.
-p, --prefix <path>
If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)
-t, --tab <chr:pos:file>
Tab-delimited file with indexes of chromosome and position columns. (1-based indexes)
-w, --win <int>
In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a
SNP or an indel).
-h, -?, --help
This help message.
EXAMPLES
bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix -s 1 -b 2 -e 2 file.tab.gz
vcf-isec 0.1.5 July 2011 VCF-ISEC(1)