I would like to remove characters from column 7 so that from an input file looking like this:
>HWI-EAS422_12:4:1:69:89 GGTTTAAATATTGCACAAAAGGTATAGAGCGT U0 1 0 0 ref_chr8.fa 6527777 F DD
I get something like that in an output file:
... (13 Replies)
I have a large text-file with tab-delimited genetic data that looks like:
KSC112 KSC234 0 0 1 1 A G C T
I simply wan to delete the first column, but since the file has 600 000 columns, it is not possible with awk (seems to be limited at 32k columns).
Does anyone have an idea how to do this? (2 Replies)
I want to add a new column to a tab delimited text file. It will be the first column and it will just be 1's. How do I go about doing that? Thanks! (1 Reply)
Hi all,
I'm new to Unix and work primarily in bioinformatics. I am in need of a script which will allow me to replace "1" with "chr1" in only the first column of a file which looks like such:
1 10327 rs112750067 T C . PASS ASP;RSPOS=10327;... (4 Replies)
I have a file which looks like this:
73450 articles and news developmental psychology 2006-03-30 16:22:40 1 http://www.usnews.com
73450 articles and news developmental psychology 2006-03-30 16:22:40 2 http://www.apa.org
73450 articles and news developmental psychology 2006-03-30... (1 Reply)
I have a file having the following entries:
test1 test2 test3
11 22 33
22 44 66
99 99 44
---
I want to add a column so that the above file becomes:
test1 test2 test3 notest
11 22 33 *
22 44 66 *
99 99 44 *
---
Thanks (6 Replies)
I am fairly new to programming and trying to resolve this problem. I have the file like this.
CHROM POS REF ALT 10_sample.bam 11_sample.bam 12_sample.bam 13_sample.bam 14_sample.bam 15_sample.bam 16_sample.bam
tg93 77 T C T T T T T
tg93 79 ... (4 Replies)
Hi all ,
I have a file having 12 columns tab delimited .
I need to read this file and remove the column 3 and column 4 and insert a word in column 3 as "AVIALABLE "
Is there a way to do this . I am trying like below
Thanks
DJ
cat $FILENAME|awk -F"\t" '{ print $1 "\t... (3 Replies)
Hello Everyone..
I want to replace the retail col from FileI with cstp1 col from FileP if the strpno matches in both files
FileP.txt
... (2 Replies)
Discussion started by: YogeshG
2 Replies
LEARN ABOUT DEBIAN
stag-flatten
STAG-FLATTEN(1p) User Contributed Perl Documentation STAG-FLATTEN(1p)NAME
stag-flatten - turns stag data into a flat table
SYNOPSIS
stag-flatten -c name -c person/name dept MyFile.xml
DESCRIPTION
reads in a file in a stag format, and 'flattens' it to a tab-delimited table format. given this data:
(company
(dept
(name "special-operations")
(person
(name "james-bond"))
(person
(name "fred"))))
the above command will return a two column table
special-operations james-bond
special-operations fred
If there are multiple values for the columns within the node, then the cartesian product will be calculated
USAGE
stag-flatten [-p PARSER] [-c COLS] [-c COLS] NODE <file>
ARGUMENTS
-p|parser FORMAT
FORMAT is one of xml, sxpr or itext
xml assumed as default
-c|column COL1,COL2,COL3,..
the name of the columns/elements to write out
this can be specified either with multiple -c arguments, or with a comma-seperated (no spaces) list of column (terminal node) names
after a single -c
-n|nest
if set, then the output will be a compress repeating values into the same row; each cell in the table will be enclosed by {}, and will
contain a comma-delimited set of values
SEE ALSO
Data::Stag
perl v5.10.0 2008-12-23 STAG-FLATTEN(1p)