Match Columns in one file and extract columns from another file
Kindly help merging information from two files with the following data structure.
I want to match for the CHR-SNP in Foo and get the columns that match from CHROM-rsID
Fields 1 & 2 of foo may have duplicates, however, a joint key of Fields $1$2$3$4 is unique.
Also would be helpful to clean up the file column delimiter to make sure spaces (more than one)are converted to single tab.
awk preferred.
Many thanks
~GH
File foo:
File bar:
required file foobar
Hi,
In ksh, I have a file with similar rows as follows:
Department = 1234 G/L Asset Acct No = 12.0000. 2/29/2008
Department = 1234 G/L Asset Acct No = 13.0000. 3/29/2008.
I want to create a new text file that contains only the numbers and date:
1234 12.0000. 2/29/2008
1234 13.0000. ... (16 Replies)
I have huge fixed width, text file in unix box and I need to extract columns found between the width 105 and 200 and output it to a new file.
Can anyone tell me how to extract it?
Thanks for your help. (1 Reply)
hi experts
lets say my format file is B
B
=========
column no,name,type,length
1,ee,N,12
3,hj,N.4
4,kl,N,5
source file
========
d e f g h i
5 8 9 7 6 5
1 3 4 5 6 6 (2 Replies)
Hi All,
Could you please help me with following:
I have to parse a .csv file.
For example: If the csv file contains 3 columns, then i have to print the column names. The field separator is (comma).
example.csv (contains 2 lines as follows)
This is,a test file, for validation... (2 Replies)
Hi All,
I have to match each row in file 1 with 1st row in file 2 and print the corresponding column from file2. I am trying to use an awk script to do this. For example
cat File1
X1
X3
X4
cat File2
ID X1 X2 X3 X4
A 1 6 2 1
B 2 7 3 3
C 3 8 4 1
D 4 9 1 1 (3 Replies)
Hi all, I know this sounds suspiciously like a homework course; but, it is not.
My goal is to take a file, and match my "ID" column to the "Date" column, if those conditions are true, add the total number of minutes worked and place it in this file, while not printing the original rows that I... (6 Replies)
Hello All,
I have a requirement in which i will be given a sql query as input in a file with dynamic number of columns. For example some times i will get 5 columns, some times 8 columns etc up to 20 columns.
So my requirement is to generate a output query which will have 20 columns all the... (7 Replies)
Hi, I have been looking everywhere for an example so I can try and do this myself but I am having difficulty. I have 2 large files of different sizes and if the pattern in the 3rd column in file 1 is in "any" column in file 2 I want to print all of the line in file 1 and append that line with the... (5 Replies)
I have a comma delimited file as per the one below and I am currently extracting the values in 2 columns (COL1 & COL6) to produce a smaller trimmed down version of the file which only contains the columns we need;
COL1,COL2,COL3,COL4,COL5,COL6,COL7,COL8,COL9... (1 Reply)
Discussion started by: Ads89
1 Replies
LEARN ABOUT DEBIAN
bio::alignio::po
Bio::AlignIO::po(3pm) User Contributed Perl Documentation Bio::AlignIO::po(3pm)NAME
Bio::AlignIO::po - po MSA Sequence input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.
DESCRIPTION
This object can transform Bio::SimpleAlign objects to and from 'po' format flat file databases. 'po' format is the native format of the POA
alignment program (Lee C, Grasso C, Sharlow MF, 'Multiple sequence alignment using partial order graphs', Bioinformatics(2002),
18(3):452-64).
FEEDBACK
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHORS - Matthew Betts
Email: matthew.betts@ii.uib.no
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
Returns : L<Bio::Align::AlignI> object - returns undef on end of file
or on error
Args : NONE
write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in po format
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
perl v5.14.2 2012-03-02 Bio::AlignIO::po(3pm)