A common bioinformatics problem, joining two tables :P I wonder why you posted your question to the "Web Development" section but it happens to be the only forum I subscribe to
Some comments about your code:
Code:
#!/usr/bin/perl -w
use strict;
#!/usr/bin/perl
use strict;
use warnings;
-w has been superseded by use warnings.
Code:
while (<F2>) {
s/\r?\n//; #remove return of carriage at the end of each line;
chomp;
The chomp() function removes return carriages and newlines.
The strategy I would use is to find some way to just capture the assembly information and using the assembly information to store the information on the line:
Code:
#note untested code
my @F=split /\t/, $_;
#use informative name for first column
my $id_seq = $f[0];
#remove anything after the first pipe
$id_seq =~ s/\|.*//;
#declare new variable for assembly information
my $assembly = '';
#store only assembly information
if ($id_seq =~ /.*(mira_.*)/){
$assembly = $1;
} else {
die "Unexpected notation on $. for $id_seq;
}
#store the line information into a hash using $assembly as the key
$line2{$assembly} = $_;
Then read file2 like you did before and get the required information from your %line2 hash.
Hi All,
I have working (Perl) code to combine 2 input files into a single output file using the join function that works to a point, but has the following limitations:
1. I am restrained to 2 input files only.
2. Only the "matched" fields are written out to the "matched" output file and... (1 Reply)
I have n files (for ex:64 files) with one similar column. Is it possible to combine them all based on that column ?
file1
ax100 20 30 40
ax200 22 33 44
file2
ax100 10 20 40
ax200 12 13 44
file2
ax100 0 0 4
ax200 2 3 4 (9 Replies)
Hi,
I have line in input file as below:
3G_CENTRAL;INDONESIA_(M)_TELKOMSEL;SPECIAL_WORLD_GRP_7_FA_2_TELKOMSEL
My expected output for line in the file must be :
"1-Radon1-cMOC_deg"|"LDIndex"|"3G_CENTRAL|INDONESIA_(M)_TELKOMSEL"|LAST|"SPECIAL_WORLD_GRP_7_FA_2_TELKOMSEL"
Can someone... (7 Replies)
Hi,
I'm dealing with an issue and losing a lot of hours figuring out how i would solve this.
I have an input file which looks like this:
('BLABLA +200-GRS','Serviço ','TarifaçãoServiço','wap.bla.us.0000000121',2985,0,55,' de conversão em escada','Dia','Domingos')
('BLABLA +200-GRR','Serviço... (6 Replies)
Hi,
I have 20 tab delimited text files that have a common column (column 1). The files are named GSM1.txt through GSM20.txt. Each file has 3 columns (2 other columns in addition to the first common column).
I want to write a script to join the files by the first common column so that in the... (5 Replies)
Hi all,
I'm trying to join two .txt file tab delimitated based on a common column.
File 1
transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct
comp1000201_c0_seq1 comp1000201_c0 337 183.51 0.00 0.00 0.00 0.00
comp1000297_c0_seq1 ... (1 Reply)
Dear Ladies & Gents,
I have a requirement to delete all the log files in /var/log/test directory that are older than 10 days and their first line begin with "MSH" or "<?xml" or "FHS". I've put together the following BASH script, but it's erroring out:
for filename in $(find /var/log/test... (2 Replies)
Hello,
This post is already here but want to do this with another way
Merge multiples files with multiples duplicates keys by filling "NULL" the void columns for anothers joinning files
file1.csv:
1|abc
1|def
2|ghi
2|jkl
3|mno
3|pqr
file2.csv:
1|123|jojo
1|NULL|bibi... (2 Replies)
Discussion started by: yjacknewton
2 Replies
LEARN ABOUT DEBIAN
monop
monop(1) General Commands Manual monop(1)NAME
monop, monop2 - Mono Class Outline Viewer
SYNOPSIS
monop [-r:assembly] [--search] class
OPTIONS
-r:assembly
Specifies the assembly to use for looking up the type
-a Renders all of the types in the specified assembly.
--search, -s, -k
Searches through all known assemblies for types containing `class'.
--refs Prints a list of the referenced assemblies for an assembly. Requires an assembly to be specified with -r:assembly.
--filter-obsolete, -f
Do not show obsolete types and members.
--declared-only, -d
Only show members declared in the type.
--private, -p
Show private members.
--runtime-version
Print runtime version.
DESCRIPTION
Monop is a tool that allows you to view the outline of a class. You can see the signature of each member of the class. Use monop to
explore 1.0 assemblies, use monop2 to explore 2.0 assemblies.
The tool takes one option, the class to view. You must specify the full name of the class, including namespace.
For generic classes, you must specify the generic arguments, for example:
monop2 'System.Collections.Generic.List`1'
The above is the string representation for the List<T> in System.Collections.Generic
If you are unsure of the full name of the class, you can use the `--search' option to search through all known assemblies.
MAILING LISTS
Visit http://lists.ximian.com/mailman/listinfo/mono-devel-list for details.
WEB SITE
Visit http://www.mono-project.com for details
monop(1)
02-05-2011
