maasha

#!/usr/bin/perl -w

use strict;

# Filenames
my $start10 = 'start10.dat';
my $res10 = 'res10.dat';

# Opening the files
open (START, '<', $start10) or die "Could not read file\n";

maasha

my %names = ();
while (defined (my $line = <START>)) {
   chomp $line;
   $names{$line};
}

maasha

#!/usr/bin/perl -w

use strict;

# Lea Benedicte Skov Hansen, Mar 2013
# This program reads a table, sums the rows and create a histogram of the sums

my $input = 'test_count.txt';                      #'count.matrix.ratio_new';
my $output = 'row_sum_his.txt';
my $interval = 5;

maasha

#!/usr/bin/env perl

use warnings;
use strict;

use Data::Dumper;

# Lea Benedicte Skov Hansen, Mar 2013
# This program reads a table, sums the rows and create a histogram of the sums

maasha

maasha@maxwell:~/data/qiime_tutorial-v1.5.0$ print_qiime_config.py -t

System information
==================
         Platform:      linux2
   Python version:      2.7.3 (default, Jan 28 2013, 09:50:08)  [GCC 4.4.5]
Python executable:      /disk/orsted/install/maasha/QIIME1.6/bin/python

Dependency versions
===================

maasha

maasha@maxwell:~/data$ unzip qiime_tutorial-v1.5.0.zip 
Archive:  qiime_tutorial-v1.5.0.zip
   creating: qiime_tutorial-v1.5.0/
   creating: qiime_tutorial-v1.5.0/18S_tutorial_files/
  inflating: qiime_tutorial-v1.5.0/18S_tutorial_files/18S_tutorial_sample_seqs.fna  
  inflating: qiime_tutorial-v1.5.0/Fasting_Example.fna  
  inflating: qiime_tutorial-v1.5.0/Fasting_Example.qual  
  inflating: qiime_tutorial-v1.5.0/Fasting_Example.sff  
  inflating: qiime_tutorial-v1.5.0/Fasting_Example.sff.txt  
  inflating: qiime_tutorial-v1.5.0/Fasting_Map.txt  

maasha

maasha@maxwell:~/data/qiime_tutorial-v1.5.0$ pick_otus_through_otu_table.py -i TEST/split_library_output/seqs.fna -o TEST/otus
Traceback (most recent call last):
  File "/home/maasha/install/QIIME1.6/bin/pick_otus_through_otu_table.py", line 131, in <module>
    main()    
  File "/home/maasha/install/QIIME1.6/bin/pick_otus_through_otu_table.py", line 128, in main
    status_update_callback=status_update_callback)
  File "/home/maasha/install/QIIME1.6/lib/python2.7/site-packages/qiime/workflow.py", line 471, in run_pick_otus_through_otu_table
    close_logger_on_success=close_logger_on_success)
  File "/home/maasha/install/QIIME1.6/lib/python2.7/site-packages/qiime/workflow.py", line 135, in call_commands_serially
    raise WorkflowError, msg

maasha

# Function to run a command and handle errors.
function run()
{
    local cmd=$@

    log "INIT" $cmd

    if error=$($cmd); then
        log "OK" $cmd
        echo_green "OK"

maasha

#!/usr/bin/env ruby -w

require 'pp'

File.open("tyt", "r") do |ios|
  ios.each_line do |line|
    line.chomp!
    
    fields = line.split("\t")
    

maasha

#!/bin/bash

function run()
{
    cmd=$1

    if error=$($cmd); then
        echo "OK"
    else
        echo "FAIL"