I have got errors like .command.sh: line 2: syntax error near unexpected token `('
/*
* Step 3
*/
chr_length = file(params.chr_length)
process create_bedgraph_and_bigwig {
publishDir "${params.outdir}/bedgraphandbigwig", mode: 'copy'
input:
set val(sample_id), file(vector_log) from vector_log_ch
set val(sample_id), file(target_query_bam) from target_query_bam_ch
file chr_length
output:
set val(sample_id), file("${sample_id}.bedgraph.log.txt") into bed_log_ch
set val(sample_id), file("${sample_id}.bed") into bed_ch
set val(sample_id), file("${sample_id}.clean.bed") into clean_bed_ch
set val(sample_id), file("${sample_id}.fragments.bed") into fragments_bed_ch
set val(sample_id), file("${sample_id}.sorted.fragments.bed") into sorted_fragments_bed_ch
shell:
'''
def fp = file(${vector_log})
def lines = fp.readLines()
def line3 = lines[3].split(' ')[4].toInteger()
def line4 = lines[4].split(' ')[4].toInteger()
def aln_sum = (10000/(line3 + line4)).toString()
bedtools bamtobed -bedpe -i !{target_query_bam} > !{sample_id}.bed 2>!{sample_id}.bedgraph.log.txt
awk '$1==$4 && $6-$2 < 1000 {{print $0}}' !{sample_id}.bed > !{sample_id}.clean.bed 2>!{sample_id}.bedgraph.log.txt
cut -f 1,2,6 !{sample_id}.clean.bed > !{sample_id}.fragments.bed 2>!{sample_id}.bedgraph.log.txt
sort -k 1,1 !{sample_id}.fragments.bed > !{sample_id}.sorted.fragments.bed
'''
}
The simple answer is to avoid using 'def' if the variable needs to be used in a shell definition or template. I couldn't actually find this after a quick search of the documentation, but I did find this note from the author:
Using groovy native string interpolation that would work, but when using the !{..} syntax scripts variable cannot be declared locally using the def keyword.
To summarise:
script/shell variable should be defensively declared in the local scope using the def keyboard
do not use def when:
i. the variable needs to be referenced as a output value
ii. the variable needs to be used in a shell template
https://github.com/nextflow-io/nextflow/issues/678#issuecomment-386206123
I have a two line json path expression that prints something and I want to put it all in one line:
Given path 'device/'
When method get
Then status 200
#This correctly prints the value:
And def device_search = $.device[?(#.manufacturer == 'a manufacturer')]
And print device_search[0].id
#This doesn't work (prints null):
And print $.device[?(#.manufacturer == 'a manufacturer')][0].id
Thanks!
This is not supported. Use 2 steps.
But if you insist, use karate.get().
And print karate.get("$.device[?(#.manufacturer == 'a manufacturer')][0].id")
I need to read values (text) from a configuration file named .env and assign them to variables so I can use them later in my program.
The .env file contains name/value pairs and looks something like this:
ENVIRONMENT_VARIABLE_ONE = AC9157847d72b1aa5370fdef36786863d9
ENVIRONMENT_VARIABLE_TWO = 73cad721b8cad6718d469acc42ffdb1f
ENVIRONMENT_VARIABLE_THREE = +13335557777
What I have tried so far
read-values.red
Red [
]
contents: read/lines %.env
env-one: first contents
env-two: second contents
env-three: third contents
print env-one ; ENVIRONMENT_VARIABLE_ONE = AC9157847d72b1aa5370fdef36786863d9
print env-two ; ENVIRONMENT_VARIABLE_ONE = 73cad721b8cad6718d469acc42ffdb1f
print env-three ; ENVIRONMENT_VARIABLE_ONE = +13335557777
What I'm looking for
print env-one ; AC9157847d72b1aa5370fdef36786863d9
print env-two ; 73cad721b8cad6718d469acc42ffdb1f
print env-three ; +13335557777
How do I continue or change my code and parse these strings such as the env- variables will contain just the values?
env-one: skip find first contents " = " 3
See help for find and skip
Another solution using parse could be:
foreach [word value] parse read %.env [collect some [keep to "=" skip keep to newline skip]] [set load word trim value]
This one will add the words to the global context ENVIRONMENT_VARIABLE_ONE will be AC9157847d72b1aa5370fdef36786863d9 and so on.
This request might seem slightly ridiculous, unfortunately however, it is direly needed by my small company and because of this I will be awarding the maximum bounty for a good solution.
We have a set of legacy order information stored in a .txt file. In order to import this order information into our new custom database system, we need to, for each row, append on a value from another set.
So, in my .txt file I have :
Trans Date,NorthTotal,NorthSoFar,SouthTotal,SouthSoFar,IsNorthWorkingDay,IsSouthWorkingDay
2012-01-01,21,0,21,0,0,0
2012-01-02,21,0,21,0,0,0
2012-01-03,21,1,21,1,1,1
...
Now, I have a set of locations in a .txt file also, for which I need to add two columns - city and country. Let's say :
City, Country
London,England
Paris,France
For each row in my first text file, I need to append on a row of my second text file! So, for my end result, using my sample data above, I wish to have :
Trans Date,NorthTotal,NorthSoFar,SouthTotal,SouthSoFar,IsNorthWorkingDay,IsSouthWorkingDay,City,Country
2012-01-01,21,0,21,0,0,0,London,England
2012-01-02,21,0,21,0,0,0,London,England
2012-01-03,21,1,21,1,1,1,London,England
2012-01-01,21,0,21,0,0,0,Paris,France
2012-01-02,21,0,21,0,0,0,Paris,France
2012-01-03,21,1,21,1,1,1,Paris,France
...
At the moment my only idea for this is to import both files into an SQL database and write a complicated function to append the two together (hence my tag) - surely someone can save me and think of something that will not take all day though! Please?! Thank you very much.
Edit : I am open to solutions written in all programming languages; but would prefer something which uses DOS or some kind of console/program that can be easily reran!
If you are open to using a database and importing these files (which should not be very difficult), then you do not need a "complicated function to append the two together". All you need is a simple cross join like this ... select t1.*, t2.* from t1, t2
See for yourself at... http://sqlfiddle.com/#!2/0c584/1
Here is a solution in C#. You run it like:
joinfiles a.txt b.txt c.txt
where a.txt is the first file, b.txt the second one, and c.txt the output file that will be created. It generates the output at 100 MB/s on my machine so that is probably fast enough.
using System;
using System.IO;
using System.Text;
namespace JoinFiles
{
class Program
{
static void Main(string[] args)
{
if (args.Length != 3)
return;
string[] file1, file2;
try
{
using (var sr1 = new StreamReader(args[0]))
using (var sr2 = new StreamReader(args[1]))
{
file1 = sr1.ReadToEnd().Split(new string[] { Environment.NewLine }, StringSplitOptions.RemoveEmptyEntries);
file2 = sr2.ReadToEnd().Split(new string[] { Environment.NewLine }, StringSplitOptions.RemoveEmptyEntries);
}
using (var outstream = new StreamWriter(args[2], false, Encoding.Default, 1048576))
{
outstream.WriteLine(file1[0] + "," + file2[0]);
for (int i = 1; i < file2.Length; i++)
for (int j = 1; j < file1.Length; j++)
outstream.WriteLine(file1[j] + "," + file2[i]);
}
}
catch (Exception ex)
{
Console.WriteLine(ex.Message);
}
}
}
}
bash script example
echo -e 'c1\na\nb' > t1
echo -e 'c2\n1\n2' > t2
while read l1;do
read -u 3 l2
echo "$l1,$l2"
done <t1 3<t2
see man bash / internal function / read
You could also write a WSH script to do this and execute from the command line. Here is a quick hack (works but will certainly need some refining). You'll need to save this as a vbs file and execute on the cli like this... wscript script.vbs infile1.txt infile2.txt outfile.txt where script.vbs is your script and infile 1 and 2 are input filenames and outfile.txt is the output file.
Set FSO_In1 = CreateObject("Scripting.FileSystemObject")
Set FSO_In2 = CreateObject("Scripting.FileSystemObject")
Set FSO_Out = CreateObject("Scripting.FileSystemObject")
Set File_Out = FSO_In1.CreateTextFile(Wscript.Arguments.Item(2),2)
Set F1_file = FSO_In1.OpenTextFile(Wscript.Arguments.Item(0),1)
HeaderWritten = False
Header = F1_File.Readline 'Read the first header line from first file
Do While F1_File.AtEndOfStream = False
F1_Line = F1_file.Readline
Set F2_File = FSO_In2.OpenTextFile(Wscript.Arguments.Item(1),1)
if HeaderWritten = False then
Header = Header & "," & F2_File.Readline
File_Out.Writeline(Header)
HeaderWritten = True
else
F2_File.Readline 'Read the first header line from second file and ignore it
end if
Do While F2_File.AtEndOfStream = False
F2_Line = F2_File.Readline
out = F1_Line & "," & F2_Line
File_Out.Writeline(out)
Loop
F2_File.Close
Loop
F1_File.Close
File_Out.Close
I'm trying to make a simple lua program that converts Fahrenheit to Celsius and kelvin and I don't know how to put an input command on the same line as a print line. Here's what I mean.
I want the program to display:
Fahrenheit = "Here's the user input"
I know how to make it say
Fahrenheit =
"User input"
I'm still a novice.
This is my code so far:
print("Fahrenheit = ") f = io.read() c = (5/9)*(f-32)
print("Celsius = "..c) k = c + 273 print("Kelvin = "..k)
Look into io.write() and io.read(). For instance, you could say:
io.write("Fahrenheit = ")
The write command writes output to the screen buffer, but doesn't add a newline. Similarly, read checks the latest input, and returns it.
For reference, I suggest this link from the tutorial.