I found the primary problem. I forgot to call one of my functions after introducing your functions to my code!
I don't know if you still willing to give me casual explanations about details in your functions. I'll ask, if you want, you reply, if you don't, no problem.
I'm actually reading/following one basic tutorial about bash script and actually running their examples. I'm also reading the links you posted.
My question is why you added the single quotes twice in the value part of the item of the list in your "make_json_object" funciton here:
I couldn't find an existing thread that addressed this question, so hopefully this isn't redundant with anything previously posted. Here goes:
I am writing a C-Shell script that runs a program that takes an arbitrary number of parameters:
myprog -a file1 \
-b file2 \
-c file3 ... \
-n... (2 Replies)
I need help in writing a BASH SCRIPT of ls command.
for example:
$ ./do_ls.sh files
f1.txt
f2.jpeg
f3.doc
$ ./do_ls.sh dirs
folder1
folder2
folder3
My attempt:
#!/bin/bash
#
if test $# -d file
then
echo $dirs
else (3 Replies)
Hello,
I would like to modify an existing script of mine that uses a manually defined "MCVERSION" variable and make it define that variable instead based on this JSON file stored online:
https://s3.amazonaws.com/Minecraft.Download/versions/versions.json
Within that JSON, I 'm looking for... (4 Replies)
All,
Have a weird issue where i need to generate a report from GitHub monthly detailing user accounts and the last time they logged in. I'm using a windows box to do this (work issued) and would like to know if anyone has any experience scripting for GitAPI using windows / cygwin / powershell?... (9 Replies)
I am trying to automate editing of a json file using bash script.
The file I initially receive is
{
"appMap": {
"URL1": {
"name": "a"
},
"URL2": {
"name": "b"
},
"URL3": {
"name": "c"
},
}
WHat I would like to do is replace... (5 Replies)
i have a json data that looks like this:
{
"ip": "16.66.35.10",
"hostname": "No Hostname",
"city": "Stepney",
"region": "England",
"country": "GB",
"loc": "51.57,-0.0333",
"org": "AS6871 British Telecommunications PLC",
"postal": "E1"
}
im looking for a way to assign... (9 Replies)
Hello guys,
I want to parse a JSON file in order to get the data in a table form.
My JSON file is like this:
{
"document":{
"page":
},
{
"column":
}
]
},
{
... (6 Replies)
One of the great thing about unix is the ability to pipe multiple programs together to manipulate data. Plain, unstructured text is the most common type of data that is passed between programs, but these days JSON is becoming more popular.
I thought it would be fun to pipe together some command... (1 Reply)
Hi All,
I am new to shell scripting, Need your help in creating a shell script which converts any unix command output to JSON format output.
example:
sample df -h command ouput :
Filesystem size used avail capacity Mounted
/dev/dsk/c1t0d0s0 8.1G 4.0G 4.0G 50% /... (13 Replies)
Discussion started by: balu1234
13 Replies
LEARN ABOUT DEBIAN
bio::index::fastq
Bio::Index::Fastq(3pm) User Contributed Perl Documentation Bio::Index::Fastq(3pm)NAME
Bio::Index::Fastq - Interface for indexing (multiple) fastq files
SYNOPSIS
# Complete code for making an index for several
# fastq files
use Bio::Index::Fastq;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fastq->new(
'-filename' => $Index_File_Name,
'-write_flag' => 1);
$inx->make_index(@ARGV);
# Print out several sequences present in the index
# in Fastq format
use Bio::Index::Fastq;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fastq->new('-filename' => $Index_File_Name);
my $out = Bio::SeqIO->new('-format' => 'Fastq','-fh' => *STDOUT);
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns Bio::Seq::Quality object
$out->write_seq($seq);
}
# or, alternatively
my $id;
my $seq = $inx->get_Seq_by_id($id); #identical to fetch
DESCRIPTION
Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing fastq files, and
retrieving the sequence from them. Note: for best results 'use strict'.
Bio::Index::Fastq supports the Bio::DB::BioSeqI interface, meaning it can be used as a Sequence database for other parts of bioperl
FEED_BACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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/
AUTHOR - Tony Cox
Email - avc@sanger.ac.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
_file_format
Title : _file_format
Function: The file format for this package, which is needed
by the SeqIO system when reading the sequence.
Returns : 'Fastq'
_index_file
Title : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index FASTQ format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
id_parser
Title : id_parser
Usage : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
parse the ID for record from a string. Useful
for (for instance) specifying a different
parser for different flavours of FASTQ file.
Returns &default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fastq
description line. An entry will be added to
the index for each string in the list returned.
Example : $index->id_parser( &my_id_parser )
Returns : ref to CODE if called without arguments
Args : CODE
default_id_parser
Title : default_id_parser
Usage : $id = default_id_parser( $header )
Function: The default Fastq ID parser for Fastq.pm
Returns $1 from applying the regexp /^>s*(S+)/
to $header.
Returns : ID string
Args : a fastq header line string
perl v5.14.2 2012-03-02 Bio::Index::Fastq(3pm)