In the bash below, if the answer is "y" then goto function remove. If the answer is "n" then goto the id variable line (where the date is inputted). However, I am getting command remove not found, but remove is a function not an command. I must have the syntax incorrect? Thank you .
Code:
#!/bin/bash
# README(v1) 12_16_2015
echo " Welcome to NGS module (v1) for medical exome analysis, the following steps will be performed
==================================
1 remove @PG tag
2 run picard markduplicates
3 run picard HSmeterics
4 run bedTools coverageBed
5 detect bases less than 30 reads
6 combine files
=================================="
printf "\n\n"
printf "What is the date to analyze : "; read id
date=$(date -d "$id" "+%m-%d-%Y") #convert to month-date-year
[ -z "$id" ] && printf "\n No date supplied. Leaving match function." && sleep 2 && printf "\n Goodbye! " && exit
for f in /home/cmccabe/Desktop/NGS/bam/$date/*.bam ; do
bname=${f##*/}
pref=${bname%%.bam}
echo "detected ${pref}.bam in the directory"
done
printf "Are all the files there? "; read match_choice
case "$match_choice" in
[yY]) remove ;;
[nN]) printf "Not all the files are there, please find the missing files(s) and try again " && sleep 2 && printf "\n Goodbye! " && exit
esac
remove() {
for f in /home/cmccabe/Desktop/NGS/bam/$date/*.bam ; do
bname=`basename $f`
pref=${bname%%.bam}
samtools view -H $f | sed '/^@PG/d' | samtools reheader - $f > home/cmccabe/Desktop/NGS/bam/$date/${pref}_newheader.bam
done
}
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Discussion started by: cmccabe
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LEARN ABOUT PHP
datetime.setisodate
DATETIME.SETISODATE(3) 1 DATETIME.SETISODATE(3)DateTime::setISODate - Sets the ISO date
Object oriented style
SYNOPSIS
public DateTime DateTime::setISODate (int $year, int $week, [int $day = 1])
DESCRIPTION
Procedural style
DateTime date_isodate_set (DateTime $object, int $year, int $week, [int $day = 1])
Set a date according to the ISO 8601 standard - using weeks and day offsets rather than specific dates.
PARAMETERS
o $object
-Procedural style only: A DateTime object returned by date_create(3). The function modifies this object.
o $year
- Year of the date.
o $week
- Week of the date.
o $day
- Offset from the first day of the week.
RETURN VALUES
Returns the DateTime object for method chaining or FALSE on failure.
CHANGELOG
+--------+---------------------------------------------------+
|Version | |
| | |
| | Description |
| | |
+--------+---------------------------------------------------+
| 5.3.0 | |
| | |
| | Changed the return value on success from NULL to |
| | DateTime. |
| | |
+--------+---------------------------------------------------+
EXAMPLES
Example #1
DateTime.setISODate(3) example
Object oriented style
<?php
$date = new DateTime();
$date->setISODate(2008, 2);
echo $date->format('Y-m-d') . "
";
$date->setISODate(2008, 2, 7);
echo $date->format('Y-m-d') . "
";
?>
Procedural style
<?php
$date = date_create();
date_isodate_set($date, 2008, 2);
echo date_format($date, 'Y-m-d') . "
";
date_isodate_set($date, 2008, 2, 7);
echo date_format($date, 'Y-m-d') . "
";
?>
The above examples will output:
2008-01-07
2008-01-13
Example #2
Values exceeding ranges are added to their parent values
<?php
$date = new DateTime();
$date->setISODate(2008, 2, 7);
echo $date->format('Y-m-d') . "
";
$date->setISODate(2008, 2, 8);
echo $date->format('Y-m-d') . "
";
$date->setISODate(2008, 53, 7);
echo $date->format('Y-m-d') . "
";
?>
The above example will output:
2008-01-13
2008-01-14
2009-01-04
Example #3
Finding the month a week is in
<?php
$date = new DateTime();
$date->setISODate(2008, 14);
echo $date->format('n');
?>
The above examples will output:
3
SEE ALSO DateTime.setDate(3), DateTime.setTime(3).
PHP Documentation Group DATETIME.SETISODATE(3)
12-17-2015
.