Peter Briggs pjbriggs

## make_nibs.sh
#!/bin/sh
#
# make_nibs.sh
#
chroms=`ls chr*.fa`
for chrom in $chroms; do
  echo $chrom
  nib=${chrom%.*}.nib
  qsub -cwd -V -b y faToNib $chrom $nib
done

## report_barcodes.py
#!/bin/env python
#
# Count and report the barcode tags in a fastq file from Illumina
# sequencing platform
#
import sys
import FASTQFile
fastq_file = sys.argv[1]
tags = {}
for read in FASTQFile.FastqIterator(fastq_file):

## usage.sh
#!/bin/sh
#
# Report disk usage
#
# Usage: usage.sh DIR
#
if [ $# -eq 0 ] ; then
  echo "Usage: $0 DIR"
  exit
fi

## make_bw_files.sh
#!/bin/sh
#
CHROMSIZE_FILE=$1
if [ -z "$CHROMSIZE_FILE" ] ; then
    echo "Usage: $0 CHROMSIZE_FILE [ DATA_DIR ]"
    exit
fi
if [ -z "$2" ] ; then
    DATA_DIR=`pwd`
else

## clean_rtf_to_fasta.sh
#!/bin/sh
#
if [ -z "$1" ] || [ -z "$2" ] ; then
  echo "Usage: $0 IN.rtf OUT.fasta"
  exit 1
fi
if [ ! -e "$1" ] ; then
  echo "Input file $1 not found"
  exit 1
fi

## sorting.py
# Compare effects of using different sort keys

import os
import locale
import re

class SortKeys:
    natural_sort_digits = re.compile(r'(\d+)')
    @classmethod
    def default(self,filename):

## load_urls.py
#!/bin/env python
#
# Open multiple arbitrary URLs in a webbrowser
import optparse
import webbrowser
import time
import sys
if __name__ == '__main__':
    p = optparse.OptionParser(usage="%prog [-f FILE] [-b BROWSER] [-p INTERVAL] "
                              "[URL [URL,...]]",

## proftpd.conf-extract
ServerName			"Galaxy FTP File Upload"
ServerType			standalone
DefaultServer			on
PidFile                         /var/run/proftpd/proftpd-galaxy.pid

# Port 21 is the standard FTP port.
Port				21

# Don't use IPv6 support by default.
UseIPv6				off

## check_gtf_exon_coverage.py
#!/bin/env python
#
# Check exon coverage in a GTF file
# Peter Briggs UoM, March 2015
#
# Purpose
# -------
# Given a GTF file, check that for each exon entry the
# associated features 'CDS', 'stop_codon' and 'start_codon'
# are consistent and specify the same range of bases as

## Galactic-Engineer-GALAXY_SLOTS-job_conf-fragment.xml
    <destinations default="dynamic">
        ...
        <!-- DRMAA runner for job using 4 cores -->
        <destination id="sge_smp_4" runner="drmaa">
           <param id="nativeSpecification">-R y -V -j n -pe smp.pe 4</param>
        </destination>
        ...
	#!/bin/sh
	#
	# make_nibs.sh
	#
	chroms=`ls chr*.fa`
	for chrom in $chroms; do
	echo $chrom
	nib=${chrom%.*}.nib
	qsub -cwd -V -b y faToNib $chrom $nib
	done
	#!/bin/env python
	#
	# Count and report the barcode tags in a fastq file from Illumina
	# sequencing platform
	#
	import sys
	import FASTQFile
	fastq_file = sys.argv[1]
	tags = {}
	for read in FASTQFile.FastqIterator(fastq_file):
	#!/bin/sh
	#
	# Report disk usage
	#
	# Usage: usage.sh DIR
	#
	if [ $# -eq 0 ] ; then
	echo "Usage: $0 DIR"
	exit
	fi
	#!/bin/sh
	#
	CHROMSIZE_FILE=$1
	if [ -z "$CHROMSIZE_FILE" ] ; then
	echo "Usage: $0 CHROMSIZE_FILE [ DATA_DIR ]"
	exit
	fi
	if [ -z "$2" ] ; then
	DATA_DIR=`pwd`
	else
	#!/bin/sh
	#
	if [ -z "$1" ] \|\| [ -z "$2" ] ; then
	echo "Usage: $0 IN.rtf OUT.fasta"
	exit 1
	fi
	if [ ! -e "$1" ] ; then
	echo "Input file $1 not found"
	exit 1
	fi
	# Compare effects of using different sort keys

	import os
	import locale
	import re

	class SortKeys:
	natural_sort_digits = re.compile(r'(\d+)')
	@classmethod
	def default(self,filename):
	#!/bin/env python
	#
	# Open multiple arbitrary URLs in a webbrowser
	import optparse
	import webbrowser
	import time
	import sys
	if __name__ == '__main__':
	p = optparse.OptionParser(usage="%prog [-f FILE] [-b BROWSER] [-p INTERVAL] "
	"[URL [URL,...]]",
	ServerName "Galaxy FTP File Upload"
	ServerType standalone
	DefaultServer on
	PidFile /var/run/proftpd/proftpd-galaxy.pid

	# Port 21 is the standard FTP port.
	Port 21

	# Don't use IPv6 support by default.
	UseIPv6 off
	#!/bin/env python
	#
	# Check exon coverage in a GTF file
	# Peter Briggs UoM, March 2015
	#
	# Purpose
	# -------
	# Given a GTF file, check that for each exon entry the
	# associated features 'CDS', 'stop_codon' and 'start_codon'
	# are consistent and specify the same range of bases as
	<destinations default="dynamic">
	...
	<!-- DRMAA runner for job using 4 cores -->
	<destination id="sge_smp_4" runner="drmaa">
	<param id="nativeSpecification">-R y -V -j n -pe smp.pe 4</param>
	</destination>
	...