import sys
import os
from os.path import *
import subprocess
import argparse
import bqd, graph_qualdepth as qd
import samtools
from bam_to_qualdepth import set_unmapped_mapped_reads
import json
import log
logc = log.get_config( 'graphsample.log' )
logger = log.setup_logger( 'graphsample', logc )
def main():
args = parse_args()
args = handle_args( args )
if not args.qualdepth:
jfile = make_json( args.bamfile, args.outpath )
else:
jfile = args.qualdepth
pngfile = make_image( jfile, args.outpath )
def make_json( bamfile, outpathprefix ):
pileup = samtools.nogap_mpileup(bamfile)
stats = bqd.parse_pileup( pileup )
set_unmapped_mapped_reads( bamfile, stats )
outfile = outpathprefix + '.qualdepth.json'
with open( outfile, 'w' ) as fh:
json.dump( stats, fh )
from glob import glob
from os.path import *
import os
import sys
import re
import log
from Bio import SeqIO
import gzip
logger = log.setup_logger(__name__, log.get_config())
ROCHE_FILE = '\S+?(?:__[0-9]){0,1}__(?:TI|RL)\d+__\d{4}_\d{2}_\d{2}__\w+.(sff|fastq)'
'''
Matches roche sff or fastq files
sample__region__barcode__year_month_day__type.filetype
'''
ROCHE_ID = '[A-Z0-9]{14}'
'''
Matches Roche accessions which are just 14 Alpha Numeric uppercase characters
@AAAAAAAAAAAAAA
'''
IONTORRENT_FILE = '\S+?__[0-9]__IX\d{3}__\d{4}_\d{2}_\d{2}__\w+.(sff|fastq)'
'''
Matches IonTorrent file names(essentially same as roche)
sample__region__barcode__year__month__day__type.filetype
'''
IONTORRENT_ID = '[A-Z]{5}:[0-9]+:[0-9]+'
'''
#!/usr/bin/env python
from subprocess import Popen, PIPE
import sys
import json
from collections import namedtuple
from itertools import izip
from matplotlib.lines import Line2D
import log
import samtools
logger = log.setup_logger(__name__, log.get_config())
# Alias our region strings
G = 'Gap'
N = 'Normal'
LC = 'LowCoverage'
LQ = 'LowQuality'
LCQ = 'LowCovQual'
# As a list
REGIONTYPES = [
G, N, LC, LQ, LCQ
]
def parse_pileup( pileup ):
'''
Parses the raw pileup output from samtools mpileup and returns a dictionary
with stats for every reference in the pileup
import argparse
import sys
import samtools
import re
import shutil
import os.path
from ngs_mapper.bam import sortbam, indexbam
import log
logger = log.setup_logger('tagreads', log.get_config())
# Exception for when headers exist
class HeaderExists(Exception):
pass
# The next 3 tuples have to be the same length and each index in each is related the same index in each tuple
# AKA zip( IDS, PLATFORMS, ID_MAP ) should work as expected
# Read group ID list
IDS = ('Roche454', 'IonTorrent', 'MiSeq', 'Sanger')
# Valid platforms for read groups
PLATFORMS = ('L454', 'IONTORRENT', 'ILLUMINA', 'CAPILLARY')
# Read name map to ID name
ID_MAP = (re.compile('[0-9A-Z]{14}'), re.compile('[A-Z0-9]{5}:\d{1,}:\d{1,}'),
re.compile('M[0-9]{5}:\d+:[\w\d-]+:\d:\d{4}:\d{4,5}:\d{4,5}'),
re.compile('.*'))
# Read Group Template
RG_TEMPLATE = {'SM': None, 'ID': None, 'PL': None, 'CN': None}
def main():
args, qsubargs = parse_args()
# Qsub job?
if qsubargs:
runsampleargs, _ = split_args(' '.join(sys.argv[1:]))
print pbs_job(runsampleargs, qsubargs)
sys.exit(1)
# So we can set the global logger
global logger
# Setup analysis directory
if os.path.isdir(args.outdir):
if os.listdir(args.outdir):
raise AlreadyExists("{0} already exists and is not empty".format(
args.outdir))
else:
os.makedirs(args.outdir)
# tempdir root will be TMPDIR environ variable if it exists
# unless outdir is set
# allows user to specify TMPDIR somewhere else if they want such as
# /dev/shm
tmpdir = args.outdir
# Directory analysis is run in will be inside of tmpdir
tdir = tempfile.mkdtemp('runsample', args.prefix, dir=tmpdir)
os.environ['TMPDIR'] = tdir
bamfile = os.path.join(tdir, args.prefix + '.bam')
flagstats = os.path.join(tdir, 'flagstats.txt')
consensus = bamfile + '.consensus.fasta'
vcf = bamfile + '.vcf'
bwalog = os.path.join(tdir, 'bwa.log')
stdlog = os.path.join(tdir, args.prefix + '.std.log')
logfile = os.path.join(tdir, args.prefix + '.log')
CN = args.CN
# Set the global logger
config = log.get_config(logfile)
logger = log.setup_logger('runsample', config)
#make_project_repo( tdir )
logger.info("--- Starting {0} --- ".format(args.prefix))
if args.config:
logger.info("--- Using custom config from {0} ---".format(args.config))
# Write all stdout/stderr to a logfile from the various commands
with open(stdlog, 'wb') as lfile:
cmd_args = {
'samplename':
args.prefix,
'tdir':
tdir,
'readsdir':
args.readsdir,
'reference':
os.path.join(tdir, os.path.basename(args.reference)),
'bamfile':
bamfile,
'flagstats':
flagstats,
'consensus':
consensus,
'vcf':
vcf,
'CN':
CN,
'trim_qual':
args.trim_qual,
'trim_outdir':
os.path.join(tdir, 'trimmed_reads'),
'filtered_dir':
os.path.join(tdir, 'filtered'),
'head_crop':
args.head_crop,
'minth':
args.minth,
'config':
args.config,
'platforms':
args.platforms,
'drop_ns':
args.drop_ns,
'index_min':
args.index_min,
'primer_info': (args.primer_file, args.primer_seed,
args.palindrom_clip, args.simple_clip)
}
# Best not to run across multiple cpu/core/threads on any of the pipeline steps
# as multiple samples may be running concurrently already
logger.debug("Copying reference file {0} to {1}".format(
args.reference, cmd_args['reference']))
shutil.copy(args.reference, cmd_args['reference'])
# Return code list
rets = []
logger.debug(cmd_args)
#Filter
def select_keys(d, keys):
return dict(((k, v) for k, v in d.items() if k in keys))
#convert sffs to fastq
print sh.convert_formats(cmd_args['readsdir'],
_out=sys.stdout,
_err=sys.stderr)
#print sh.sff_to_fastq(cmd_args['readsdir'], _out=sys.stdout, _err=sys.stderr)
try:
if cmd_args['config']:
__result = sh.ngs_filter(cmd_args['readsdir'],
config=cmd_args['config'],
outdir=cmd_args['filtered_dir'])
else:
filter_args = select_keys(
cmd_args, ["drop_ns", "platforms", "index_min"])
__result = sh.ngs_filter(cmd_args['readsdir'],
outdir=cmd_args['filtered_dir'],
**filter_args)
logger.debug('ngs_filter: %s' % __result)
except sh.ErrorReturnCode, e:
logger.error(e.stderr)
sys.exit(1)
#Trim reads
cmd = 'trim_reads {filtered_dir} -q {trim_qual} -o {trim_outdir} --head-crop {head_crop}'
if cmd_args['config']:
cmd += ' -c {config}'
primer_info = cmd_args['primer_info']
if primer_info[0]:
cmd += " --primer-file %s --primer-seed %s --palindrome-clip %s --simple-clip %s " % primer_info
p = run_cmd(cmd.format(**cmd_args),
stdout=lfile,
stderr=subprocess.STDOUT)
rets.append(p.wait())
if rets[-1] != 0:
logger.critical("{0} did not exit sucessfully".format(
cmd.format(**cmd_args)))
# Filter on index quality and Ns
# Mapping
with open(bwalog, 'wb') as blog:
cmd = 'run_bwa_on_samplename {trim_outdir} {reference} -o {bamfile}'
if cmd_args['config']:
cmd += ' -c {config}'
p = run_cmd(cmd.format(**cmd_args),
stdout=blog,
stderr=subprocess.STDOUT)
# Wait for the sample to map
rets.append(p.wait())
# Everything else is dependant on bwa finishing so might as well die here
if rets[-1] != 0:
cmd = cmd.format(**cmd_args)
logger.critical(
"{0} failed to complete sucessfully. Please check the log file {1} for more details"
.format(cmd, bwalog))
sys.exit(1)
# Tag Reads
cmd = 'tagreads {bamfile} -CN {CN}'
if cmd_args['config']:
cmd += ' -c {config}'
p = run_cmd(cmd.format(**cmd_args),
stdout=lfile,
stderr=subprocess.STDOUT)
r = p.wait()
if r != 0:
logger.critical("{0} did not exit sucessfully".format(
cmd.format(**cmd_args)))
rets.append(r)
# Variant Calling
cmd = 'base_caller {bamfile} {reference} {vcf} -minth {minth}'
if cmd_args['config']:
cmd += ' -c {config}'
p = run_cmd(cmd.format(**cmd_args),
stdout=lfile,
stderr=subprocess.STDOUT)
r = p.wait()
if r != 0:
logger.critical("{0} did not exit sucessfully".format(
cmd.format(**cmd_args)))
rets.append(r)
if rets[-1] != 0:
cmd = cmd.format(**cmd_args)
logger.critical('{0} failed to complete successfully'.format(
cmd.format(**cmd_args)))
# Flagstats
with open(flagstats, 'wb') as flagstats:
cmd = 'samtools flagstat {bamfile}'
p = run_cmd(cmd.format(**cmd_args),
stdout=flagstats,
stderr=lfile,
script_dir='')
r = p.wait()
if r != 0:
logger.critical("{0} did not exit sucessfully".format(
cmd.format(**cmd_args)))
rets.append(r)
# Graphics
cmd = 'graphsample {bamfile} -od {tdir}'
p = run_cmd(cmd.format(**cmd_args),
stdout=lfile,
stderr=subprocess.STDOUT)
r = p.wait()
if r != 0:
logger.critical("{0} did not exit sucessfully".format(
cmd.format(**cmd_args)))
rets.append(r)
# Read Graphics
fastqs = ' '.join(
glob.glob(os.path.join(cmd_args['trim_outdir'], '*.fastq')))
cmd = 'fqstats -o {0}.reads.png {1}'.format(
cmd_args['bamfile'].replace('.bam', ''), fastqs)
p = run_cmd(cmd, stdout=lfile, stderr=subprocess.STDOUT)
r = p.wait()
if r != 0:
logger.critical("{0} did not exit sucessfully".format(cmd))
rets.append(r)
# Consensus
cmd = 'vcf_consensus {vcf} -i {samplename} -o {consensus}'
p = run_cmd(cmd.format(**cmd_args),
stdout=lfile,
stderr=subprocess.STDOUT)
r = p.wait()
if r != 0:
logger.critical("{0} did not exit sucessfully".format(
cmd.format(**cmd_args)))
rets.append(r)
# If sum is > 0 then one of the commands failed
if sum(rets) != 0:
logger.critical(
"!!! There was an error running part of the pipeline !!!")
logger.critical("Please check the logfile {0}".format(logfile))
sys.exit(1)
logger.info("--- Finished {0} ---".format(args.prefix))
#subprocess.call( 'git add -A', cwd=tdir, shell=True, stdout=lfile, stderr=subprocess.STDOUT )
#subprocess.call( 'git commit -am \'runsample\'', cwd=tdir, shell=True, stdout=lfile, stderr=subprocess.STDOUT )
logger.debug("Moving {0} to {1}".format(tdir, args.outdir))
# Cannot log any more below this line as the log file will be moved in the following code
if not os.path.isdir(args.outdir):
shutil.move(tdir, args.outdir)
else:
file_list = [os.path.join(tdir, m) for m in os.listdir(tdir)]
for f in file_list:
shutil.move(f, args.outdir)
"""
import subprocess
import os
import argparse
import sys
from os.path import basename, join, isdir, dirname, expandvars
from glob import glob
import tempfile
import reads
import shlex
import data
from ngs_mapper import compat
import log
lconfig = log.get_config()
logger = log.setup_logger( 'trim_reads', lconfig )
def main():
args = parse_args()
trim_reads_in_dir(
args.readsdir,
args.q,
args.outputdir,
head_crop=args.headcrop,
platforms=args.platforms,
primer_info=[args.primer_file, args.primer_seed, args.palindrom_clip, args.simple_clip]
)
def trim_reads_in_dir( *args, **kwargs ):
'''
#. Symlink all original .ab1 files into this directory
#. Convert all .ab1 to .fastq
#. Parse the sanger filename and create ReadsBySample/samplename directory
#. Symlink all .fastq and .ab1 files for that samplename from ReadData into Samplename directory
"""
import shutil
from os.path import *
import os
from glob import glob
from Bio import SeqIO
import re
import sys
import log
logger = log.setup_logger(basename(__file__), log.get_config())
# For invalid formatted filenames
class InvalidFormat(Exception):
pass
def sync_sanger(runpath, ngsdata):
rund = basename(runpath)
rawd = join(ngsdata, 'RawData', 'Sanger', rund)
readd = join(ngsdata, 'ReadData', 'Sanger', rund)
sync_run(runpath, ngsdata)
sync_readdata(rawd, ngsdata)
link_reads(readd, ngsdata)
def main():
args,qsubargs = parse_args()
# Qsub job?
if qsubargs:
runsampleargs, _ = split_args(' '.join(sys.argv[1:]))
print pbs_job(runsampleargs, qsubargs)
sys.exit(1)
# So we can set the global logger
global logger
# Setup analysis directory
if os.path.isdir( args.outdir ):
if os.listdir( args.outdir ):
raise AlreadyExists( "{0} already exists and is not empty".format(args.outdir) )
else:
os.makedirs(args.outdir)
# tempdir root will be TMPDIR environ variable if it exists
# unless outdir is set
# allows user to specify TMPDIR somewhere else if they want such as
# /dev/shm
tmpdir = args.outdir
# Directory analysis is run in will be inside of tmpdir
tdir = tempfile.mkdtemp('runsample', args.prefix, dir=tmpdir)
os.environ['TMPDIR'] = tdir
bamfile = os.path.join( tdir, args.prefix + '.bam' )
flagstats = os.path.join( tdir, 'flagstats.txt' )
consensus = bamfile+'.consensus.fasta'
vcf = bamfile+'.vcf'
bwalog = os.path.join( tdir, 'bwa.log' )
stdlog = os.path.join( tdir, args.prefix + '.std.log' )
logfile = os.path.join( tdir, args.prefix + '.log' )
CN = args.CN
# Set the global logger
config = log.get_config( logfile )
logger = log.setup_logger( 'runsample', config )
#make_project_repo( tdir )
logger.info( "--- Starting {0} --- ".format(args.prefix) )
if args.config:
logger.info( "--- Using custom config from {0} ---".format(args.config) )
# Write all stdout/stderr to a logfile from the various commands
with open(stdlog,'wb') as lfile:
cmd_args = {
'samplename': args.prefix,
'tdir': tdir,
'readsdir': args.readsdir,
'reference': os.path.join(tdir, os.path.basename(args.reference)),
'bamfile': bamfile,
'flagstats': flagstats,
'consensus': consensus,
'vcf': vcf,
'CN': CN,
'trim_qual': args.trim_qual,
'trim_outdir': os.path.join(tdir,'trimmed_reads'),
'filtered_dir' : os.path.join(tdir, 'filtered'),
'head_crop': args.head_crop,
'minth': args.minth,
'config': args.config,
'platforms': args.platforms,
'drop_ns': args.drop_ns,
'index_min': args.index_min,
'primer_info' : (args.primer_file, args.primer_seed, args.palindrom_clip, args.simple_clip)
}
# Best not to run across multiple cpu/core/threads on any of the pipeline steps
# as multiple samples may be running concurrently already
logger.debug( "Copying reference file {0} to {1}".format(args.reference,cmd_args['reference']) )
shutil.copy( args.reference, cmd_args['reference'] )
# Return code list
rets = []
logger.debug(cmd_args)
#Filter
def select_keys(d, keys):
return dict( ((k, v) for k, v in d.items() if k in keys))
#convert sffs to fastq
print sh.convert_formats(cmd_args['readsdir'], _out=sys.stdout, _err=sys.stderr)
#print sh.sff_to_fastq(cmd_args['readsdir'], _out=sys.stdout, _err=sys.stderr)
try:
if cmd_args['config']:
__result = sh.ngs_filter(cmd_args['readsdir'], config=cmd_args['config'], outdir=cmd_args['filtered_dir'])
else:
filter_args = select_keys(cmd_args, ["drop_ns", "platforms", "index_min"])
__result = sh.ngs_filter(cmd_args['readsdir'], outdir=cmd_args['filtered_dir'], **filter_args)
logger.debug( 'ngs_filter: %s' % __result )
except sh.ErrorReturnCode, e:
logger.error(e.stderr)
sys.exit(1)
#Trim reads
cmd = 'trim_reads {filtered_dir} -q {trim_qual} -o {trim_outdir} --head-crop {head_crop}'
if cmd_args['config']:
cmd += ' -c {config}'
primer_info = cmd_args['primer_info']
if primer_info[0]:
cmd += " --primer-file %s --primer-seed %s --palindrome-clip %s --simple-clip %s " % primer_info
p = run_cmd( cmd.format(**cmd_args), stdout=lfile, stderr=subprocess.STDOUT )
rets.append( p.wait() )
if rets[-1] != 0:
logger.critical( "{0} did not exit sucessfully".format(cmd.format(**cmd_args)) )
# Filter on index quality and Ns
# Mapping
with open(bwalog, 'wb') as blog:
cmd = 'run_bwa_on_samplename {trim_outdir} {reference} -o {bamfile}'
if cmd_args['config']:
cmd += ' -c {config}'
p = run_cmd( cmd.format(**cmd_args), stdout=blog, stderr=subprocess.STDOUT )
# Wait for the sample to map
rets.append( p.wait() )
# Everything else is dependant on bwa finishing so might as well die here
if rets[-1] != 0:
cmd = cmd.format(**cmd_args)
logger.critical( "{0} failed to complete sucessfully. Please check the log file {1} for more details".format(cmd,bwalog) )
sys.exit(1)
# Tag Reads
cmd = 'tagreads {bamfile} -CN {CN}'
if cmd_args['config']:
cmd += ' -c {config}'
p = run_cmd( cmd.format(**cmd_args), stdout=lfile, stderr=subprocess.STDOUT )
r = p.wait()
if r != 0:
logger.critical( "{0} did not exit sucessfully".format(cmd.format(**cmd_args)) )
rets.append( r )
# Variant Calling
cmd = 'base_caller {bamfile} {reference} {vcf} -minth {minth}'
if cmd_args['config']:
cmd += ' -c {config}'
p = run_cmd( cmd.format(**cmd_args), stdout=lfile, stderr=subprocess.STDOUT )
r = p.wait()
if r != 0:
logger.critical( "{0} did not exit sucessfully".format(cmd.format(**cmd_args)) )
rets.append( r )
if rets[-1] != 0:
cmd = cmd.format(**cmd_args)
logger.critical( '{0} failed to complete successfully'.format(cmd.format(**cmd_args)) )
# Flagstats
with open(flagstats,'wb') as flagstats:
cmd = 'samtools flagstat {bamfile}'
p = run_cmd( cmd.format(**cmd_args), stdout=flagstats, stderr=lfile, script_dir='' )
r = p.wait()
if r != 0:
logger.critical( "{0} did not exit sucessfully".format(cmd.format(**cmd_args)) )
rets.append( r )
# Graphics
cmd = 'graphsample {bamfile} -od {tdir}'
p = run_cmd( cmd.format(**cmd_args), stdout=lfile, stderr=subprocess.STDOUT )
r = p.wait()
if r != 0:
logger.critical( "{0} did not exit sucessfully".format(cmd.format(**cmd_args)) )
rets.append( r )
# Read Graphics
fastqs = ' '.join( glob.glob( os.path.join( cmd_args['trim_outdir'], '*.fastq' ) ) )
cmd = 'fqstats -o {0}.reads.png {1}'.format(cmd_args['bamfile'].replace('.bam',''),fastqs)
p = run_cmd( cmd, stdout=lfile, stderr=subprocess.STDOUT )
r = p.wait()
if r != 0:
logger.critical( "{0} did not exit sucessfully".format(cmd) )
rets.append( r )
# Consensus
cmd = 'vcf_consensus {vcf} -i {samplename} -o {consensus}'
p = run_cmd( cmd.format(**cmd_args), stdout=lfile, stderr=subprocess.STDOUT )
r = p.wait()
if r != 0:
logger.critical( "{0} did not exit sucessfully".format(cmd.format(**cmd_args)) )
rets.append( r )
# If sum is > 0 then one of the commands failed
if sum(rets) != 0:
logger.critical( "!!! There was an error running part of the pipeline !!!" )
logger.critical( "Please check the logfile {0}".format(logfile) )
sys.exit( 1 )
logger.info( "--- Finished {0} ---".format(args.prefix) )
#subprocess.call( 'git add -A', cwd=tdir, shell=True, stdout=lfile, stderr=subprocess.STDOUT )
#subprocess.call( 'git commit -am \'runsample\'', cwd=tdir, shell=True, stdout=lfile, stderr=subprocess.STDOUT )
logger.debug( "Moving {0} to {1}".format( tdir, args.outdir ) )
# Cannot log any more below this line as the log file will be moved in the following code
if not os.path.isdir( args.outdir ):
shutil.move( tdir, args.outdir )
else:
file_list = [os.path.join(tdir,m) for m in os.listdir(tdir)]
for f in file_list:
shutil.move( f, args.outdir )
#. Symlink all original .ab1 files into this directory
#. Convert all .ab1 to .fastq
#. Parse the sanger filename and create ReadsBySample/samplename directory
#. Symlink all .fastq and .ab1 files for that samplename from ReadData into Samplename directory
"""
import shutil
from os.path import *
import os
from glob import glob
from Bio import SeqIO
import re
import sys
import log
logger = log.setup_logger( basename(__file__), log.get_config() )
# For invalid formatted filenames
class InvalidFormat(Exception): pass
def sync_sanger( runpath, ngsdata ):
rund = basename( runpath )
rawd = join( ngsdata, 'RawData', 'Sanger', rund )
readd = join( ngsdata, 'ReadData', 'Sanger', rund )
sync_run( runpath, ngsdata )
sync_readdata( rawd, ngsdata )
link_reads( readd, ngsdata )
def sync_run( runpath, ngsdata ):
'''
import sys
import os
from os.path import *
import subprocess
import argparse
import bqd, graph_qualdepth as qd
import samtools
from bam_to_qualdepth import set_unmapped_mapped_reads
import json
import log
logc = log.get_config('graphsample.log')
logger = log.setup_logger('graphsample', logc)
def main():
args = parse_args()
args = handle_args(args)
if not args.qualdepth:
jfile = make_json(args.bamfile, args.outpath)
else:
jfile = args.qualdepth
pngfile = make_image(jfile, args.outpath)
def make_json(bamfile, outpathprefix):
pileup = samtools.nogap_mpileup(bamfile)
stats = bqd.parse_pileup(pileup)
set_unmapped_mapped_reads(bamfile, stats)
outfile = outpathprefix + '.qualdepth.json'
import argparse
import sys
import samtools
import re
import shutil
import os.path
from ngs_mapper.bam import sortbam, indexbam
import log
logger = log.setup_logger('tagreads',log.get_config())
# Exception for when headers exist
class HeaderExists(Exception): pass
# The next 3 tuples have to be the same length and each index in each is related the same index in each tuple
# AKA zip( IDS, PLATFORMS, ID_MAP ) should work as expected
# Read group ID list
IDS = ('Roche454', 'IonTorrent', 'MiSeq', 'Sanger')
# Valid platforms for read groups
PLATFORMS = ('L454', 'IONTORRENT', 'ILLUMINA', 'CAPILLARY')
# Read name map to ID name
ID_MAP = (
re.compile( '[0-9A-Z]{14}' ),
re.compile( '[A-Z0-9]{5}:\d{1,}:\d{1,}' ),
re.compile( 'M[0-9]{5}:\d+:[\w\d-]+:\d:\d{4}:\d{4,5}:\d{4,5}' ),
re.compile( '.*' )
)
# Read Group Template
RG_TEMPLATE = {
'SM': None,
'ID': None,
from glob import glob
from os.path import *
import numpy as np
import matplotlib.pyplot as plt
from nose.tools import ok_, eq_
from datetime import datetime
import log
logc = log.get_config()
logger = log.setup_logger( 'graph_times', logc )
def main():
ss = start_stop( 'Projects' )
logger.info( "Plotting all projects inside of {0}".format('Projects') )
x,y = [],[]
samplenames = sorted(ss.keys())
for sn in samplenames:
x.append( sn )
y.append( ss[sn] )
fig = plt.figure()
fig.set_size_inches( 20.0, 8.0 )
fig.suptitle( 'Pipeline Time per Sample' )
ax = plt.gca()
ax.plot( range(len(x)), y )
ax.set_xlim([0,len(x)-1])
ax.set_ylim([0,max(y)])
ax.set_xticks( range(0,len(x)) )
ax.set_xticklabels( x, rotation='vertical' )
ax.set_ylabel( 'Seconds' )
