def view(request, response, xfer_msg=None):
samplesheet = Samplesheet(request.path_named_values['fcid'])
if not samplesheet.exists():
raise HTTP_NOT_FOUND(str(samplesheet))
samplesheet.read()
problems = list()
header = TR(TH(), TH('FCID'), TH('Lane'),
TH('SampleID', BR(), '(as "ID_index-spec")'), TH('SampleRef'),
TH('Index', BR(), '(sequence)'), TH('Description'),
TH('Control'), TH('Recipe'), TH('Operator'))
rows = []
seqindex_lookup = dict() # Key: lane number, value: seq index
# Figure out whether that extra A has been appended previously.
append_a = None
for record in samplesheet.records:
if append_a is None or append_a == True:
append_a = len(record[4]) > 6 and record[4][-1] == 'A'
if append_a is None:
append_a = False
index_sequence_length = None
for pos, record in enumerate(samplesheet.records):
# Same length of index sequence required for entire samplesheet!
if index_sequence_length is None and record[4]:
index_sequence_length = len(record[4])
lanes = []
for i in xrange(1, 9):
if i == record[1]:
lanes.append(OPTION(str(i), selected=True))
else:
lanes.append(OPTION(str(i)))
samplerefs = _get_sampleref_options(record[3])
warning = []
if record[4]: # Check index sequence
if set(record[4].upper()).difference(set('ATGC')):
warning.append('Invalid nucleotide in index sequence!')
if index_sequence_length:
if index_sequence_length != len(record[4]):
warning.append('Unequal length of index sequence!')
other_seqindices = seqindex_lookup.get(record[1], set())
if record[4] in other_seqindices:
warning.append('Index sequence already used in lane!')
else:
for other_seqindex in other_seqindices:
try:
hd = hamming_distance(record[4], other_seqindex)
except ValueError:
pass
else:
if hd < MIN_HAMMING_DISTANCE:
warning.append('Too small difference between'
' this index sequence and'
' another in lane!')
break
seqindex_lookup.setdefault(record[1], set()).add(record[4])
if interpret_sampleid_for_index(record[2], append_a) != record[4]:
warning.append('SampleID and index sequence inconsistent!')
else:
warning.append('Missing sequence!')
if warning:
problems.append(str(pos + 1))
warning = B(' '.join(warning), style='color: red;')
# The abominable dot '.' in project identifiers is stored as
# double underscore, since CASAVA cannot handle dot.
# For display purposes, the dot is shown instead of double underscore.
description = record[5].replace('__', '.')
rows.append(
TR(
TD(str(pos + 1)), TD(record[0]),
TD(SELECT(name="lane%i" % pos, *lanes)),
TD(
INPUT(type='text',
name="sampleid%i" % pos,
value=record[2],
size=30)),
TD(SELECT(name="sampleref%i" % pos, *samplerefs)),
TD(
INPUT(type='text',
name="index%i" % pos,
value=record[4],
size=10), warning),
TD(
INPUT(type='text',
name="description%i" % pos,
value=description,
size=24)),
TD(
INPUT(type='radio',
name="control%i" % pos,
value='N',
checked=record[6] == 'N'), 'N ',
INPUT(type='radio',
name="control%i" % pos,
value='Y',
checked=record[6] == 'Y'), 'Y'),
TD(
INPUT(type='text',
name="recipe%i" % pos,
value=record[7],
size=4)),
TD(
INPUT(type='text',
name="operator%i" % pos,
value=record[8],
size=4))))
try:
previous_lane = samplesheet.records[-1][1]
previous_sampleref = samplesheet.records[-1][3]
except IndexError:
previous_lane = None
previous_sampleref = None
lanes = []
for i in xrange(1, 9):
if i == previous_lane:
lanes.append(OPTION(str(i), selected=True))
else:
lanes.append(OPTION(str(i)))
samplerefs = _get_sampleref_options(previous_sampleref)
rows.append(
TR(
TD(str(len(samplesheet.records) + 1)), TD(samplesheet.fcid),
TD(SELECT(name='lane', multiple=True, *lanes)),
TD(INPUT(type='text', name='sampleid', size=30)),
TD(SELECT(name='sampleref', *samplerefs)),
TD(INPUT(type='text', name='index', size=10)),
TD(INPUT(type='text', name='description', size=24)),
TD(INPUT(type='radio', checked=True, name='control', value='N'),
'N ', INPUT(type='radio', name='control', value='Y'), 'Y'),
TD(INPUT(type='text', name='recipe', size=4)),
TD(INPUT(type='text', name='operator', size=4))))
rows.reverse()
rows.insert(0, header)
table = TABLE(border=1, *rows)
instructions = P(
UL(
LI('To add several records, cut-and-paste'
' from the Google Docs spreadsheet'
' into the text box to the right.'),
LI('To add another record,'
' fill in values in the first row.'),
LI('To delete a record, set its SampleID'
' to a blank character.'),
LI('To modify a record, change the value'
' in the field.'),
LI('NOTE: Sample and project identifiers are now'
' strictly controlled: Offensive characters are'
' automatically converted to underscores.'),
LI(
'Specify index number for the sample like so:',
TABLE(TR(TH('Index type'), TH('Standard name'),
TH('Alternate short name')),
TR(TD('Ordinary Illumina'), TD('samplename_index3'),
TD('samplename_3')),
TR(TD('Small RNA'), TD('samplename_rpi6'),
TD('samplename_r6')),
TR(TD('Agilent'), TD('samplename_agilent14'),
TD('samplename_a14')),
TR(TD('Mondrian'), TD('samplename_mondrian11'),
TD('samplename_m11')),
TR(TD('Haloplex'), TD('samplename_halo11'),
TD('samplename_h11')),
border=1)),
LI('Click "Save" to store the samplesheet.'
' Comicbookguy will fetch it automatically'
' within 15 minutes.')))
ops = TABLE(
TR(
TD(
FORM(I('Cut-and-paste 4 columns'
' (Lane, Sample, Project, Ref.genome).'),
TEXTAREA(name='cutandpaste', cols=40, rows=4),
INPUT(type='submit', value='Add'),
method='POST',
action=samplesheet.url))),
TR(
TD(
FORM(INPUT(type='submit', value='Sort samplesheet records'),
INPUT(type='hidden', name='sort', value='default'),
method='POST',
action=samplesheet.url))),
## TR(TD(FORM(INPUT(type='submit',
## value='Download CSV file (obsolete)'),
## method='GET',
## action=samplesheet.file_url))),
TR(
TD(
FORM(INPUT(type='submit',
value='Delete this samplesheet',
onclick="return confirm('Really delete?');"),
INPUT(type='hidden', name='http_method', value='DELETE'),
method='POST',
action=samplesheet.url))),
width='100%')
warning = []
if xfer_msg:
warning.append(P(xfer_msg))
if problems:
warning.append(
P("There are problems regarding records %s!" %
', '.join(problems)))
warning = DIV(style='color: red;', *warning)
form = FORM(
P(INPUT(type='submit', value='Save')),
## INPUT(type='checkbox', name='append_a',
## value='y', checked=append_a),
## " Append an 'A' to a newly defined index sequence."),
P(table),
method='POST',
action=samplesheet.url)
response['Content-Type'] = 'text/html'
response.append(
str(
HTML(
HEAD(TITLE(str(samplesheet))),
BODY(A('Home', href=get_url()), H1(str(samplesheet)),
TABLE(TR(TD(instructions), TD(ops))), warning, form))))
def view(request, response, xfer_msg=None):
if invalid_data_dir(request, response): return
samplesheet = Samplesheet(request.path_named_values['fcid'])
if not samplesheet.exists:
raise HTTP_NOT_FOUND(str(samplesheet))
samplesheet.read()
problems = set()
header = TR(TH(),
TH('FCID'),
TH('Lane'),
TH('SampleID + index-spec',
BR(),
'(format: see above)',
width='20%'),
TH('SampleRef'),
TH('Index', BR(), '(sequence)'),
TH('ProjectID'),
TH('Control'),
TH('Recipe'),
TH('Operator'))
rows = []
# Key: lane number, value: tuple (seq index, SampleID)
seqindex_lookup = dict()
# Figure out whether that extra A has been appended previously.
append_a = None
for record in samplesheet.records:
if append_a is None or append_a == True:
append_a = len(record[4]) > 6 and record[4][-1] == 'A'
if append_a is None:
append_a = False
# Require same index sequence length within each lane.
index_sequence_lengths = [None] * 9 # 1-based index for max 8 lanes.
for pos, record in enumerate(samplesheet.records):
lane = record[1]
lanes = []
for i in xrange(1, 9):
if i == lane:
lanes.append(OPTION(str(i), selected=True))
else:
lanes.append(OPTION(str(i)))
samplerefs = _get_sampleref_options(record[3])
sample_warning = []
project_warning = []
# Check valid sampleid
sampleid = record[2]
if not SAMPLEID_RX.match(sampleid):
sampleid = '_'.join(sampleid.split('_')[:-1])
if not SAMPLEID_RX.match(sampleid):
sample_warning.append('Invalid SampleID.')
if record[3] == 'unknown':
sample_warning.append('Unknown SampleRef.')
if record[4]: # Check index sequence; '-' for dual
if set(record[4].upper()).difference(set('ATGC-')):
sample_warning.append('Invalid nucleotide in index sequence.')
if index_sequence_lengths[lane] is None:
index_sequence_lengths[lane] = len(record[4])
else:
if index_sequence_lengths[lane] != len(record[4]):
sample_warning.append('Unequal length of index sequence in lane.')
other_seqindices = seqindex_lookup.get(lane, set())
if record[4] in other_seqindices:
sample_warning.append('Index sequence already used in lane.')
else:
for other_seqindex, other_sampleid in other_seqindices:
ld = levenshtein_distance(record[4], other_seqindex,
shortest=True)
if ld < MIN_LEVENSHTEIN_DISTANCE:
sample_warning.append('Too small Levenshtein distance'
' between this index sequence'
' and sample %s in lane.'
% other_sampleid)
break
hd = hamming_distance(record[4], other_seqindex,
shortest=True)
if hd < MIN_HAMMING_DISTANCE:
sample_warning.append('Too small Hamming distance'
' between this index sequence'
' and sample %s in lane.'
% other_sampleid)
break
seqindex_lookup.setdefault(lane, set()).add((record[4], record[2]))
indexseq = interpret_sampleid_for_index(record[2], append_a)
if indexseq and indexseq != record[4]:
sample_warning.append('SampleID and index sequence inconsistent.')
if not record[4]:
sample_warning.append('Index sequence missing.')
else:
sample_warning.append('Missing sequence.')
if sample_warning:
problems.add(pos+1)
sample_warning = B('<br>'.join(sample_warning), style='color: red;')
# The abominable dot '.' in project identifiers is stored as
# double underscore, since CASAVA cannot handle dot.
# For display purposes, the dot is shown instead of double underscore.
description = record[5].replace('__', '.')
if not PROJECTID_RX.match(record[5]):
project_warning.append('Project ID is malformed')
if project_warning:
problems.add(pos+1)
project_warning = B('<br>'.join(project_warning), style='color: red;')
rows.append(TR(TD(str(pos+1)),
TD(record[0]),
TD(SELECT(name="lane%i" % pos, *lanes)),
TD(INPUT(type='text', name="sampleid%i" % pos,
value=record[2], size=24),
sample_warning),
TD(SELECT(name="sampleref%i" % pos, *samplerefs)),
TD(INPUT(type='text', name="index%i" % pos,
value=record[4], size=16)),
TD(INPUT(type='text', name="description%i" % pos,
value=description, size=24),
project_warning),
TD(INPUT(type='radio', name="control%i" % pos,
value='N', checked=record[6]=='N'), 'N ',
BR(),
INPUT(type='radio', name="control%i" % pos,
value='Y', checked=record[6]=='Y'), 'Y'),
TD(INPUT(type='text', name="recipe%i" % pos,
value=record[7], size=4)),
TD(INPUT(type='text', name="operator%i" % pos,
value=record[8], size=4))))
try:
previous_lane = samplesheet.records[-1][1]
previous_sampleref = samplesheet.records[-1][3]
except IndexError:
previous_lane = None
previous_sampleref = None
lanes = []
for i in xrange(1, 9):
if i == previous_lane:
lanes.append(OPTION(str(i), selected=True))
else:
lanes.append(OPTION(str(i)))
samplerefs = _get_sampleref_options(previous_sampleref)
rows.append(TR(TD(str(len(samplesheet.records)+1)),
TD(samplesheet.fcid),
TD(SELECT(name='lane', multiple=True, *lanes)),
TD(INPUT(type='text', name='sampleid', size=24)),
TD(SELECT(name='sampleref', *samplerefs)),
TD(INPUT(type='text', name='index', size=16)),
TD(INPUT(type='text', name='description', size=24)),
TD(INPUT(type='radio', checked=True,
name='control', value='N'), 'N ',
BR(),
INPUT(type='radio', name='control', value='Y'), 'Y'),
TD(INPUT(type='text', name='recipe', size=4)),
TD(INPUT(type='text', name='operator', size=4))))
rows.reverse()
rows.insert(0, header)
table = TABLE(border=1, cellpadding=2, *rows)
instructions = P(UL(LI('To add several records, cut-and-paste'
' from the Google Docs spreadsheet'
' into the text box to the right, then save.'),
LI('To add another record, fill in values'
' in the first row, then save.'),
LI('To delete a record, set its SampleID'
' to a blank character, then save.'),
LI('To modify a record, change the value'
' in the field, then save.'),
LI('Offensive characters in Project Identifiers'
' will be automatically converted'
' to underscores.'),
LI('SampleID must look like ',
B('P123_456'), ', possibly with any of the'
' characters B, C, D or F attached.'),
LI('If the index suffix looks like a nucleotide'
' sequence with at least 6 bases, it will be used.'),
LI('Specify index number for the sample by adding the'
' appropriate suffix using underscore, like so:',
TABLE(TR(TH('Index type'),
TH('Standard index spec'),
TH('Alternate short index spec')),
TR(TD('Illumina'),
TD('sampleid_index3'),
TD('sampleid_i3')),
TR(TD('Small RNA'),
TD('sampleid_rpi6'),
TD('sampleid_r6')),
TR(TD('Agilent'),
TD('sampleid_agilent14'),
TD('sampleid_a14')),
TR(TD('Mondrian'),
TD('sampleid_mondrian11'),
TD('sampleid_m11')),
TR(TD('Haloplex'),
TD('sampleid_halo11'),
TD('sampleid_h11')),
TR(TD('Haloplex HT 8-bp'),
TD('sampleid_haloht31'),
TD('sampleid_hht31')),
TR(TD('SureSelect'),
TD('sampleid_sureselect9'),
TD('sampleid_ss9')),
TR(TD('TruSeq DNA Dual HT'),
TD('sampleid_dual13')),
TR(TD('Nextera Dual HT'),
TD('sampleid_nxdual15')),
TR(TD('Halo HT Dual'),
TD('sampleid_haloht15dual')),
TR(TD('Illumina Dual'),
TD('sampleid_index15dual')),
TR(TD('Agilent SureSelect XT'),
TD('sampleid_xtd04')),
border=1,
cellpadding=2))))
ops = TABLE(TR(TD(FORM(I('Cut-and-paste 4 columns'
' (Lane, Sample, Project, Ref.genome).'),
TEXTAREA(name='cutandpaste', cols=40, rows=4),
INPUT(type='submit', value='Add'),
method='POST',
action=samplesheet.url))),
TR(TD(FORM(INPUT(type='submit',
value='Sort samplesheet records'),
INPUT(type='hidden',
name='sort', value='default'),
method='POST',
action=samplesheet.url))),
TR(TD(FORM(INPUT(type='submit',
value='Delete this samplesheet',
onclick="return confirm('Really delete?');"),
INPUT(type='hidden',
name='http_method', value='DELETE'),
method='POST',
action=samplesheet.url))),
width='100%')
title = "%s (%s)" % (samplesheet,
A("CSV file", href=samplesheet.file_url))
warning = []
if xfer_msg:
warning.append(P(xfer_msg))
if problems:
problems = sorted(problems)
problems = ', '.join(map(str, problems))
warning.append(P("There are problems regarding records %s!" % problems))
warning = DIV(style='color: red;', *warning)
form = FORM(P(INPUT(type='submit', value='Save'),
' Store the samplesheet. The pipeline computer (comicbookguy)'
' will fetch it automatically within 15 minutes.'),
P(table),
method='POST',
action=samplesheet.url)
response['Content-Type'] = 'text/html'
response.append(str(HTML(HEAD(TITLE(str(samplesheet))),
BODY(A('Home', href=get_url()),
H1(title),
TABLE(TR(TD(instructions),
TD(ops))),
warning,
form))))
