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Fixes error with only integer-like sample names #78

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merged 1 commit into from
Mar 8, 2021
Merged

Fixes error with only integer-like sample names #78

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20 changes: 14 additions & 6 deletions bin/summary_report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,10 +127,11 @@ def check_and_init_tabledata(self, t_index):
if self.tabledata is None:
self.tabledata = pd.DataFrame(index=sorted(t_index))
self.tabledata.columns.name = 'Sample'
self.force_index_dtype_string(self.tabledata)
self.add_col_description(f'Missing values (\'<font color="{self.color_error_red}">n/a</font>\') denote cases where the respective program could not determine a result.')
else:
for item in t_index:
assert item in self.tabledata.index, f'Index not found in existing table: {item}'
assert item in self.tabledata.index, f'Index not found in existing table: {item}. Available: {self.tabledata.index}'


def add_col_description(self, desc):
Expand Down Expand Up @@ -242,11 +243,15 @@ def write_html_report(self):

### functions to add columns

def force_index_dtype_string(self, dataframe):
dataframe.index = dataframe.index.astype('string')

def add_pangolin_results(self, pangolin_results):
log(f'Adding Pangolin results ...')
# column names:
# taxon,lineage,probability,pangoLEARN_version,status,note
res_data = pd.read_csv(pangolin_results, index_col='taxon')
res_data = pd.read_csv(pangolin_results, index_col='taxon', dtype={'taxon': str})
self.force_index_dtype_string(res_data)
self.check_and_init_tabledata(res_data.index)

res_data['lineage_prob'] = [f'<b>{l}</b><br>({p:.2f})' for l,p in zip(res_data['lineage'], res_data['probability'])]
Expand All @@ -258,7 +263,8 @@ def add_pangolin_results(self, pangolin_results):
def add_president_results(self, president_results):
log(f'Adding President results ...')

res_data = pd.read_csv(president_results, index_col='query_name', sep='\t')
res_data = pd.read_csv(president_results, index_col='query_name', sep='\t', dtype={'query_name': str})
self.force_index_dtype_string(res_data)
self.check_and_init_tabledata(res_data.index)

def identity_markup(ident, mismatches):
Expand Down Expand Up @@ -308,7 +314,8 @@ def percN_markup(nn, ql):
def add_nextclade_results(self, nextclade_results):
log(f'Adding Nextclade results ...')

res_data = pd.read_csv(nextclade_results, index_col='seqName', sep='\t')
res_data = pd.read_csv(nextclade_results, index_col='seqName', sep='\t', dtype={'seqName': str})
self.force_index_dtype_string(res_data)
self.check_and_init_tabledata(res_data.index)

res_data['mutations_formatted'] = [m.replace(',', ', ') if type(m) == str else '-' for m in res_data['aaSubstitutions']]
Expand Down Expand Up @@ -342,8 +349,9 @@ def spike_markup(field):
def add_kraken2_results(self, kraken2_results):
log(f'Adding Kraken2 results ...')
# column names:
#sample,num_sarscov2,num_human
res_data = pd.read_csv(kraken2_results, index_col=0)
# sample,num_unclassified,num_sarscov2,num_human
res_data = pd.read_csv(kraken2_results, index_col='sample', dtype={'sample': str})
self.force_index_dtype_string(res_data)
self.check_and_init_tabledata(res_data.index)

def readable_si_units(number):
Expand Down
2 changes: 1 addition & 1 deletion workflows/process/summary_report.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ process summary_report {
'''
else
'''
echo '#sample,num_unclassified,num_sarscov2,num_human' > kraken2_results.csv
echo 'sample,num_unclassified,num_sarscov2,num_human' > kraken2_results.csv
for KF in !{kraken2_results}; do
echo -n "${KF%.kreport}," >> kraken2_results.csv
NUNCLASS=$(awk -v ORS= '$5=="0" {print $3 "," }' $KF)
Expand Down