Unable to create ign_sample_report with swedish number formatting
Smeds opened this issue · comments
ngi_reports are unable to parse genome_results.txt file from qualimap, when the output has been generated using swedish number formatting, i.e with spaces and commas.
Example
number of windows = 483 number of reads = 1 066 442 816 number of mapped reads = 1 049 993 798 (98,46%) number of mapped bases = 151 315 373 336 bp number of sequenced bases = 151 253 112 265 bp number of aligned bases = 0 bp
sample reports can be generated if the example is changed to
number of windows = 483 number of reads = 1,066,442,816 number of mapped reads = 1,049,993,798 (98.46%) number of mapped bases = 151,315,373,336 bp number of sequenced bases = 151,253,112,265 bp number of aligned bases = 0 bp
Hi @Smeds - is there a traceback associated?
I got no traceback
Here's the terminal output I got:
ngi_reports -n uppsala ign_sample_report --samples 235
2015-12-09 11:24:54,883 - NGI Reports - INFO - Report type: ign_sample_report
2015-12-09 11:24:55,563 - NGI Reports - INFO - Found 304 Piper setup XML files..
2015-12-09 11:25:01,797 - NGI Reports - ERROR - Could not parse the ign_sample_report template for sample 235 - skipping
Closing this issue as ign_sample_report has been retired.