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rki-mf1 / covsonar

A database-driven system for handling genomic sequences of SARS-CoV-2 and screening genomic profiles.
GNU General Public License v3.0
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Broken pipe error on using `head` on output of `match` command #100

Open matthuska opened 1 year ago

matthuska commented 1 year ago

This is not critical to fix, but sonar errors when you pipe the output of match to head:

$ sonar match --db test.db | head -n 2
SAMPLE_NAME     IMPORTED        GENOMIC_PROFILE PROTEOMIC_PROFILE       FRAMESHIFT_MUTATIONS
IMS-10116-CVDP-0039B345-A3B6-475D-A50C-543AFBA039D8             T670G C1627T C1884T C2790T C3037T A3039G G4184A A4236C C4321T C5178T C5284T C9344T A9424G C9534T C10029T C10198T G10447A C10449A del:11288-11296 G12160A G12761A C12880T C14408T C15714T C17410T A18163G C19955T A20055G C21618T del:21633-21641 del:21765-21770 G21987A T22200G G22578A C22674T T22679C C22686T A22688G G22775A A22786C G22813T T22882G T22917G G22992A C22995A A23013C T23018G A23055G A23063T T23075C A23403G C23525T T23599G C23604A C23854A G23948T A24424T T24469A C25000T C25584T C26060T C26270T G26529A C26577G G26709A A27038G C27807T C27889T A28271T C28311T A28330G del:28361-28369 A28370T G28371T G28881A G28882A G28883C A29510C del:29734-29759  E:T9I M:D3N M:Q19E M:A63T N:P13L N:del:30-32 N:S33F N:R203K N:G204R N:S413R ORF1ab:S135R ORF1ab:A540V ORF1ab:T842I ORF1ab:Y925C ORF1ab:G1307S ORF1ab:N1324T ORF1ab:T1638I ORF1ab:L3027F ORF1ab:T3090I ORF1ab:T3255I ORF1ab:P3395H ORF1ab:del:3675-3677 ORF1ab:D4166N ORF1ab:P4715L ORF1ab:R5716C ORF1ab:I5967V ORF1ab:T6564I ORF3a:T223I S:T19I S:del:24-27 S:del:68-70 S:G142D S:V213G S:G339D S:S371F S:S373P S:S375F S:T376A S:D405N S:R408S S:K417N S:N440K S:L452R S:S477N S:T478K S:E484A S:F486V S:Q498R S:N501Y S:Y505H S:D614G S:H655Y S:N679K S:P681H S:N764K S:D796Y S:Q954H S:N969K
Traceback (most recent call last):
  File "<snip>/bin/sonar", line 6, in <module>
    sys.exit(main())
  File "<snip>/src/covsonar/src/covsonar/sonar.py", line 1134, in main
    execute_commands(args)
  File "<snip>/src/covsonar/src/covsonar/sonar.py", line 1091, in execute_commands
    handle_match(args)
  File "<snip>/src/covsonar/src/covsonar/sonar.py", line 1003, in handle_match
    sonarUtils.match(
  File "<snip>/src/covsonar/src/covsonar/utils.py", line 882, in match
    sonarUtils._export_query_results(rows, format, reference, outfile)
  File "<snip>/src/covsonar/src/covsonar/utils.py", line 902, in _export_query_results
    sonarUtils.export_csv(
  File "<snip>/src/covsonar/src/covsonar/utils.py", line 1104, in export_csv
    writer.writerow(row)
  File "<snip>/envs/covsonar-dev/lib/python3.9/csv.py", line 154, in writerow
    return self.writer.writerow(self._dict_to_list(rowdict))
BrokenPipeError: [Errno 32] Broken pipe