[Bioperl-guts-l] [Bug 2077] bp_sreformat.pl creates broken GenBank formatted file from EMBL input

bugzilla-daemon at newportal.open-bio.org bugzilla-daemon at newportal.open-bio.org
Wed Aug 30 08:34:33 EDT 2006


http://bugzilla.open-bio.org/show_bug.cgi?id=2077





------- Comment #10 from mmokrejs at ribosome.natur.cuni.cz  2006-08-30 08:34 -------
ID   5CAR000173 standard; mRNA; PLN; 60 BP.
XX
AC   BB187974;
XX
DT   20-NOV-2002 (Rel. 16, Created)
DT   20-NOV-2002 (Rel. 16, Last updated, Version 1)
XX
DE   5'UTR in Cicer arietinum mRNA for putative epsilon subunit of
mitochondrial
DE   F1-ATPase (f19c24.25 gene)
XX
DR   EMBL; AJ487471;
DR   UTR; CC208061;
XX
OS   Cicer arietinum (chickpea)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids I; Fabales; Fabaceae; Papilionoideae; Cicereae; Cicer.
XX
UT   5'UTR;
XX
FH   Key             Location/Qualifiers
FH
FT   5'UTR           1..60
FT                   /source="EMBL::AJ487471:1..60"
FT                   /gene="f19c24.25""
FT                   /product="putative epsilon subunit of mitochondrial
F1-ATPase"
XX
SQ   Sequence 60 BP; 19 A; 16 C; 9 G; 16 T; 0 other;
     gttcacattc atttttcaga gaacacacag agcgtatcgt atcaaatcac cgatcgatcc       
60
//


The message is unclear. Is it warning or error or info mesage? Is the user
supposed to verify the content of the resulting file? Did the process continue
after that problematic "feature" tag or not? That's what is unclear, sorry.
Sure, the creator of the file should fix the format, but not an issue here.

Thanks for you effort.


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