Hi Charles, this is a side effect of the automatic parsing of EMBOSS USAs. If there is a ":" present it can be interpreted as file:entry or dbname:entry. http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html#eg And if the part before the ":" stands for a database, then you can specify to search in indexed database fields by adding "-<index>". In this case EMBOSS interprets the present directory "test" as a database (I'm not sure if this is a feature or a bug :-) ) and then assumes that "1.fa" is the name of an index where it should look for "A".
Cheers, David. -----Ursprüngliche Nachricht----- Von: [email protected] [mailto:[email protected]] Im Auftrag von Charles Plessy Gesendet: 05 June 2014 07:36 An: [email protected] Betreff: [EMBOSS] Bug with file names containing a dash. Dear all, I just encountered the following bug: If a file name contains a dash, then EMBOSS will be disturbed when a directory named as the string before that dash is present in the same directory. echo -e '>A\nAAAAAA' > test-1.fa cat test-1.fa # >A # AAAAAA seqret test-1.fa:A stdout # Read and write (return) sequences # >A # AAAAAA mkdir test seqret test-1.fa:A stdout # Read and write (return) sequences # Error: Query 'test-1.fa:A' query field '1.fa' not defined for datatype 'sequence' # Error: Unable to read sequence 'test-1.fa:A' # Died: seqret terminated: Bad value for '-sequence' and no prompt Cheers, -- Charles Plessy, Tsurumi, Kanagawa, Japan. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
