QA tests for seqret are defined in the file:
.../emboss/emboss/test/qatest.dat |
The test data for the application is given under the /test directory and consists of input files, application parameters and the corresponding output files.
You'll see from inspecting the file that many tests are defined for the application, testing it under all sorts of input conditions in order to be as robust as possible. These are performed frequently to ensure the applications work as advertised and are not broken by (e.g.) recent changes to the library code.
Quality assurance testing, including how to write entries in qatest.dat, is covered in detail elsewhere (Chapter 7, Quality Assurance).
Test 1. This test extracts an entry from a database and write it to a file:
ID seqret-ex1 UC Extract an entry from a database and write it to a file: AP seqret IN tembl:x65923 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.fasta FP /X65923/ //
The command line session is below:
% qatest.pl -simple -testfile=seqret_1.dat seqret-ex1 Tests total: 1 pass: 1 fail: 0 Time: 0 seconds
Test 2. This test reads all entries in the database tembl that start with ab and write them to a file. In this example the specification is all done on the command line. To stop Unix getting confused by the * character, it has a backslash (\) before it:
ID seqret-ex2 UC Display the contents of the sequence on the screen: AP seqret IN tembl:x65923 IN stdout FI stdout FP /X65923/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / //
The command line session is below:
% qatest.pl -simple -testfile=seqret_2.dat seqret-ex2 Tests total: 1 pass: 1 fail: 0 Time: 0 seconds
Test 3. seqret does not read in features by default as this results in slightly faster performance. If, however, you wish to read in features with your sequence and also write them out then using -feature will change the default behaviour. Note EMBL format is used for the output file. The default FASTA format would report the features in GFF format (file seqname.gff
ID seqret-ex3 UC Write the result in GCG format by using the qualifier '-osformat'. AP seqret CL -osf gcg IN tembl:x65923 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.gcg FP /X65923/ //
The command line session is below:
% qatest.pl -simple -testfile=seqret_3.dat seqret-ex3 Tests total: 1 pass: 1 fail: 0 Time: 0 seconds
Test 4. Display the contents of the sequence on the screen:
ID seqret-ex4 UC Write the result in GCG format by specifying the format UC in the output USA on the command line. AP seqret CL -outseq gcg::x65923.gcg IN tembl:x65923 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.gcg FP /X65923/ //
The command line session is below:
% qatest.pl -simple -testfile=seqret_4.dat seqret-ex4 Tests total: 1 pass: 1 fail: 0 Time: 0 seconds
Test 5. Write the result in GCG format by using the qualifier -osformat:
ID seqret-ex5 UC Write the result in GCG format by specifying the format UC in the output USA at the prompt. AP seqret IN tembl:x65923 IN gcg::x65923.gcg FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.gcg FP /X65923/ //
The command line session is below:
% qatest.pl -simple -testfile=seqret_5.dat seqret-ex5 Tests total: 1 pass: 1 fail: 0 Time: 0 seconds
Test 6. Write the result in GCG format by specifying the format in the output USA on the command line.
ID seqret-ex6 UC Write the reverse-complement of a sequence: AP seqret CL -srev IN tembl:x65923 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.fasta FP /X65923/
The command line session is below:
% qatest.pl -simple -testfile=seqret_6.dat seqret-ex6 Tests total: 1 pass: 1 fail: 0 Time: 0 seconds
Test 7. Write the result in GCG format by specifying the format in the output USA at the prompt.
ID seqret-ex7 UC Extract the bases between the positions starting at 5 and ending at 25: AP seqret CL -sbegin 5 -send 25 IN tembl:x65923 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.fasta FP /X65923/ //
The command line session is below:
% qatest.pl -simple -testfile=seqret_7.dat seqret-ex7 Tests total: 1 pass: 1 fail: 0 Time: 0 seconds
Test 8. Write the reverse complement of a sequence:
ID seqret-ex8 UC Extract the bases between the positions starting at 5 UC and ending at 5 bases before the end of the sequence: AP seqret CL -sbegin 5 -send -5 IN tembl:x65923 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.fasta FP /X65923/ //
The command line session is below:
% qatest.pl -simple -testfile=seqret_8.dat seqret-ex8 Tests total: 1 pass: 1 fail: 0 Time: 0 seconds
Test 9. Extract the bases between the positions starting at 5 and ending at 25:
ID seqret-ex9 UC Read all entries in the database 'tembl' that start with 'h' UC and write them to a file: AP seqret IN tembl:h* IN hall.seq FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hall.seq FP /H45989/ //
The command line session is below:
% qatest.pl -simple -testfile=seqret_9.dat seqret-ex9 Tests total: 1 pass: 1 fail: 0 Time: 0 seconds
Test 10. Extract the bases between the positions starting at 5 and ending at 5 bases before the end of the sequence:
ID seqret-ex10
UC Read all entries in the database 'tembl' that start with 'ab'
UC and write them to a file.
UC In this example the specification is all done in the command line
UC and to stop Unix getting confused by the '*' character,
UC it has to have a backslash ('\') before it:
AP seqret
CL 'tembl:ab*' aball.seq
FI stderr
FC = 1
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI aball.seq
FP /^>AB000095/
FP 4 /^>/
//
The command line session is below:
% qatest.pl -simple -testfile=seqret_10.dat seqret-ex10 Tests total: 1 pass: 1 fail: 0 Time: 0 seconds
Test 11. Read all entries in the database tembl that start with h and write them to a file:
ID seqret-ex11 UC seqret does not read in features by default because this results in UC slightly faster performance. If however you wish to read in features UC with your sequence and write them out on output, using '-feature' will UC change the default behaviour to use any features present in the sequence. UC N.B. use embl format for the output file as the default format 'fasta' UC reports the features in gff (file "<seqname>.gff") AP seqret CL -feature IN tembl:x65923 IN embl::x65923.embl FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.embl FP /X65923/ //
The command line session is below:
% qatest.pl -simple -testfile=seqret_11.dat seqret-ex11 Tests total: 1 pass: 1 fail: 0 Time: 0 seconds