Skip to content
Browse files

Test EMBL files with missing sequence type in ID line

  • Loading branch information...
1 parent f6ea866 commit 0c4831d41a6b90f9695812791309001d7aa34c6d @peterjc peterjc committed Jul 22, 2013
Showing with 33 additions and 0 deletions.
  1. +32 −0 Tests/output/test_SeqIO
  2. +1 −0 Tests/test_SeqIO.py
View
32 Tests/output/test_SeqIO
@@ -2284,6 +2284,38 @@ Testing reading embl format file EMBL/DD231055_edited.embl
Checking can write/read as 'tab' format
Checking can write/read as 'nexus' format
Checking can write/read as 'phylip-sequential' format
+Testing reading embl format file EMBL/DD231055_edited2.embl
+ ID = 'DD231055.1', Name='DD231055',
+ Seq='GCCGAGCTGACCCAGTCTCCATCCTCCCTGTCTGCATCTG...TATGAGA', length=315
+ Checking can write/read as 'fasta' format
+ Checking can write/read as 'clustal' format
+ Checking can write/read as 'phylip' format
+ Checking can write/read as 'stockholm' format
+ Checking can write/read as 'phylip-relaxed' format
+ Checking can write/read as 'embl' format
+ Failed: Need a DNA, RNA or Protein alphabet
+ Checking can write/read as 'fastq' format
+ Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
+ Checking can write/read as 'fastq-illumina' format
+ Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
+ Checking can write/read as 'fastq-solexa' format
+ Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
+ Checking can write/read as 'genbank' format
+ Failed: Need a Nucleotide or Protein alphabet
+ Checking can write/read as 'imgt' format
+ Failed: Need a DNA, RNA or Protein alphabet
+ Checking can write/read as 'phd' format
+ Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
+ Checking can write/read as 'qual' format
+ Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
+ Checking can write/read as 'seqxml' format
+ Failed: Need a DNA, RNA or Protein alphabet
+ Checking can write/read as 'sff' format
+ Failed: Missing SFF flow information
+ Checking can write/read as 'tab' format
+ Checking can write/read as 'nexus' format
+ Failed: Need a DNA, RNA or Protein alphabet
+ Checking can write/read as 'phylip-sequential' format
Testing reading embl format file EMBL/SC10H5.embl
ID = 'AL031232', Name='SC10H5',
Seq='GATCAGTAGACCCAGCGACAGCAGGGCGGGGCCCAGCAGG...CGAGCAT', length=4870
View
1 Tests/test_SeqIO.py
@@ -151,6 +151,7 @@
("embl", False, 'EMBL/epo_prt_selection.embl', 9), # proteins
("embl", False, 'EMBL/TRBG361.embl', 1),
("embl", False, 'EMBL/DD231055_edited.embl', 1),
+ ("embl", False, 'EMBL/DD231055_edited2.embl', 1), #Partial ID line
("embl", False, 'EMBL/SC10H5.embl', 1), # Pre 2006 style ID line
("embl", False, 'EMBL/U87107.embl', 1), # Old ID line with SV line
("embl", False, 'EMBL/AAA03323.embl', 1), # 2008, PA line but no AC

0 comments on commit 0c4831d

Please sign in to comment.
Something went wrong with that request. Please try again.