Cope with malformed EMBL (or GenBank) files where the features are ov…

…er-indented (Bug 3062)

Bio/GenBank/Scanner.py

@@ -167,7 +167,9 @@ def parse_features(self, skip=False):
                 line = self.handle.readline()
                 while line[:self.FEATURE_QUALIFIER_INDENT] == self.FEATURE_QUALIFIER_SPACER \
                 or line.rstrip() == "" : # cope with blank lines in the midst of a feature
-                    feature_lines.append(line[self.FEATURE_QUALIFIER_INDENT:].rstrip())
+                    #Use strip to remove any harmless trailing white space AND and leading
+                    #white space (e.g. out of spec files with too much intentation)
+                    feature_lines.append(line[self.FEATURE_QUALIFIER_INDENT:].strip())
                     line = self.handle.readline()
                 features.append(self.parse_feature(feature_key, feature_lines))
         self.line = line

Tests/EMBL/A04195_bad_indent.embl

@@ -0,0 +1,36 @@
+ID   A04195 IMGT/LIGM annotation : by annotators; RNA; SYN; 51 BP.
+XX
+AC   A04195;
+XX
+DT   15-MAY-1995 (Rel. 2, arrived in LIGM-DB )
+DT   20-APR-1999 (Rel. 11, Last updated, Version 4)
+XX
+DE   Artificial Ig lambda-chain mRNA ;
+DE   RNA; rearranged configuration; Ig-Light-Lambda; regular. 
+XX
+KW   antigen receptor; Immunoglobulin superfamily (IgSF); 
+KW   Immunoglobulin (IG); IG-Light; IG-Light-Lambda; cDNA; rearranged. 
+XX
+OS   synthetic construct
+OC   other sequences; artificial sequences. 
+XX
+RN   [1]
+RP   1-51
+RA   ;
+RT   ;
+RL   Patent number WO8403712-A/4, 27-SEP-1984.
+XX
+DR   EMBL; A04195.
+XX
+FH   Key                 Location/Qualifiers 
+FH   
+FT   L-REGION            10..51
+FT                       /partial
+FT                       /organism="Artificial sequence"
+FT                       /product="Ig Lambda"
+FT                       /translation="MQAVMTQESALTTS"
+FT   INIT-CODON          10..12
+XX
+SQ   Sequence 51 BP; 15 A; 13 C; 10 G; 13 T; 0 other;
+     gattgatcaa tgcaggctgt tatgactcag gaatctgcac tcaccacatc a                 51
+//

Tests/output/test_SeqIO

@@ -1829,6 +1829,29 @@ Testing reading embl format file EMBL/Human_contigs.embl
  Checking can write/read as 'genbank' format
  Checking can write/read as 'qual' format
  Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL954800.2).
+Testing reading embl format file EMBL/A04195_bad_indent.embl
+ ID and Name='A04195',
+ Seq='GATTGATCAATGCAGGCTGTTATGACTCAGGAATCTGCAC...CACATCA', length=51
+ 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 'embl' format
+ Checking can write/read as 'fastq' format
+ Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
+ Checking can write/read as 'fastq-illumina' format
+ Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
+ Checking can write/read as 'fastq-solexa' format
+ Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
+ Checking can write/read as 'genbank' format
+ Checking can write/read as 'phd' format
+ Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
+ Checking can write/read as 'qual' format
+ Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
+ 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
 Testing reading stockholm format file Stockholm/simple.sth
  ID and Name='AP001509.1',
  Seq='UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAU...UUAAUGU', length=104

Tests/test_SeqIO.py

@@ -139,6 +139,7 @@ def send_warnings_to_stdout(message, category, filename, lineno,
     ("embl",   False, 'EMBL/AAA03323.embl', 1), # 2008, PA line but no AC
     ("embl",   False, 'EMBL/AE017046.embl', 1), #See also NC_005816.gb
     ("embl",   False, 'EMBL/Human_contigs.embl', 2), #contigs, no sequences
+    ("embl",   False, 'EMBL/A04195_bad_indent.embl', 1), # features over indented
     ("stockholm", True,  'Stockholm/simple.sth', 2),
     ("stockholm", True,  'Stockholm/funny.sth', 5),
 #Following PHYLIP files are currently only used here and in test_AlignIO.py,