diff --git a/Tests/Stockholm/funny.sth b/Tests/Stockholm/funny.sth index 559b9ba39d3..e9afaf86090 100644 --- a/Tests/Stockholm/funny.sth +++ b/Tests/Stockholm/funny.sth @@ -11,16 +11,17 @@ #=GS O83071/259-312 AC O83071 #=GS O31698/88-139 AC O31698 #=GS O31698/88-139 OS Bacillus subtilis -O83071/192-246 MTCRAQLIAVPRASSLAE..AIACAQKM....RVSRVPVYERS -#=GR O83071/192-246 SA 999887756453524252..55152525....36463774777 -O83071/259-312 MQHVSAPVFVFECTRLAY..VQHKLRAH....SRAVAIVLDEY -#=GR O83071/259-312 SS CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEE -O31698/18-71 MIEADKVAHVQVGNNLEH..ALLVLTKT....GYTAIPVLDPS -#=GR O31698/18-71 SS CCCHHHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEHHH -O31698/88-139 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE -#=GR O31698/88-139 SS CCCCCCCHHHHHHHHHHH..HEEEEEEE....EEEEEEEEEEH -#=GC SS_cons CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEH -O31699/88-139 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE -#=GR O31699/88-139 AS ________________*__________________________ -#=GR_O31699/88-139_IN ____________1______________2__________0____ -// \ No newline at end of file +O83071/192-246 MTCRAQLIAVPRASSLAE..AIACAQKM....RVSRVPVYERS +#=GR O83071/192-246 SA 999887756453524252..55152525....36463774777 +O83071/259-312 MQHVSAPVFVFECTRLAY..VQHKLRAH....SRAVAIVLDEY +#=GR O83071/259-312 SS CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEE +O31698/18-71 MIEADKVAHVQVGNNLEH..ALLVLTKT....GYTAIPVLDPS +#=GR O31698/18-71 SS CCCHHHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEHHH +O31698/88-139 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE +#=GR O31698/88-139 SS CCCCCCCHHHHHHHHHHH..HEEEEEEE....EEEEEEEEEEH +#=GC SS_cons CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEH +O31699/88-139 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE +#=GR O31699/88-139 AS ________________*__________________________ +#=GR_O31699/88-139_IN ____________1______________2__________0____ +363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE +// diff --git a/Tests/output/test_AlignIO b/Tests/output/test_AlignIO index 093f4a74b46..88ca28ba657 100644 --- a/Tests/output/test_AlignIO +++ b/Tests/output/test_AlignIO @@ -149,14 +149,14 @@ Testing reading stockholm format file Stockholm/simple.sth with 1 alignments Checking can write/read as 'fasta' format Checking can write/read as 'tab' format Testing reading stockholm format file Stockholm/funny.sth with 1 alignments - Alignment 0, with 5 sequences of length 43 - MMMEE alignment column 0 - TQIVV alignment column 1 - CHEMM alignment column 2 - RVALL alignment column 3 - ASDTT alignment column 4 - ||||| ... - SYSEE alignment column 42 + Alignment 0, with 6 sequences of length 43 + MMMEEE alignment column 0 + TQIVVV alignment column 1 + CHEMMM alignment column 2 + RVALLL alignment column 3 + ASDTTT alignment column 4 + |||||| ... + SYSEEE alignment column 42 Checking can write/read as 'clustal' format Checking can write/read as 'nexus' format Failed: Need a DNA, RNA or Protein alphabet diff --git a/Tests/output/test_SeqIO b/Tests/output/test_SeqIO index f7027c9ce86..a2e2ffc218e 100644 --- a/Tests/output/test_SeqIO +++ b/Tests/output/test_SeqIO @@ -2512,16 +2512,16 @@ Testing reading stockholm format file Stockholm/funny.sth ID = 'O31698/18-71', Name='O31698', Seq='MIEADKVAHVQVGNNLEH--ALLVLTKT----GYTAIPVLDPS', length=43 ... - ID = 'O31699/88-139', Name='O31699', + ID and Name='363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00', Seq='EVMLTDIPRLHINDPIMK--GFGMVINN------GFVCVENDE', length=43 Testing reading stockholm format file Stockholm/funny.sth as an alignment - MMMEE alignment column 0 - TQIVV alignment column 1 - CHEMM alignment column 2 - RVALL alignment column 3 - ASDTT alignment column 4 - ||||| ... - SYSEE alignment column 42 + MMMEEE alignment column 0 + TQIVVV alignment column 1 + CHEMMM alignment column 2 + RVALLL alignment column 3 + ASDTTT alignment column 4 + |||||| ... + SYSEEE alignment column 42 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format @@ -2530,19 +2530,19 @@ Testing reading stockholm format file Stockholm/funny.sth as an alignment 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=O31699/88-139). + Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00). Checking can write/read as 'fastq-illumina' format - Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O31699/88-139). + Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00). Checking can write/read as 'fastq-solexa' format - Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O31699/88-139). + Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00). Checking can write/read as 'genbank' format - Failed: Need a Nucleotide or Protein alphabet + Failed: Locus identifier '363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00' is too long 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=O31699/88-139). + Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00). Checking can write/read as 'qual' format - Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O31699/88-139). + Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00). Checking can write/read as 'seqxml' format Failed: Need a DNA, RNA or Protein alphabet Checking can write/read as 'sff' format diff --git a/Tests/test_AlignIO.py b/Tests/test_AlignIO.py index 01878c74a57..e926b616a00 100644 --- a/Tests/test_AlignIO.py +++ b/Tests/test_AlignIO.py @@ -37,7 +37,7 @@ #Following example is also used in test_Nexus.py ("nexus", 9, 1, 'Nexus/test_Nexus_input.nex'), ("stockholm", 2, 1, 'Stockholm/simple.sth'), - ("stockholm", 5, 1, 'Stockholm/funny.sth'), + ("stockholm", 6, 1, 'Stockholm/funny.sth'), ("phylip", 6, 1, 'Phylip/reference_dna.phy'), ("phylip", 6, 1, 'Phylip/reference_dna2.phy'), ("phylip",10, 1, 'Phylip/hennigian.phy'), diff --git a/Tests/test_SeqIO.py b/Tests/test_SeqIO.py index 06d4c10e059..7a112783a6d 100644 --- a/Tests/test_SeqIO.py +++ b/Tests/test_SeqIO.py @@ -158,7 +158,7 @@ def send_warnings_to_stdout(message, category, filename, lineno, ("embl", False, 'EMBL/A04195.imgt', 1), # features over indented for EMBL ("imgt", False, 'EMBL/A04195.imgt', 1), # features over indented for EMBL ("stockholm", True, 'Stockholm/simple.sth', 2), - ("stockholm", True, 'Stockholm/funny.sth', 5), + ("stockholm", True, 'Stockholm/funny.sth', 6), #Following PHYLIP files are currently only used here and in test_AlignIO.py, #and are mostly from Joseph Felsenstein's PHYLIP v3.6 documentation: ("phylip", True, 'Phylip/reference_dna.phy', 6),