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Fixing Bio.Clustalw when parsing non-standard header lines, and addin…

…g a test case from PROMALS3D (Bug 2564)
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1 parent a2cd967 commit d33cf1af5568e87eb5859a9ce264a9d9cbd6b60e @peterjc peterjc committed Aug 7, 2008
Showing with 167 additions and 14 deletions.
  1. +14 −14 Bio/Clustalw/__init__.py
  2. +135 −0 Tests/Clustalw/promals3d.aln
  3. +17 −0 Tests/output/test_AlignIO
  4. +1 −0 Tests/test_AlignIO.py
@@ -39,6 +39,8 @@ def parse_file(file_name, alphabet = IUPAC.unambiguous_dna, debug_level = 0):
Defaults to be unambiguous_dna sequence.
There is a deprecated optional argument debug_level which has no effect.
+
+ Since Biopython 1.46, this has called Bio.AlignIO internally.
"""
# Avoid code duplication by calling Bio.AlignIO to do this for us.
@@ -56,8 +58,18 @@ def parse_file(file_name, alphabet = IUPAC.unambiguous_dna, debug_level = 0):
clustal_alignment._records = generic_alignment._records
for record in clustal_alignment._records :
record.seq.alphabet = alpha
- clustal_alignment._version = generic_alignment._version
- clustal_alignment._star_info = generic_alignment._star_info
+
+ try :
+ clustal_alignment._version = generic_alignment._version
+ except AttributeError :
+ #Missing the version, could be a 3rd party tool's output
+ pass
+
+ try :
+ clustal_alignment._star_info = generic_alignment._star_info
+ except AttributeError :
+ #Missing the consensus, again, this is not always present
+ pass
return clustal_alignment
@@ -156,18 +168,6 @@ def __str__(self):
handle.seek(0)
return handle.read()
-
- def _add_star_info(self, stars):
- """Add all of the stars, which indicate consensus sequence.
- """
- self._star_info = stars
-
- def _add_version(self, version):
- """Add the version information about the clustal file being read.
- """
- self._version = version
-
-
class MultipleAlignCL:
"""Represent a clustalw multiple alignment command line.
@@ -0,0 +1,135 @@
+CLUSTAL format multiple sequence alignment by PROMALS3D
+
+
+gi_13925890_gb_AAK49457.1 M------VTVEEFRRAQCAEGPATVMAIGTATPSNCVDQSTYPDYYFRITNSEHKVELKEKFKRMCEKSM
+gi_13936399_dbj_BAB47196. M---SSSITVDQIRKAQRAEGPATILAIGTATPANFIIQADYPDYYFRVTKSEHMTNLKKRFQRICDRTM
+gi_13936397_dbj_BAB47195. M----TSMTVDQIRRPLRAEGLATILAIGTANPANYITQADYPDYYFRVTKSEHMTDLKNKFQRMCDRSM
+gi_13936395_dbj_BAB47194. M----TSMTVDQIRRPLRAEGLATILAIGTANPANYITQADYPDYYFRVTKSEHMTDLKNKFQRMCDRSM
+gi_12644514_sp_Q9MB41_CHS M------VTVEEVRKAQRAEGPATILAIGTVTPANCVNQSTYPDYYFRITNSEHKTELKEKFQRMCDKSM
+gi_12644512_sp_Q9MB39_CHS M------VTVEEVRKAQRAEGPATILAIGTVTPANCVNQSTYPDYYFRITNSEHKTELKERFQRMCDKSM
+gi_12644509_sp_Q9MB36_CHS M------VTVEEVRKAQRAEGPATILAIGTVTPANCVNQSTYPDYYFRITNSEHKTELKEKFQRMCDKSM
+gi_12644511_sp_Q9MB38_CHS M------VTVEEVRKAQRAEGPATILAIGTATPANCVNQSTYPDYYFRITNSEHKTELKEKFQRMCDKSM
+gi_12644510_sp_Q9MB37_CHS M------VTVEEVRKAKRAEGPATILAIGTATPANCVNQSTYPDYYFRITNSEHKTELKEKFQRMCDKSM
+gi_12644513_sp_Q9MB40_CHS M------VTVGEVRKAQRAEGPATILAIGTATPANCVNQSTYPDYYFRITNSEHKTELKEKFQRMCDKSM
+gi_13774969_gb_AAK39112.1 M------VTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPDYYFRITNSDHMTDLKQKFQRMCDKSM
+gi_13774971_gb_AAK39113.1 M------VTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPDYYFRITKSDHMTDLKQKFQRMCDKSM
+gi_13774967_gb_AAK39111.1 M------VTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPDYYFRITKSDHMTDLKQKFQRMCDKSM
+gi_13774975_gb_AAK39115.1 M------VTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPDYYFRITKSDHMTDLKQKFQRMCDKSM
+gi_13774965_gb_AAK39110.1 M------VTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPDYYFRITKSDHMTDLKQKFQRMCDKSM
+gi_13774973_gb_AAK39114.1 M------VTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPDYYFRITKSDHMTDLKQKFQRMCDKSM
+gi_14150838_gb_AAK54648.1 ----------------------------------------------------------------------
+gi_12644515_sp_Q9MBB1_CHS MTVLEESADASSRRLAQRANGPATVLAIGTANPANVFEQSSYPDFYFDITNSQHMTELKLKFSRMCQKSG
+gi_13919613_gb_AAK33142.1 -----------------------------------------YPDYYFRITNREHKAELKEKFQRMCDKSM
+gi_13919597_gb_AAK33134.1 -----------------------------------------YPDYYFRITNSEHKAELKEKFQRMCDKSM
+
+
+gi_13925890_gb_AAK49457.1 IKKRYMHLTEEILKENPNICAYMAPSLDARQDIVVVEVPKLGKEAAQKAIKEWGQPKSKITHLVFCTTSG
+gi_13936399_dbj_BAB47196. IKKRHLVLSEDHLKENPNMCEFMAPSLDVRQDILVVEVPKLGKEACMKAIKEWDQPKSKITHFIFATTSG
+gi_13936397_dbj_BAB47195. IKKRHMYFTEEHLKQNPNMCDYTAPSLDARQSILVVEVPKLGKEACIKAIKEWNQPKSKITHFIFTTISG
+gi_13936395_dbj_BAB47194. IKKRHMYFTEEHLKQNPNMCDYTAPSLDARQSILVVEVPKLGKEACIKAIKEWNQPKSKITHFIFTTISG
+gi_12644514_sp_Q9MB41_CHS ITKRYMHLTEEILKENPSFCEYMAPSLDARQDIAVVEVPKLGKEAAQSAIKEWGQPKSKITHVVFCTTSG
+gi_12644512_sp_Q9MB39_CHS ITKRYMHLTEEILKENPSFCEYMAPSLDARQDIAVVEVPKLGKEAAQSAIKEWGQPKSKITHVVFCTTSG
+gi_12644509_sp_Q9MB36_CHS ITKRYMHLTEEILKENPSFCEYMAPSLDARQDIAVVEVPKLGKEAAQSAIKEWGQPKSKITHVVFCTTSG
+gi_12644511_sp_Q9MB38_CHS ITKRYMHLTEEILKENPSFCEYMAPSLDARQDIAVVEVPKLGKEAAQSAIKEWGQPKSKITHVVFCTTSG
+gi_12644510_sp_Q9MB37_CHS ITKRYMHLTEEILKENPSFCEYMAPSLDARQDIAVVEVPKLGKEAAQSAIKEWGQPKSKITHVFFCTTSG
+gi_12644513_sp_Q9MB40_CHS ITKRYMHLTEEILKENPSFCEYMAPSLDARQDIAVVEVPKLGKEAAQSAIKGWGQPKSKITHVVFCTTSG
+gi_13774969_gb_AAK39112.1 ITKRYMHLTEEILKENPSFCEYMAPSLDARQDIVVVEVPKLGKEAAQSAIKEWGQPKSKITHVIFCTTSG
+gi_13774971_gb_AAK39113.1 ITKRYMHLTEEILKENPSFCEYMAPSLDARQDIVVVEVPKLGKEAAQSAIKEWGQPKSKITHVIFCTTSG
+gi_13774967_gb_AAK39111.1 ITKRYMHLTEEILKENPSFCEYMAPSLDARQDIVVVEVPKLGKEAAQSAIKEWGQPKSKITHVIFCTTSG
+gi_13774975_gb_AAK39115.1 ITKRYMHLTEEILKENPSFCEYMAPSLDARQDIVVVEVPKLGKEAAQSAIKEWGQPKSKITHVIFCTTSG
+gi_13774965_gb_AAK39110.1 ITKRYMHLTEEILKENPSFCEYMAPSLDARQDIVVVEVPKLGKEAAQSAIKEWGQPKSKITHVIFCTTSG
+gi_13774973_gb_AAK39114.1 ITKRYMHLTEEILKENPSFCEYMAPSLDARQDIVVVEVPKLGKEAAQSAIKEWGQPKSKITHVIFCTTSG
+gi_14150838_gb_AAK54648.1 ----------------------------------------------------------------------
+gi_12644515_sp_Q9MBB1_CHS IKKRYMHLNSEILKANPSLCAYWEKSLDVRQDIAVVEVPKLGKEASLKAIKEWGQPKSKITHLVFCTTSG
+gi_13919613_gb_AAK33142.1 IKKRYMYLTEEILKENPSMCEYMAPSLDARQDMVVVEIPKLGKEAAVKAIKEWGQ---------------
+gi_13919597_gb_AAK33134.1 IKKRYMYLTEEILKENPSMCEYMAPSLDARQDMVVVEIPKLGKEAAVKAIKEWGQ---------------
+
+
+gi_13925890_gb_AAK49457.1 VDMPGCDYQLTKLLGLRPSVKRFMMYQQGCFAGGTVLRMAKDLAENNKGARVLVVCSEITAVTFRGPNDT
+gi_13936399_dbj_BAB47196. VDMPGADYQCAKLLGLSSSVKRVMMYQQGCFAGGTVLRIAKDIAENNKGARVLALCSEITTCMFHGPTES
+gi_13936397_dbj_BAB47195. IDMPGADYQCSKLLGLNPSVKRVMLYNLGCHASGTILRMAKDIAENNKGARVLAVCSDIMTGHFRGPAES
+gi_13936395_dbj_BAB47194. IDMPGADYQCSKLLGLNPSVKRVMLYNLGCHASGTILRMAKDIAENNKGARVLAVCSDIMTGHFRGPAES
+gi_12644514_sp_Q9MB41_CHS VDMPGADYQLTKLLGLSPSVKRLMMYQQGCFAGGTVLRLAKDLAENNKGARVLIVCSEITVVTFRGPSET
+gi_12644512_sp_Q9MB39_CHS VDMPGADYQLTKLLGLRPSVKRLMMYQQGCFAGGTVLRLAKDLAENNKGARVLIVCSEITVVTFRGPSET
+gi_12644509_sp_Q9MB36_CHS IDMPGADYQLTKLLGLRPSVKRLMMYQQGCFAGGTVLRLAKDLAENNKGARVLIVCSEITVVTFRGPSET
+gi_12644511_sp_Q9MB38_CHS VDMPGADYQLTKLLGLRPSVKRLMMYQQGCFAGGTVLRLAKDLAENNKGARVLIVCSEITVVTFRGPSET
+gi_12644510_sp_Q9MB37_CHS VDMPGADYQLTKLLGLRPSVKRLMMYQQGCFAGGTVLRLAKDLAENNKGARVLIVCSEITVVTFRGPSET
+gi_12644513_sp_Q9MB40_CHS VDMPGADYQLTKLLGLRPSVKRLMMYQQGCFAGGTVLRLAKDLAENNKGARVLIVCSEITVVTFRGPSEA
+gi_13774969_gb_AAK39112.1 VDMPGADYQLTKLLGLRPSVKRLMMYQQGCFAGGTVLRVAKDLAENNKGARVLVVCSEITVVTFRGPNET
+gi_13774971_gb_AAK39113.1 VDMPGADYQLTKLLGLRPSVKRLMMYQQGLFAGGTVLRVAKDLAENNKGARVLVVCSEITVVTFRGPNET
+gi_13774967_gb_AAK39111.1 VDMPGADYQLTKLLGLRPSVKRLMMYQQGCFAGGTVLRVAKDLAENNKGARVLVVCSEITVVTFRGPNET
+gi_13774975_gb_AAK39115.1 VDMPGADYQLTKLLGLRPSVKRLMMYQQGCFAGGTVLRVAKDLAENNKGARVLVVCSEITVVTFRGPNET
+gi_13774965_gb_AAK39110.1 VDMPGADYQLTKLLGLRPSVKRLMMYQQGCFAGGTVLRVAKDLVENNKGARVLVVCSEITVVTFRGPNET
+gi_13774973_gb_AAK39114.1 VDMPGADYQLTKLLGLRPSVKRLMMYQQGCFAGGTVLRVAKDLAENNKGARVLVVCSEITVVTFRGPNET
+gi_14150838_gb_AAK54648.1 -----------------------MMYQQGCFAGGTVLRLAKDLAENNRGARVLVVCSEITAVTFRGPSET
+gi_12644515_sp_Q9MBB1_CHS VDMPGADWALTKLLGLRPSVKRLMMYQQGCFAGGTVLRVAKDVAENNKGARVLVVCSEITCVTFRGPSET
+gi_13919613_gb_AAK33142.1 ----------------------------------------------------------------------
+gi_13919597_gb_AAK33134.1 ----------------------------------------------------------------------
+
+
+gi_13925890_gb_AAK49457.1 HLDSLVGQALFGDGAAAVIIGSDPIPEV-ERPLFELVSAAQTLLPDSEGAIDGHLREVGLTFHLLKDVPG
+gi_13936399_dbj_BAB47196. HLDSMVGQALFGDGASAVIVGAEPDESAGERPIYELVSAAQTILPNSEGAIDGHLMETRLTFHLLKDVPG
+gi_13936397_dbj_BAB47195. HLDSMIGQALFGDGASAIIVGAEPDESAGEQPIFELVSTAQTTLPDSDGVARGHLKEAGVVIHLHQSLPG
+gi_13936395_dbj_BAB47194. HLDSMIGQALFGDGASAIIVGAEPDESAGEQPIFELVSTAQTTLPDSDGVARGHLKEAGVVIHLHQSLPG
+gi_12644514_sp_Q9MB41_CHS HLDSLVGQALFGDGAAAVIVGADPTPA--EKPLFQLVSAAQTLAPDSCGAIDGHLREVGLTFHLLKDVPS
+gi_12644512_sp_Q9MB39_CHS HLDSLVGQALFGDGAAAVIVGADPTPA--EKPLFQLVSAAQNLAPDSCGAIDGHLREVGLTFHLLKDVPS
+gi_12644509_sp_Q9MB36_CHS HLDSLVGQALFGDGAAAVIVGADPTPA--EKPLFQLVSAAQTLAPNSCGAIDGHLREVGLTFHLLKDVPS
+gi_12644511_sp_Q9MB38_CHS HLDSLVGQALFGDGAAAVIVGADPTPA--EKPLFQLVSAAQTLAPNSCGAIDGHLREVGLTFHLLKDVPS
+gi_12644510_sp_Q9MB37_CHS HLDSLVGQALFGDGAAAVIVGADPTPA--EKPLFQLVSAAQTLAPDSCGAIDGHLREVGLTFHLLKDVPS
+gi_12644513_sp_Q9MB40_CHS HLDSLVGQALFGDGAAAVIVGADPTPA--EKPLFQLVSAAQTLAPDSCGAIDGHLREVGLTFHLLKDVPS
+gi_13774969_gb_AAK39112.1 HLDSLVGQALFGDGAAAIIVGSDPTPV--EKPLFQLVSAAQTLAPDSCGAIDGHLREVGLTFHLLKDVPS
+gi_13774971_gb_AAK39113.1 HLDSLVGQALFGDGAAAIIVGSDPTPV--EKALFQLVSAAQTLAPDSCGAIDGHLREVGLTFHLLKDVPS
+gi_13774967_gb_AAK39111.1 HLDSLVGQALFGDGAAAIIVGSDPTPV--EKPLFQLVSAAQTLAPDSCGAIDGHLREVGLTFHLLKDVPS
+gi_13774975_gb_AAK39115.1 HLDSLVGQALFGDGAAAIIVGSDPTPV--EKPLFQLVSAAQTLAPDSCGAIDGHLREVGLTFHLLKDVPS
+gi_13774965_gb_AAK39110.1 HLDSLVGQALFGDGAAAIIVGSDPTPV--EEPLFQLVSAAQTLAPDSCGAIDGHLREVGLTFHLLKDVPS
+gi_13774973_gb_AAK39114.1 HLDSLVGQALFGDGAAAIIVGSDPTPV--EKPLFQLVSAAQTLAPDSCGAIDGHLREVGLTFHLLKDVPS
+gi_14150838_gb_AAK54648.1 HLDSMVGQALFGDGAGAVIVGSDPDLSV-ERPLYELVWTGATLLPDSEGAIDGHLREVGLTFHLLKDVPG
+gi_12644515_sp_Q9MBB1_CHS HLDSLVGQALFGDGAAAVILGSDPLPE--ENPCFELHWSGSNILPDSDGAIDGHLREVGLTFHLMKDVPG
+gi_13919613_gb_AAK33142.1 ----------------------------------------------------------------------
+gi_13919597_gb_AAK33134.1 ----------------------------------------------------------------------
+
+
+gi_13925890_gb_AAK49457.1 LISKNIEKSLVEAF------------QPLGISDWNSLFWIAHPGGPAILDQVELKLGLKQEKLKATRKVL
+gi_13936399_dbj_BAB47196. LISNNIEKSLIEAF------------TPIGINDWNSIFWVTHPGGPAILDEVEAKLELKKEKLAISRHVL
+gi_13936397_dbj_BAB47195. LISTNIEKSLTEAF------------APIGISDWNSIFWITHPAGRAVLEEIEAKLQLKNEKLADSRHVL
+gi_13936395_dbj_BAB47194. LISTNIEKSLTEAF------------APIGISDWNSIFWITHPAGRAVLEEIEAKLQLKNEKLADSRHVL
+gi_12644514_sp_Q9MB41_CHS VVSNNIEKCLFEAF------------NPLGISDWNSVFWIAHPGGPAILDQVEDKLGLKPEKLRATRHVL
+gi_12644512_sp_Q9MB39_CHS VVSNNIEKCLFEAF------------NPLGISDWNSVFWIAHPGGPAILDQVEDKLGLKPEKLRATRHVL
+gi_12644509_sp_Q9MB36_CHS VVSNNIEKCLFEAF------------NPLGISDWNSVFWIAHPGGPAILDQVEDKLGLKPEKLRATRHVL
+gi_12644511_sp_Q9MB38_CHS VVSNNIEKCLFEAF------------NPLGISDWNSVFWIAHPGGPAILDQVEDKLGLKPEKLRATRHVL
+gi_12644510_sp_Q9MB37_CHS VVSNNIEKCLFEAF------------NPLGISDWNSVFWIAHPGGPAILDQVEDKLGLKPEKLRATRHVL
+gi_12644513_sp_Q9MB40_CHS VVSNNIEKCLFEAF------------NPLGISDWNSVFWIAHPGGPAILDQVEDKLGLKPEKLRATRHVL
+gi_13774969_gb_AAK39112.1 IVSNNIEKCLSEAF------------NPLGISDWNSIFWIAHPGGPAILDQVEDKLGLKPEKLRATRHVL
+gi_13774971_gb_AAK39113.1 IVSNNIEKCLSEAF------------NPLGISDWNSIFWIAHPGGPAILDQVEDKLGLKPEKLRATRHVL
+gi_13774967_gb_AAK39111.1 IVSNNIEKCLSEAF------------NPLGISDWNSIFWIAHPGGPAILDQVEDKLGLKPEKLRATRHVL
+gi_13774975_gb_AAK39115.1 IVSNNIEKCLSEAF------------NPLGISDWNSIFWIAHPGGPAILDQVEDKLGLKPEKLRATRHVL
+gi_13774965_gb_AAK39110.1 IVSNNIEKCLSEAF------------NPLGISDWNSIFWIAHPGGPAILDQVEDKLGLKPEKLRATRHVL
+gi_13774973_gb_AAK39114.1 IVSNNIEKCLSEAF------------NPLGISDWNSIFWIAHPGGPAILDQVEDKLGLKPEKLRATRHVL
+gi_14150838_gb_AAK54648.1 LISKNIEKSLKEAF------------TPLGISDWNSTFWIAHPGGPAILDQVEAKLGLKEEKMRATREVL
+gi_12644515_sp_Q9MBB1_CHS IISKNIGKVLNDAFRSAFDESGNAEDRPASVND---IFWIAHPGGPAILDQVEEKMKLAPEKMRATRDVL
+gi_13919613_gb_AAK33142.1 ----------------------------------------------------------------------
+gi_13919597_gb_AAK33134.1 ----------------------------------------------------------------------
+
+
+gi_13925890_gb_AAK49457.1 SNYGNMSSACVLFILDEMRKASAKEGLGTTGEGLEWGVLFGFGPGLTVETVVLHSVAT------
+gi_13936399_dbj_BAB47196. SEYGNMSSASVFFVMDELRKRSLEEGKSTTGDGLDWGVLFGFGPGLTVEMVVLHSVENKVKSET
+gi_13936397_dbj_BAB47195. SEYGNMSSACVFFIMDKLRKRSLEQRKSTTGDGLEWGVLFGFGPGLTVETVVLHSVANKF----
+gi_13936395_dbj_BAB47194. SEYGNMSSACVFFIMDKLRKRSLEQRKSTTGDGLEWGVLFGFGPGLTVETVVLHSVANKF----
+gi_12644514_sp_Q9MB41_CHS SEYGNMSSACVLFILDEMRKASSNAGLGTTGEGLEWGVLFGFGPGLTIETVVLHSVPIKPGPH-
+gi_12644512_sp_Q9MB39_CHS SEYGNMSSACVLFILDEMRKASSNAGLGTTGEGLEWGVLFGFGPGLTIETVVLHSVPIKPGPH-
+gi_12644509_sp_Q9MB36_CHS SEYGNMSSACVLFILDEMRKASSNAGLGTTGEGLEWGVLFGFGPGLTIETVVLHSVPT------
+gi_12644511_sp_Q9MB38_CHS SEYGNMSSACVLFILDEMRKASSNAGLGTTGEGLEWGVLFGFGPGLTIETVVLHSVLIKPGPH-
+gi_12644510_sp_Q9MB37_CHS SEYGNMSSACVLFILDEMRKASSNAGLGTTGEGLEWGVLFGFGPGLTIETVVLHSVPIKPGPH-
+gi_12644513_sp_Q9MB40_CHS SEYGNMSSACVLFILDEMRKASSNDGLGTTGEGLEWGVLFGFGPGLTIETVVLHSVPT------
+gi_13774969_gb_AAK39112.1 SEYGNMSSACVLFILDEMRKASSNDGLGTTGEGLEWGV--------------------------
+gi_13774971_gb_AAK39113.1 SEYGNMSSACVLFILDEMRKASSNDGLGTTGEGLEWGVLFGFGPGLTIETVVLHSVPA------
+gi_13774967_gb_AAK39111.1 SEYGNMSSACVLFILDEMRKASSNDGLGTTGEGLEWGVLFGFGPGLTIETVVLHSVPA------
+gi_13774975_gb_AAK39115.1 SEYGNMSSACVLFILDEMRKASSNDGLGTTGEGLEWGVLFGFGPGLTIETVVLHSVPA------
+gi_13774965_gb_AAK39110.1 SEYGNMSSACVLFILDEMRKASSNDGLGTTGEGLEWGVLFGFGPGLTIETVVLHSVPA------
+gi_13774973_gb_AAK39114.1 SEYGNMSSACVLFILDEMRKAASNDGLGTTGEGLEWGVLFGLGPGLTIETVALHSVPA------
+gi_14150838_gb_AAK54648.1 SEYGNMSSAC------------------------------------------------------
+gi_12644515_sp_Q9MBB1_CHS SEYGNMSSACVLFIMDHMRRMSAQNKLQTTGEGLDWGVLLGFGPGLTVETVLLKSIRLAC----
+gi_13919613_gb_AAK33142.1 ----------------------------------------------------------------
+gi_13919597_gb_AAK33134.1 ----------------------------------------------------------------
+
+
@@ -71,6 +71,23 @@ Testing reading clustal format file Clustalw/protein.aln with 1 alignments
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
+Testing reading clustal format file Clustalw/promals3d.aln with 1 alignments
+ Alignment 0, with 20 sequences of length 414
+ MMMMMMMMMMMMMMMM-M-- alignment column 0
+ -----------------T-- alignment column 1
+ -----------------V-- alignment column 2
+ -----------------L-- alignment column 3
+ -S---------------E-- alignment column 4
+ |||||||||||||||||||| ...
+ -T------------------ alignment column 413
+ Checking can write/read as 'nexus' format
+ Failed: Need a DNA, RNA or Protein alphabet
+ Checking can write/read as 'phylip' format
+ Failed: Repeated identifier, possibly due to truncation
+ Checking can write/read as 'clustal' format
+ Checking can write/read as 'stockholm' format
+ Checking can write/read as 'fasta' format
+ Checking can write/read as 'tab' format
Testing reading fasta format file GFF/multi.fna with 1 alignments
Alignment 0, with 3 sequences of length 8
ACGTCGCG test1
@@ -28,6 +28,7 @@
("clustal", 5, 1, 'Clustalw/hedgehog.aln'),
("clustal", 2, 1, 'Clustalw/odd_consensus.aln'),
("clustal",20, 1, 'Clustalw/protein.aln'), #Used in the tutorial
+ ("clustal",20, 1, 'Clustalw/promals3d.aln'), #Nonstandard header
#Following examples are also used in test_GFF.py
("fasta", 3, 1, 'GFF/multi.fna'), #Trivial nucleotide alignment
#Following example is also used in test_Nexus.py

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