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Added sequential Phylip test cases and updated test_AlignIO.py accord…

…ingly
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1 parent ec546dd commit 243085e2bb4b1ee4a20a0718829491ef1af1da20 @brandoninvergo brandoninvergo committed with peterjc Nov 2, 2011
Showing with 32 additions and 0 deletions.
  1. +22 −0 Tests/Phylip/sequential.phy
  2. +5 −0 Tests/Phylip/sequential2.phy
  3. +5 −0 Tests/test_AlignIO.py
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22 Tests/Phylip/sequential.phy
@@ -0,0 +1,22 @@
+ 3 384
+CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---- --------SQ
+ FLEFQDKFNK KY-SHEEYLE RFEIFKSNLG KIEELNLIAI NHKADTKFGV NKFADLSSDE
+ FKNYYLNNKE AIFTDDLPVA DYLDDEFINS IPTAFDWRTR G-AVTPVKNQ GQCGSCWSFS
+ TTGNVEGQHF ISQNKLVSLS EQNLVDCDHE CMEYEGEEAC DEGCNGGLQP NAYNYIIKNG
+ GIQTESSYPY TAETGTQCNF NSANIGAKIS NFTMIP-KNE TVMAGYIVST GPLAIAADAV
+ E-WQFYIGGV F-DIPCN--P NSLDHGILIV GYSAKNTIFR KNMPYWIVKN SWGADWGEQG
+ YIYLRRGKNT CGVSNFVSTS II--
+ALEU_HORVU MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG ALGRTRHALR
+ FARFAVRYGK SYESAAEVRR RFRIFSESLE EVRSTN---- RKGLPYRLGI NRFSDMSWEE
+ FQATRL-GAA QTCSATLAGN HLMRDA--AA LPETKDWRED G-IVSPVKNQ AHCGSCWTFS
+ TTGALEAAYT QATGKNISLS EQQLVDCAGG FNNF------ --GCNGGLPS QAFEYIKYNG
+ GIDTEESYPY KGVNGV-CHY KAENAAVQVL DSVNITLNAE DELKNAVGLV RPVSVAFQVI
+ DGFRQYKSGV YTSDHCGTTP DDVNHAVLAV GYGVENGV-- ---PYWLIKN SWGADWGDNG
+ YFKMEMGKNM CAIATCASYP VVAA
+CATH_HUMAN ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK---- --------FH
+ FKSWMSKHRK TY-STEEYHH RLQTFASNWR KINAHN---- NGNHTFKMAL NQFSDMSFAE
+ IKHKYLWSEP QNCSAT--KS NYLRGT--GP YPPSVDWRKK GNFVSPVKNQ GACGSCWTFS
+ TTGALESAIA IATGKMLSLA EQQLVDCAQD FNNY------ --GCQGGLPS QAFEYILYNK
+ GIMGEDTYPY QGKDGY-CKF QPGKAIGFVK DVANITIYDE EAMVEAVALY NPVSFAFEVT
+ QDFMMYRTGI YSSTSCHKTP DKVNHAVLAV GYGEKNGI-- ---PYWIVKN SWGPQWGMNG
+ YFLIERGKNM CGLAACASYP IPLV
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5 Tests/Phylip/sequential2.phy
@@ -0,0 +1,5 @@
+ 4 131
+IXI_234 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE
+IXI_235 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE
+IXI_236 TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--GSRPPRFAPPLMSSCITSTTGPPPPAGDRSHE
+IXI_237 TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQATGGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--GSRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE
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5 Tests/test_AlignIO.py
@@ -46,6 +46,8 @@
("phylip", 3, 1, 'Phylip/interlaced.phy'),
("phylip", 4, 1, 'Phylip/interlaced2.phy'),
("phylip-relaxed", 12, 1, 'ExtendedPhylip/primates.phyx'),
+ ("phylip-sequential", 3, 1, 'Phylip/sequential.phy'),
+ ("phylip-sequential", 4, 1, 'Phylip/sequential.phy'),
("emboss", 4, 1, 'Emboss/alignret.txt'),
("emboss", 2, 5, 'Emboss/needle.txt'),
("emboss", 2, 1, 'Emboss/needle_asis.txt'),
@@ -177,6 +179,9 @@ def simple_alignment_comparison(alignments, alignments2, format):
assert r1.id.replace("[","").replace("]","")[:10] == r2.id, \
"'%s' vs '%s'" % (r1.id, r2.id)
elif format=="phylip-relaxed":
+ assert r1.id.replace("[","").replace("]","")[:10] == r2.id, \
+ "'%s' vs '%s'" % (r1.id, r2.id)
+ elif format=="phylip-relaxed":
assert r1.id.replace(" ", "").replace(':', '|') == r2.id, \
"'%s' vs '%s'" % (r1.id, r2.id)
elif format=="clustal":

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