diff --git a/lib/galaxy/datatypes/phylip.py b/lib/galaxy/datatypes/phylip.py index ed18d779d7c..5d05461363a 100644 --- a/lib/galaxy/datatypes/phylip.py +++ b/lib/galaxy/datatypes/phylip.py @@ -51,6 +51,14 @@ class Phylip(Text): """ All Phylip files starts with the number of sequences so we can use this to count the following number of sequences in the first 'stack' + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname('test.phylip') + >>> Phylip().sniff(fname) + True + >>> fname = get_test_fname('sequence.fasta') + >>> Phylip().sniff(fname) + False """ with open(filename, "r") as f: # Get number of sequence from first line diff --git a/lib/galaxy/datatypes/test/test.phylip b/lib/galaxy/datatypes/test/test.phylip new file mode 100644 index 00000000000..b3f413e5ad3 --- /dev/null +++ b/lib/galaxy/datatypes/test/test.phylip @@ -0,0 +1,30 @@ + 9 144 +OM-RGC.v1.012162940 ---------- ---------- RVFERFGLAP MDKPFDPITT FDYD-SRQVF IQ-----TDA +FELIC KMKIL-I--- -CYGFIIRRL IVNERFGRTS MDKPNDTIES FSME-KEDVF PQLFPKVLDA +OM-RGC.v1.010553481 MKKIFLL--- -NDGITIREI SIIEVFAKRK LNKPFDTIEP FSE--TQKVR PAVRKNGNSS +OM-RGC.v1.001504500 YLKLFLLNHP TFSGIQYPF- NDRRTSQTRQ FNSPFDKYAD STFEMTDRFW TFTRKTLEEF +OM-RGC.v1.012274392 ---------- ----IQYPF- NNRRTSQTRQ FNSPFDKYAD STFEMTDRFW TFTKKTLDEF +OM-RGC.v1.003588026 ------D-QF SWTLIQNESG DSEQEGFVYD FNSPFDKIYD DFYRLENRLF SRSMRDLDYF +OM-RGC.v1.002677074 -----YD-QF SWTDIEYEFG DSSQEGFISD FNSPFDKIYD EFYKLDSRLF SRTMRDLNYF +OM-RGC.v1.012568023 ---------- ---------- ----KGFTSK YNAPFDNIID LSRSLDWFME NWTQWLLEDY +OM-RGC.v1.002130110 --LLR-N--- ----VND--- --LQNVFLKK SDKPFDTAEF QDSDLSLNLY ---QPELTIH + + SFRAEW---- -NQISGTTK- -DTYPVVSLI AIASFLESSV SDQASFTVLT IVAFNLVADK + S-YEEWDKKD YNHLSANKK- -ESFSRAIWF GVVSFV--DF ANQNSFTLMT MVTFNFTSSL + VDI--WKFKV E--------- -DR------- ----ILAPGS KN-------S LMT------- + MDDSGWKY-- ERDTVDVPGQ YDA---LHFI ILSCVVDPEL EARTTIVCLS LIAYNVIDAE + MDDSGWKY-- ERDTVDVPGQ YDA---LHFI ILSCVVDPEL EARTTIVCLS LIAYNVIDAE + VKKVGWNA-- EQDPNRATA- -SA---IHFI ILMCVVDPEL ESRTTIVCLS LIAYNVIDSE + LKKNGWDA-- KQDPNRSSE- -SA---IHFI ILMCVVDPEL ESRTTIVCLS LIAYNVIDSE + AGEIEWDA-- YKDPVYLSQ- -IG---IFFI ILLCFIHPEL ESKTTIICLS LIAYNVIDED + KEIYEWD--- HTEIYGQGS- -QT---IFLI IVWSFIRAEL ESKASMGSLT LVAYNVFGDD + + PAFALMFLSV ASSSI-DTRF PLAF + TPFIISSL-L TYSV--NFQF PLLI + ---------- ---------- ---- + KEVWVIYVPF FRK-L-EIKG LSSN + KEVWVIYVPF FRK-L-EIKG LSS- + KEVWVIYVPF FRK-I-EIKG LSSN + KE-------- ---------- ---- + KSIYILFVPF YQM-V-DKRG PILN + KNIAILFLSV YFLTINDKRV PGLL