# HG changeset patch # User peterjc # Date 1422356778 18000 # Node ID b19b6addd05c620c3d0b1f002eb9fffe04a74782 # Parent d0de6862cda19966557ef8f49c4e9fa2d50d41f5 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc diff -r d0de6862cda1 -r b19b6addd05c test-data/blastdb.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastdb.loc Tue Jan 27 06:06:18 2015 -0500 @@ -0,0 +1,7 @@ +# This is a test file distributed with the Galaxy BLAST+ wrapper for +# defining a list of nucleotide BLAST databases used in functional +# tests for blastn etc. +# +# See the file tool-data/blastdb.loc.sample for more information. +# +three_human_mRNA Three Human mRNAs ${__HERE__}/three_human_mRNA.fasta diff -r d0de6862cda1 -r b19b6addd05c test-data/blastdb_d.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastdb_d.loc Tue Jan 27 06:06:18 2015 -0500 @@ -0,0 +1,7 @@ +# This is a test file distributed with the Galaxy BLAST+ wrapper for +# defining a list of protein domain BLAST databases used in functional +# tests of rpsblast etc. +# +# See the file tool-data/blastdb_d.loc.sample for more information. +# +cd00003_and_cd00008 Domains CD00003 (PNPsynthase) and CD00008 (PIN_53EXO-like) ${__HERE__}/cd00003_and_cd00008 diff -r d0de6862cda1 -r b19b6addd05c test-data/blastdb_p.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastdb_p.loc Tue Jan 27 06:06:18 2015 -0500 @@ -0,0 +1,8 @@ +# This is a test file distributed with the Galaxy BLAST+ wrapper for +# defining a list of protein BLAST databases used in functional tests +# for blastp etc. +# +# See the file tool-data/blastdb_p.loc.sample for more information. +# +four_human_proteins Four Human Proteins (no taxid) ${__HERE__}/four_human_proteins.fasta +four_human_proteins_taxid Four Human Proteins (with taxid) ${__HERE__}/four_human_proteins_taxid.fasta diff -r d0de6862cda1 -r b19b6addd05c test-data/blastn_chimera_vs_three_human_max1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_chimera_vs_three_human_max1.tabular Tue Jan 27 06:06:18 2015 -0500 @@ -0,0 +1,1 @@ +chimera ENA|AB011145|AB011145.1 100.00 4560 0 0 1 4560 121 4680 0.0 8421 diff -r d0de6862cda1 -r b19b6addd05c test-data/blastn_chimera_vs_three_human_max1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_chimera_vs_three_human_max1.txt Tue Jan 27 06:06:18 2015 -0500 @@ -0,0 +1,356 @@ +BLASTN 2.2.30+ + + +Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb +Miller (2000), "A greedy algorithm for aligning DNA sequences", J +Comput Biol 2000; 7(1-2):203-14. + + + +Database: Just 3 human mRNA sequences + 3 sequences; 10,732 total letters + + + +Query= chimera chunks of AB011145 plus M10051 plus BC112106 + +Length=9973 + Score E +Sequences producing significant alignments: (Bits) Value + + ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein,... 8421 0.0 + + +> ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, +partial cds. +Length=4796 + + Score = 8421 bits (4560), Expect = 0.0 + Identities = 4560/4560 (100%), Gaps = 0/4560 (0%) + Strand=Plus/Plus + +Query 1 GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC 60 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 121 GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC 180 + +Query 61 CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA 120 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 181 CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA 240 + +Query 121 TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC 180 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 241 TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC 300 + +Query 181 TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT 240 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 301 TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT 360 + +Query 241 TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA 300 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 361 TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA 420 + +Query 301 CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA 360 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 421 CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA 480 + +Query 361 TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA 420 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 481 TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA 540 + +Query 421 CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC 480 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 541 CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC 600 + +Query 481 TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA 540 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 601 TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA 660 + +Query 541 TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT 600 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 661 TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT 720 + +Query 601 TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG 660 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 721 TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG 780 + +Query 661 GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA 720 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 781 GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA 840 + +Query 721 TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA 780 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 841 TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA 900 + +Query 781 ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG 840 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 901 ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG 960 + +Query 841 TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA 900 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 961 TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA 1020 + +Query 901 CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC 960 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1021 CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC 1080 + +Query 961 AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT 1020 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1081 AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT 1140 + +Query 1021 CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA 1080 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1141 CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA 1200 + +Query 1081 ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC 1140 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1201 ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC 1260 + +Query 1141 CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA 1200 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1261 CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA 1320 + +Query 1201 TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG 1260 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1321 TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG 1380 + +Query 1261 CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC 1320 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1381 CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC 1440 + +Query 1321 TATGTGTatttttattttgaataaacagaaagaaattttgggtttttaatttttttCTCC 1380 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1441 TATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCC 1500 + +Query 1381 CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTaaaaaaaaaaaaaCCTGCTA 1440 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1501 CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTA 1560 + +Query 1441 GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT 1500 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1561 GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT 1620 + +Query 1501 ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA 1560 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1621 ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA 1680 + +Query 1561 GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT 1620 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1681 GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT 1740 + +Query 1621 CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT 1680 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1741 CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT 1800 + +Query 1681 GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA 1740 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1801 GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA 1860 + +Query 1741 TTGCTTATGAAAATTCCATAGTGGTAtttttttGGATTCTTAATGTGTAACTTAAACATA 1800 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1861 TTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATA 1920 + +Query 1801 CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA 1860 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1921 CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA 1980 + +Query 1861 AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG 1920 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1981 AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG 2040 + +Query 1921 GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG 1980 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2041 GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG 2100 + +Query 1981 AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT 2040 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2101 AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT 2160 + +Query 2041 TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT 2100 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2161 TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT 2220 + +Query 2101 TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACtt 2160 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2221 TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACTT 2280 + +Query 2161 tttttCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG 2220 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2281 TTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG 2340 + +Query 2221 CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA 2280 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2341 CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA 2400 + +Query 2281 CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT 2340 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2401 CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT 2460 + +Query 2341 TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC 2400 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2461 TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC 2520 + +Query 2401 TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT 2460 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2521 TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT 2580 + +Query 2461 GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT 2520 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2581 GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT 2640 + +Query 2521 AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT 2580 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2641 AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT 2700 + +Query 2581 TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT 2640 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2701 TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT 2760 + +Query 2641 GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT 2700 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2761 GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT 2820 + +Query 2701 TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA 2760 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2821 TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA 2880 + +Query 2761 GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA 2820 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2881 GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA 2940 + +Query 2821 TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA 2880 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2941 TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA 3000 + +Query 2881 TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT 2940 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3001 TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT 3060 + +Query 2941 AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT 3000 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3061 AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT 3120 + +Query 3001 TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT 3060 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3121 TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT 3180 + +Query 3061 ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT 3120 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3181 ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT 3240 + +Query 3121 GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA 3180 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3241 GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA 3300 + +Query 3181 GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT 3240 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3301 GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT 3360 + +Query 3241 GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT 3300 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3361 GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT 3420 + +Query 3301 TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT 3360 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3421 TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT 3480 + +Query 3361 TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT 3420 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3481 TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT 3540 + +Query 3421 AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG 3480 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3541 AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG 3600 + +Query 3481 AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC 3540 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3601 AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC 3660 + +Query 3541 TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT 3600 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3661 TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT 3720 + +Query 3601 CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAA 3660 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3721 CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAA 3780 + +Query 3661 GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT 3720 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3781 GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT 3840 + +Query 3721 TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT 3780 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3841 TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT 3900 + +Query 3781 GAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCT 3840 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3901 GAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCT 3960 + +Query 3841 TTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGG 3900 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3961 TTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGG 4020 + +Query 3901 GCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA 3960 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4021 GCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA 4080 + +Query 3961 CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCA 4020 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4081 CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCA 4140 + +Query 4021 CGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTA 4080 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4141 CGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTA 4200 + +Query 4081 GAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGA 4140 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4201 GAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGA 4260 + +Query 4141 GGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT 4200 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4261 GGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT 4320 + +Query 4201 GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATG 4260 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4321 GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATG 4380 + +Query 4261 GAAACTTTTAGATGACATTCTACAAATTAtttttttCTTTAAATTAAAAGAACCTAGCCA 4320 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4381 GAAACTTTTAGATGACATTCTACAAATTATTTTTTTCTTTAAATTAAAAGAACCTAGCCA 4440 + +Query 4321 ATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCA 4380 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4441 ATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCA 4500 + +Query 4381 AAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA 4440 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4501 AAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA 4560 + +Query 4441 ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAA 4500 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4561 ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAA 4620 + +Query 4501 GGTTGTCAAGAAGGCttttttttttttcttttttAAACCTGAGGGCAAAAAGGAATGGAT 4560 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4621 GGTTGTCAAGAAGGCTTTTTTTTTTTTCTTTTTTAAACCTGAGGGCAAAAAGGAATGGAT 4680 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 106299490 + + + Database: Just 3 human mRNA sequences + Posted date: Dec 26, 2014 5:54 AM + Number of letters in database: 10,732 + Number of sequences in database: 3 + + + +Matrix: blastn matrix 1 -2 +Gap Penalties: Existence: 0, Extension: 2.5 diff -r d0de6862cda1 -r b19b6addd05c test-data/blastn_rhodopsin_vs_three_human.xml --- a/test-data/blastn_rhodopsin_vs_three_human.xml Fri Oct 31 11:43:23 2014 -0400 +++ b/test-data/blastn_rhodopsin_vs_three_human.xml Tue Jan 27 06:06:18 2015 -0500 @@ -2,7 +2,7 @@ blastn - BLASTN 2.2.29+ + BLASTN 2.2.30+ Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. Query_1 diff -r d0de6862cda1 -r b19b6addd05c test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Fri Oct 31 11:43:23 2014 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Tue Jan 27 06:06:18 2015 -0500 @@ -2,7 +2,7 @@ blastp - BLASTP 2.2.29+ + BLASTP 2.2.30+ Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. sp|Q9BS26|ERP44_HUMAN diff -r d0de6862cda1 -r b19b6addd05c test-data/blastx_rhodopsin_vs_four_human.xml --- a/test-data/blastx_rhodopsin_vs_four_human.xml Fri Oct 31 11:43:23 2014 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Tue Jan 27 06:06:18 2015 -0500 @@ -2,7 +2,7 @@ blastx - BLASTX 2.2.29+ + BLASTX 2.2.30+ Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query_1 diff -r d0de6862cda1 -r b19b6addd05c test-data/blastx_rhodopsin_vs_four_human_all.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_all.tabular Fri Oct 31 11:43:23 2014 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_all.tabular Tue Jan 27 06:06:18 2015 -0500 @@ -1,10 +1,10 @@ -gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 sp|P08100|OPSD_HUMAN 1647 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A 0 gi|57163782|ref|NM_001009242.1| gi|57163782|ref|NM_001009242.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 15KA71FL4TS79VA9ML34VI71LI7SASA21LI13TA1GV11 99 99 N/A N/A N/A N/A N/A -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 sp|P08100|OPSD_HUMAN 1419 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 N/A 0 gi|2734705|gb|U59921.1|BBU59921 gi|2734705|gb|U59921.1|BBU59921 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 3/0 10IV1MF2KA20YF1IM1CA7LV7ML5IV17FV1NDHL4CG3VS1ML1ST1MLNH3IVLF1AP3YNVL36SG4VI7IV3SA2VA3LA9ML5VI26LM8RQ2CF30VIFA13FY2STNH3EN7VI7SASA9LM8IL2LI6FL1ED1DE 63 63 N/A N/A N/A N/A N/A -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 3e-67 220 sp|P08100|OPSD_HUMAN 561 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 5KA9HY61FL4TS28 22 8 N/A N/A N/A N/A N/A -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 sp|P08100|OPSD_HUMAN 319 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 3/0 18LV3GS19LI7SASA13 22 5 N/A N/A N/A N/A N/A -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 304 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 2/0 6ML34VI14VARASA 22 4 N/A N/A N/A N/A N/A -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 sp|P08100|OPSD_HUMAN 240 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 3/0 1AG36LV1LF13VA4 22 4 N/A N/A N/A N/A N/A -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 sp|P08100|OPSD_HUMAN 136 23 24 0 92.31 1 0 QFRNCMLTTLCCGKNPLGDDEASTTA QFRNCMLTTICCGKNPLGDDEASATV 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 9LI13TA1AV 22 2 N/A N/A N/A N/A N/A -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 sp|P08100|OPSD_HUMAN 1518 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 N/A 0 gi|283855822|gb|GQ290312.1| gi|283855822|gb|GQ290312.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 5KA66ND4FL4TS5ML7AP49LV25ML34VI40VI6LV19VI11SASA21LI13TA1 99 99 N/A N/A N/A N/A N/A -gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 sp|P08100|OPSD_HUMAN 1596 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A 0 gi|18148870|dbj|AB062417.1| gi|18148870|dbj|AB062417.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 15KA9AY22MV38FL4TS79VA9ML10PLHKEP1TV14IT2LM1VI47LV3GS11DN14TSSA1VI17VL2LI13TA13 99 99 N/A N/A N/A N/A N/A -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 sp|P08100|OPSD_HUMAN 1371 272 307 0 92.19 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA 1344 348 N/A 0 gi|12583664|dbj|AB043817.1| gi|12583664|dbj|AB043817.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 2/0 10IV1MF22AQ2AM1SA4FL2IVAL12IVEQ23FL4TS1ML3ML12IL14CS8WYMV5VMTS6SN6MAVF2TV6LA3FA20RLAK1GEIV10TVCV2ST2LMAIVI1SF4RQ2CF12EA3RK2RK6VI4SA2VI9WF8TN9SA5SA1LI3MV3CM6HN2IL2LI6FLEGEDEDDEGA 74 74 N/A N/A N/A N/A N/A +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 sp|P08100|OPSD_HUMAN 1647 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A 0 gi|57163782|ref|NM_001009242.1| gi|57163782|ref|NM_001009242.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 15KA71FL4TS79VA9ML34VI71LI7SASA21LI13TA1GV11 99 33 N/A N/A N/A N/A N/A +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 sp|P08100|OPSD_HUMAN 1419 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 N/A 0 gi|2734705|gb|U59921.1|BBU59921 gi|2734705|gb|U59921.1|BBU59921 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 3/0 10IV1MF2KA20YF1IM1CA7LV7ML5IV17FV1NDHL4CG3VS1ML1ST1MLNH3IVLF1AP3YNVL36SG4VI7IV3SA2VA3LA9ML5VI26LM8RQ2CF30VIFA13FY2STNH3EN7VI7SASA9LM8IL2LI6FL1ED1DE 63 21 N/A N/A N/A N/A N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 3e-67 220 sp|P08100|OPSD_HUMAN 561 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 5KA9HY61FL4TS28 22 3 N/A N/A N/A N/A N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 sp|P08100|OPSD_HUMAN 319 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 3/0 18LV3GS19LI7SASA13 22 2 N/A N/A N/A N/A N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 304 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 2/0 6ML34VI14VARASA 22 1 N/A N/A N/A N/A N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 sp|P08100|OPSD_HUMAN 240 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 3/0 1AG36LV1LF13VA4 22 1 N/A N/A N/A N/A N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 sp|P08100|OPSD_HUMAN 136 23 24 0 92.31 1 0 QFRNCMLTTLCCGKNPLGDDEASTTA QFRNCMLTTICCGKNPLGDDEASATV 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 9LI13TA1AV 22 1 N/A N/A N/A N/A N/A +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 sp|P08100|OPSD_HUMAN 1518 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 N/A 0 gi|283855822|gb|GQ290312.1| gi|283855822|gb|GQ290312.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 5KA66ND4FL4TS5ML7AP49LV25ML34VI40VI6LV19VI11SASA21LI13TA1 99 33 N/A N/A N/A N/A N/A +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 sp|P08100|OPSD_HUMAN 1596 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A 0 gi|18148870|dbj|AB062417.1| gi|18148870|dbj|AB062417.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 15KA9AY22MV38FL4TS79VA9ML10PLHKEP1TV14IT2LM1VI47LV3GS11DN14TSSA1VI17VL2LI13TA13 99 33 N/A N/A N/A N/A N/A +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 sp|P08100|OPSD_HUMAN 1371 272 307 0 92.19 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA 1344 348 N/A 0 gi|12583664|dbj|AB043817.1| gi|12583664|dbj|AB043817.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 2/0 10IV1MF22AQ2AM1SA4FL2IVAL12IVEQ23FL4TS1ML3ML12IL14CS8WYMV5VMTS6SN6MAVF2TV6LA3FA20RLAK1GEIV10TVCV2ST2LMAIVI1SF4RQ2CF12EA3RK2RK6VI4SA2VI9WF8TN9SA5SA1LI3MV3CM6HN2IL2LI6FLEGEDEDDEGA 74 25 N/A N/A N/A N/A N/A diff -r d0de6862cda1 -r b19b6addd05c test-data/chimera.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chimera.fasta Tue Jan 27 06:06:18 2015 -0500 @@ -0,0 +1,168 @@ +>chimera chunks of AB011145 plus M10051 plus BC112106 +GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC +CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA +TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC +TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT +TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA +CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA +TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA +CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC +TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA +TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT +TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG +GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA +TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA +ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG +TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA +CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC +AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT +CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA +ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC +CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA +TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG +CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC +TATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCC +CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTA +GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT +ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA +GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT +CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT +GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA +TTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATA +CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA +AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG +GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG +AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT +TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT +TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACTT +TTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG +CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA +CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT +TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC +TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT +GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT +AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT +TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT +GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT +TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA +GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA +TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA +TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT +AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT +TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT +ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT +GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA +GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT +GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT +TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT +TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT +AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG +AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC +TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT +CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAA +GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT +TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT +GAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCT +TTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGG +GCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA +CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCA +CGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTA +GAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGA +GGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT +GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATG +GAAACTTTTAGATGACATTCTACAAATTATTTTTTTCTTTAAATTAAAAGAACCTAGCCA +ATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCA +AAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA +ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAA +GGTTGTCAAGAAGGCTTTTTTTTTTTTCTTTTTTAAACCTGAGGGCAAAAAGGAATGGAT +TGGGGGCCGCCTCGGAGCATGACCCCCGCGGGCCAGCGCCGCGCGCCTGATCCGAGGAGA +CCCCGCGCTCCCGCAGCCATGGGCACCGGGGGCCGGCGGGGGGCGGCGGCCGCGCCGCTG +CTGGTGGCGGTGGCCGCGCTGCTACTGGGCGCCGCGGGCCACCTGTACCCCGGAGAGGTG +TGTCCCGGCATGGATATCCGGAACAACCTCACTAGGTTGCATGAGCTGGAGAATTGCTCT +GTCATCGAAGGACACTTGCAGATACTCTTGATGTTCAAAACGAGGCCCGAAGATTTCCGA +GACCTCAGTTTCCCCAAACTCATCATGATCACTGATTACTTGCTGCTCTTCCGGGTCTAT +GGGCTCGAGAGCCTGAAGGACCTGTTCCCCAACCTCACGGTCATCCGGGGATCACGACTG +TTCTTTAACTACGCGCTGGTCATCTTCGAGATGGTTCACCTCAAGGAACTCGGCCTCTAC +AACCTGATGAACATCACCCGGGGTTCTGTCCGCATCGAGAAGAACAATGAGCTCTGTTAC +TTGGCCACTATCGACTGGTCCCGTATCCTGGATTCCGTGGAGGATAATCACATCGTGTTG +AACAAAGATGACAACGAGGAGTGTGGAGACATCTGTCCGGGTACCGCGAAGGGCAAGACC +AACTGCCCCGCCACCGTCATCAACGGGCAGTTTGTCGAACGATGTTGGACTCATAGTCAC +TGCCAGAAAGTTTGCCCGACCATCTGTAAGTCACACGGCTGCACCGCCGAAGGCCTCTGT +TGCCACAGCGAGTGCCTGGGCAACTGTTCTCAGCCCGACGACCCCACCAAGTGCGTGGCC +TGCCGCAACTTCTACCTGGACGGCAGGTGTGTGGAGACCTGCCCGCCCCCGTACTACCAC +TTCCAGGACTGGCGCTGTGTGAACTTCAGCTTCTGCCAGGACCTGCACCACAAATGCAAG +AACTCGCGGAGGCAGGGCTGCCACCAATACGTCATTCACAACAACAAGTGCATCCCTGAG +TGTCCCTCCGGGTACACGATGAATTCCAGCAACTTGCTGTGCACCCCATGCCTGGGTCCC +TGTCCCAAGGTGTGCCACCTCCTAGAAGGCGAGAAGACCATCGACTCGGTGACGTCTGCC +CAGGAGCTCCGAGGATGCACCGTCATCAACGGGAGTCTGATCATCAACATTCGAGGAGGC +AACAATCTGGCAGCTGAGCTAGAAGCCAACCTCGGCCTCATTGAAGAAATTTCAGGGTAT +CTAAAAATCCGCCGATCCTACGCTCTGGTGTCACTTTCCTTCTTCCGGAAGTTACGTCTG +ATTCGAGGAGAGACCTTGGAAATTGGGAACTACTCCTTCTATGCCTTGGACAACCAGAAC +CTAAGGCAGCTCTGGGACTGGAGCAAACACAACCTCACCACCACTCAGGGGAAACTCTTC +TTCCACTATAACCCCAAACTCTGCTTGTCAGAAATCCACAAGATGGAAGAAGTTTCAGGA +ACCAAGGGGCGCCAGGAGAGAAACGACATTGCCCTGAAGACCAATGGGGACAAGGCATCC +TGTGAAAATGAGTTACTTAAATTTTCTTACATTCGGACATCTTTTGACAAGATCTTGCTG +AGATGGGAGCCGTACTGGCCCCCCGACTTCCGAGACCTCTTGGGGTTCATGCTGTTCTAC +AAAGAGGCCCCTTATCAGAATGTGACGGAGTTCGATGGGCAGGATGCGTGTGGTTCCAAC +AGTTGGACGGTGGTAGACATTGACCCACCCCTGAGGTCCAACGACCCCAAATCACAGAAC +CACCCAGGGTGGCTGATGCGGGGTCTCAAGCCCTGGACCCAGTATGCCATCTTTGTGAAG +ACCCTGGTCACCTTTTCGGATGAACGCCGGACCTATGGGGCCAAGAGTGACATCATTTAT +GTCCAGACAGATGCCACCAACCCCTCTGTGCCCCTGGATCCAATCTCAGTGTCTAACTCA +TCATCCCAGATTATTCTGAAGTGGAAACCACCCTCCGACCCCAATGGCAACATCACCCAC +TACCTGGTTTTCTGGGAGAGGCAGGCGGAAGACAGTGAGCTGTTCGAGCTGGATTATTGC +CTCAAAGGGCTGAAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCT +CAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAG +ACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGAT +TACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGAC +CCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTG +CCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAG +CACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACAC +TTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGC +AGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTT +GGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCG +AAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAG +GAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGT +GGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGC +TCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATT +GCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGT +ATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCT +TCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGAC +GAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTC +GGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTG +GCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAG +GCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCC +AAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTAC +CTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAA +GAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAG +TTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAA +ATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGC +AAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACC +ACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAA +CAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTAT +CTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAA +TTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTG +CACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGT +GAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCAC +TGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGC +TACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTG +ACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTT +CCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCT +CCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTG +GCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGC +TTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCT +CTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTC +ACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAAT +TTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTG +GCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAAC +CATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCA +CTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTAC +TACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCAC +TTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAG +GAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACC +CGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTG +GCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCA +GCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAG +CAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGAT +GAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTG +CCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACA +GCCATCCCACCAG diff -r d0de6862cda1 -r b19b6addd05c test-data/four_human_proteins.dbinfo.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.dbinfo.txt Tue Jan 27 06:06:18 2015 -0500 @@ -0,0 +1,7 @@ +Database: Just 4 human proteins + 4 sequences; 3,297 total residues + +Date: Feb 10, 2014 6:40 PM Longest sequence: 1,382 residues + +Volumes: + /mnt/galaxy/galaxy_blast/test-data/four_human_proteins_taxid.fasta diff -r d0de6862cda1 -r b19b6addd05c test-data/four_human_proteins.fasta --- a/test-data/four_human_proteins.fasta Fri Oct 31 11:43:23 2014 -0400 +++ b/test-data/four_human_proteins.fasta Tue Jan 27 06:06:18 2015 -0500 @@ -1,61 +1,48 @@ >sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 -MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRF -SQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMK -REYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFER -VANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK -CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHAD -CDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREF -HHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL +MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFP +NENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSK +RNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK +CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPV +IAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLL +RDRDEL >sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 -MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEG -GFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSIS -DNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRD -LKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG -KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEP -DPEHRPDIFQVSYFAFKFAKKDCPVSNINNSSIPSALPEPMTASEAAARKSQIKARITDT -IGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLAPGEFGNHRPKGALRPGNGPE -ILLGQGPPQQPPQQHRVLQQLQQGDWRLQQLHLQHRHPHQQQQQQQQQQQQQQQQQQQQQ -QQQQQQHHHHHHHHLLQDAYMQQYQHATQQQQMLQQQFLMHSVYQPQPSASQYPTMMPQY -QQAFFQQQMLAQHQPSQQQASPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSV -ADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTEEELLDREFDLLRSNRLEERASSD -KNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD -QRTGKKTSVQGQVQKGNDESESDFESDPPSPKSSEEEEQDDEEVLQGEQGDFNDDDTEPE -NLGHRPLLMDSEDEEEEEKHSSDSDYEQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSA -QLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNLPQHRFPAAGLEQEEFDVFTK -APFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD -EITGSQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHHGTPTSTKKTLKPTYRTPERARR -HKKVGRRDSQSSNEFLTISDSKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLS -WHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKMDDFGAVPFTELVVQSITPHQ -SQQSQPVELDPFGAAPFPSKQ +MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEGGFSTVFLVRTHGGIRCALKR +MYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFC +DTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG +KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQVSYFAFKFAK +KDCPVSNINNSSIPSALPEPMTASEAAARKSQIKARITDTIGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLA +PGEFGNHRPKGALRPGNGPEILLGQGPPQQPPQQHRVLQQLQQGDWRLQQLHLQHRHPHQQQQQQQQQQQQQQQQQQQQQ +QQQQQQHHHHHHHHLLQDAYMQQYQHATQQQQMLQQQFLMHSVYQPQPSASQYPTMMPQYQQAFFQQQMLAQHQPSQQQA +SPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSVADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTEEEL +LDREFDLLRSNRLEERASSDKNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD +QRTGKKTSVQGQVQKGNDESESDFESDPPSPKSSEEEEQDDEEVLQGEQGDFNDDDTEPENLGHRPLLMDSEDEEEEEKH +SSDSDYEQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSAQLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNL +PQHRFPAAGLEQEEFDVFTKAPFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD +EITGSQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHHGTPTSTKKTLKPTYRTPERARRHKKVGRRDSQSSNEFLTISD +SKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLSWHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKM +DDFGAVPFTELVVQSITPHQSQQSQPVELDPFGAAPFPSKQ >sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 -MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHL -QILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYAL -VIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNE -ECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL -GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG -CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGC -TVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETL -EIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE -RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQ -NVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFS -DERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWE -RQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL -KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAF -PNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYV -SARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCV -SRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG -PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSR -EKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKG -FTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMA -AEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV -RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDN -CPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEME -FEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIPYTHMNGGKKNGRILTLPRSN -PS +MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPK +LIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDW +SRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL +GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYT +MNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRS +YALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE +RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVD +IDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIIL +KWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL +KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEK +VVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGL +IVLYEVSYRRYGDEELHLCVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG +PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSREKITLLRELGQGSFGMVYEG +NARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRP +EAENNPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV +RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMR +PTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEMEFEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIP +YTHMNGGKKNGRILTLPRSNPS >sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 -MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY -VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG -GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP -EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES -ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI -YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA +MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA +VADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFT +WVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES +ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTT +ICCGKNPLGDDEASATVSKTETSQVAPA diff -r d0de6862cda1 -r b19b6addd05c test-data/tblastn_four_human_vs_rhodopsin.html --- a/test-data/tblastn_four_human_vs_rhodopsin.html Fri Oct 31 11:43:23 2014 -0400 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Tue Jan 27 06:06:18 2015 -0500 @@ -3,7 +3,7 @@ 
 
-TBLASTN 2.2.29+
+TBLASTN 2.2.30+
 
 
 Query= sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
diff -r d0de6862cda1 -r b19b6addd05c test-data/tblastn_four_human_vs_rhodopsin.xml
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -2,7 +2,7 @@
 
 
   tblastn
-  TBLASTN 2.2.29+
+  TBLASTN 2.2.30+
   Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
   
   Query_1
diff -r d0de6862cda1 -r b19b6addd05c test-data/three_human_mRNA.dbinfo.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/three_human_mRNA.dbinfo.txt	Tue Jan 27 06:06:18 2015 -0500
@@ -0,0 +1,7 @@
+Database: Just 3 human mRNA sequences
+	3 sequences; 10,732 total bases
+
+Date: Dec 26, 2014  5:54 AM	Longest sequence: 4,796 bases
+
+Volumes:
+	/mnt/galaxy/galaxy_blast/test-data/three_human_mRNA.fasta
diff -r d0de6862cda1 -r b19b6addd05c test-data/three_human_mRNA.fasta.log.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/three_human_mRNA.fasta.log.txt	Tue Jan 27 06:06:18 2015 -0500
@@ -0,0 +1,5 @@
+New DB title:  Just 3 human mRNA sequences
+Sequence type: Nucleotide
+Keep Linkouts: T
+Keep MBits: T
+Maximum file size: 1000000000B
diff -r d0de6862cda1 -r b19b6addd05c test-data/three_human_mRNA.fasta.nhd
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/three_human_mRNA.fasta.nhd	Tue Jan 27 06:06:18 2015 -0500
@@ -0,0 +1,3 @@
+12956943350
+13082197871
+19180330422
diff -r d0de6862cda1 -r b19b6addd05c test-data/three_human_mRNA.fasta.nhi
Binary file test-data/three_human_mRNA.fasta.nhi has changed
diff -r d0de6862cda1 -r b19b6addd05c test-data/three_human_mRNA.fasta.nhr
Binary file test-data/three_human_mRNA.fasta.nhr has changed
diff -r d0de6862cda1 -r b19b6addd05c test-data/three_human_mRNA.fasta.nin
Binary file test-data/three_human_mRNA.fasta.nin has changed
diff -r d0de6862cda1 -r b19b6addd05c test-data/three_human_mRNA.fasta.nog
Binary file test-data/three_human_mRNA.fasta.nog has changed
diff -r d0de6862cda1 -r b19b6addd05c test-data/three_human_mRNA.fasta.nsd
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/three_human_mRNA.fasta.nsd	Tue Jan 27 06:06:18 2015 -0500
@@ -0,0 +1,3 @@
+gnl|bl_ord_id|00
+gnl|bl_ord_id|11
+gnl|bl_ord_id|22
diff -r d0de6862cda1 -r b19b6addd05c test-data/three_human_mRNA.fasta.nsi
Binary file test-data/three_human_mRNA.fasta.nsi has changed
diff -r d0de6862cda1 -r b19b6addd05c test-data/three_human_mRNA.fasta.nsq
Binary file test-data/three_human_mRNA.fasta.nsq has changed
diff -r d0de6862cda1 -r b19b6addd05c test-data/tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tool_data_table_conf.xml.test	Tue Jan 27 06:06:18 2015 -0500
@@ -0,0 +1,15 @@
+
+    
+    
+        value, name, path
+        
+    

+    
+        value, name, path
+        
+    

+    
+        value, name, path
+        
+    

+
diff -r d0de6862cda1 -r b19b6addd05c tool-data/tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tool_data_table_conf.xml.sample	Tue Jan 27 06:06:18 2015 -0500
@@ -0,0 +1,14 @@
+
+    
+        value, name, path
+        
+    

+    
+        value, name, path
+        
+    

+    
+        value, name, path
+        
+    

+
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/README.rst
--- a/tools/ncbi_blast_plus/README.rst	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/README.rst	Tue Jan 27 06:06:18 2015 -0500
@@ -7,7 +7,7 @@
 
 See the licence text below.
 
-Currently tested with NCBI BLAST 2.2.29+ (i.e. version 2.2.29 of BLAST+),
+Currently tested with NCBI BLAST 2.2.30+ (i.e. version 2.2.30 of BLAST+),
 and does not work with the NCBI 'legacy' BLAST suite (e.g. ``blastall``).
 
 Note that these wrappers (and the associated datatypes) were originally
@@ -20,6 +20,22 @@
 http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
 
 
+Citation
+========
+
+Please cite the following paper (currently available as a preprint):
+
+NCBI BLAST+ integrated into Galaxy.
+P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
+bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint)
+
+You should also cite the NCBI BLAST+ tools:
+
+BLAST+: architecture and applications.
+C. Camacho et al. BMC Bioinformatics 2009, 10:421.
+DOI: http://dx.doi.org/10.1186/1471-2105-10-421
+
+
 Automated Installation
 ======================
 
@@ -35,8 +51,7 @@
 
 For those not using Galaxy's automated installation from the Tool Shed, put
 the XML and Python files in the ``tools/ncbi_blast_plus/`` folder and add the
-XML files to your ``tool_conf.xml`` as normal (and do the same in
-``tool_conf.xml.sample`` in order to run the unit tests). For example, use::
+XML files to your ``tool_conf.xml`` as normal.  For example, use::
 
   

     
@@ -61,15 +76,16 @@
 
 As described above for an automated installation, you must also tell Galaxy
 about any system level BLAST databases using the ``tool-data/blastdb*.loc``
-files.
+files. Also merge the ``tool-data/tool_data_table_conf.xml.sample`` contents
+into your ``tool_data_table_conf.xml`` file.
 
 You must install the NCBI BLAST+ standalone tools somewhere on the system
-path. Currently the unit tests are written using BLAST 2.2.29+.
+path. Currently the unit tests are written using BLAST+ 2.2.30.
 
 Run the functional tests (adjusting the section identifier to match your
 ``tool_conf.xml.sample`` file)::
 
-    ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools
+    ./run_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools
 
 Configuration
 =============
@@ -157,7 +173,7 @@
         - Set number of threads via ``$GALAXY_SLOTS`` environment variable.
         - More descriptive default output names.
         - Tests require updated BLAST DB definitions (``blast_datatypes`` v0.0.18).
-        - Pre-check for duplicate identifiers in makeblastdb wrapper.
+        - Pre-check for duplicate identifiers in ``makeblastdb`` wrapper.
         - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27.
         - Now depends on ``package_blast_plus_2_2_28`` in ToolShed.
         - Extended tabular output includes 'salltitles' as column 25.
@@ -170,8 +186,8 @@
         - More detailed descriptions for BLASTN and BLASTP task option.
         - Wrappers for segmasker, dustmasker and convert2blastmask
           (contribution from Bjoern Gruening).
-        - Supports using maskinfo with makeblastdb wrapper.
-        - Supports setting a taxonomy ID in makeblastdb wrapper.
+        - Supports using maskinfo with ``makeblastdb`` wrapper.
+        - Supports setting a taxonomy ID in ``makeblastdb`` wrapper.
         - Subtle changes like new conditional settings will require some old
           workflows be updated to cope.
 v0.1.01 - Requires ``blastdbd`` datatype (``blast_datatypes`` v0.0.19).
@@ -181,6 +197,19 @@
           domain database from the user's history.
         - Tool definitions now embed citation information (by John Chilton).
         - BLAST tools support GI and SeqID filters (added by Bjoern Gruening).
+v0.1.02 - Now depends on ``package_blast_plus_2_2_30`` in ToolShed.
+        - Tests updated for BLAST+ 2.2.30 instead of BLAST+ 2.2.29.
+        - New tasks ``blastp-fast``, ``blastx-fast`` and ``tblastn-fast``.
+        - New minimum query HSP coverage option, ``-qcov_hsp_perc``.
+        - Removed ``-word_size`` from RPS-BLAST and RPS-TBLASTN wrappers, this
+          is set during database construction and should not have been offered
+          as a command line option in releases prior to BLAST+ 2.2.30.
+        - BLAST database ``blastdb*.loc`` files now accessed via the XML
+          table definitions in Galaxy's ``tool_data_table_conf.xml`` file,
+          setup via ``tool-data/tool_data_table_conf.xml.sample``
+        - Replace ``.extra_files_path`` with ``.files_path`` (internal change,
+	  thanks to Bjoern Gruening and John Chilton).
+        - Added "NCBI BLAST+ integrated into Galaxy" preprint citation.
 ======= ======================================================================
 
 
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/blastxml_to_tabular.py
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py	Tue Jan 27 06:06:18 2015 -0500
@@ -66,7 +66,7 @@
 from optparse import OptionParser
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.1.01"
+    print "v0.1.04"
     sys.exit(0)
 
 if sys.version_info[:2] >= ( 2, 5 ):
@@ -162,7 +162,7 @@
     blast_program = None
     # get an iterable
     try: 
-        context = ElementTree.iterparse(in_file, events=("start", "end"))
+        context = ElementTree.iterparse(blastxml_filename, events=("start", "end"))
     except:
         stop_err("Invalid data format.")
     # turn it into an iterator
@@ -321,7 +321,7 @@
                         #Only a subset of the columns are needed
                         values = [values[colnames.index(c)] for c in cols]
                     #print "\t".join(values) 
-                    outfile.write("\t".join(values) + "\n")
+                    output_handle.write("\t".join(values) + "\n")
             # prevents ElementTree from growing large datastructure
             root.clear()
             elem.clear()
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/blastxml_to_tabular.xml
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     Convert BLAST XML output to tabular
     blastxml_to_tabular.py --version
     
@@ -9,7 +9,7 @@
 #else
 -c "$output.out_format"
 #end if
-#for i in $blastxml_file#${i} #end for#
+#for i in $blastxml_file#"${i}" #end for#
     
     
         
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     Show BLAST database information from blastdbcmd
     
         blastdbcmd
@@ -15,6 +15,18 @@
     
         
     
+    
+        
+            
+            
+            
+        
+        
+            
+            
+            
+        
+    
     
     
 **What it does**
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     Extract sequence(s) from BLAST database
     
         blastdbcmd
@@ -70,6 +70,16 @@
     
         
     
+    
+        
+            
+            
+            
+            
+            
+            
+        
+    
     
     
 **What it does**
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     Search nucleotide database with nucleotide query sequence(s)
     
     
@@ -19,12 +19,15 @@
 @THREADS@
 #if $adv_opts.adv_opts_selector=="advanced":
 $adv_opts.strand
-@ADVANCED_OPTIONS@
+@ADV_FILTER_QUERY@
+@ADV_MAX_HITS@
+@ADV_WORD_SIZE@
 #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ):
 -perc_identity $adv_opts.identity_cutoff
 #end if
 $adv_opts.ungapped
 @ADV_ID_LIST_FILTER@
+@ADV_QCOV_HSP_PERC@
 ## End of advanced options:
 #end if
     
@@ -64,6 +67,7 @@
             
             
             
+            
         
     
     
@@ -104,6 +108,24 @@
             
             
         
+        
+            
+            
+            
+            
+            
+            
+            
+        
+        
+            
+            
+            
+            
+            
+            
+            
+        
     
     
     
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     Search protein database with protein query sequence(s)
     
     
@@ -19,10 +19,13 @@
 @THREADS@
 #if $adv_opts.adv_opts_selector=="advanced":
 -matrix $adv_opts.matrix
-@ADVANCED_OPTIONS@
+@ADV_FILTER_QUERY@
+@ADV_MAX_HITS@
+@ADV_WORD_SIZE@
 ##Ungapped disabled for now - see comments below
 ##$adv_opts.ungapped
 @ADV_ID_LIST_FILTER@
+@ADV_QCOV_HSP_PERC@
 ## End of advanced options:
 #end if
     
@@ -36,6 +39,7 @@
 
         
             
+            
             
         
         
@@ -54,6 +58,7 @@
             -->
             
             
+            
         
     
     
@@ -76,6 +81,7 @@
             
             
             
+            
             
         
         
@@ -92,6 +98,7 @@
             
             
             
+            
             
         
         
@@ -108,6 +115,7 @@
             
             
             
+            
             
         
         
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     Search protein database with translated nucleotide query sequence(s)
     
     
@@ -14,15 +14,19 @@
 -query "$query"
 @BLAST_DB_SUBJECT@
 -query_gencode $query_gencode
+-task $blast_type
 -evalue $evalue_cutoff
 @BLAST_OUTPUT@
 @THREADS@
 #if $adv_opts.adv_opts_selector=="advanced":
 $adv_opts.strand
 -matrix $adv_opts.matrix
-@ADVANCED_OPTIONS@
+@ADV_FILTER_QUERY@
+@ADV_MAX_HITS@
+@ADV_WORD_SIZE@
 $adv_opts.ungapped
 @ADV_ID_LIST_FILTER@
+@ADV_QCOV_HSP_PERC@
 ## End of advanced options:
 #end if
     
@@ -34,6 +38,10 @@
 
         
         
+        
+            
+            
+        
         
 
         
@@ -47,6 +55,7 @@
             
             
             
+            
         
     
     
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb
     
         convert2blastmask
@@ -80,7 +80,7 @@
 **References**
 
 If you use this Galaxy tool in work leading to a scientific publication please
-cite the following papers (a more specific paper covering this wrapper is planned):
+cite the following papers:
 
 @REFERENCES@
     
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     
     masks low complexity regions
     
@@ -13,7 +13,7 @@
 #if $db_opts.db_opts_selector == "db":
   -in "${db_opts.database.fields.path}" -infmt blastdb
 #elif $db_opts.db_opts_selector == "histdb":
-  -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb
+  -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb
 #else:
   -in "$subject" -infmt fasta
 #end if
@@ -92,7 +92,7 @@
 **References**
 
 If you use this Galaxy tool in work leading to a scientific publication please
-cite the following papers (a more specific paper covering this wrapper is planned):
+cite the following papers:
 
 @REFERENCES@
     
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_macros.xml
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,11 @@
 
+    
+        
+            @BINARY@
+            blast+
+        
+        @BINARY@ -version
+    
     
         
             
@@ -175,11 +182,7 @@
             
             
                 
-                    
-                      
-                      
-                      
-                    
+                    
                 
                 
                  
@@ -205,11 +208,7 @@
             
             
                 
-                    
-                      
-                      
-                      
-                    
+                    
                 
                 
                 
@@ -234,11 +233,7 @@
             
             
                 
-                    
-                      
-                      
-                      
-                    
+                    
                 
                 
                 
@@ -258,20 +253,12 @@
             
             
                 
-                    
-                      
-                      
-                      
-                    
+                    
                 
             
             
                 
-                    
-                      
-                      
-                      
-                    
+                    
                 
             
         
@@ -305,12 +292,8 @@
             
         
     
-    
-        
-            @BINARY@
-            blast+
-        
-        @BINARY@ -version
+    
+        
     
     
         
@@ -349,6 +332,11 @@
             
         
     
+    
+#if float(str($adv_opts.qcov_hsp_perc)) > 0:
+    -qcov_hsp_perc $adv_opts.qcov_hsp_perc
+#end if
+    
     
 #if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'negative_gilist':
     -negative_gilist $adv_opts.adv_optional_id_files_opts.negative_gilist
@@ -363,7 +351,7 @@
 #if $db_opts.db_opts_selector == "db":
   -db "${db_opts.database.fields.path}"
 #elif $db_opts.db_opts_selector == "histdb":
-  -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
+  -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}"
 #else:
   -subject "$db_opts.subject"
 #end if
@@ -381,12 +369,22 @@
     -outfmt $output.out_format
 #end if
     
-    $adv_opts.filter_query
+    $adv_opts.filter_query
+    
 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
+## Note -max_target_seqs used to simply override -num_descriptions and -num_alignments
+## but this was changed in BLAST+ 2.2.27 onwards to force their use (raised with NCBI)
 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
+#if str($output.out_format) in ["6", "ext", "cols", "5"]:
+## Most output formats use this, including tabular and XML:
 -max_target_seqs $adv_opts.max_hits
+#else
+## Text and HTML output formats 0-4 currently need this instead:
+-num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits
 #end if
+#end if
+    
+    
 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
 -word_size $adv_opts.word_size
 #end if
@@ -401,14 +399,18 @@
 ${db_opts.subject.name}
 #end if
     
+Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015).
+NCBI BLAST+ integrated into Galaxy. *BioRxiv* preprint.
+http://dx.doi.org/10.1101/014043
+
 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
 Galaxy tools and workflows for sequence analysis with applications
-in molecular plant pathology. PeerJ 1:e167
+in molecular plant pathology. *PeerJ* 1:e167
 http://dx.doi.org/10.7717/peerj.167
 
 Christiam Camacho et al. (2009).
 BLAST+: architecture and applications.
-BMC Bioinformatics. 15;10:421.
+*BMC Bioinformatics*. 15;10:421.
 http://dx.doi.org/10.1186/1471-2105-10-421
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
@@ -418,7 +420,9 @@
         
             10.1186/1471-2105-10-421
             10.7717/peerj.167
-            
+            
+            10.1101/014043
+            
         
     
     **Output format**
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_makeblastdb.xml
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     Make BLAST database
     
         makeblastdb
@@ -10,7 +10,7 @@
 ##and abort (via the ampersand ampersand trick) if any are found.
 #for i in $input_file#"${i}" #end for#
 &&
-makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}"
+makeblastdb -out "${os.path.join($outfile.files_path,'blastdb')}"
 $parse_seqids
 $hash_index
 ## Single call to -in with multiple filenames space separated with outer quotes
@@ -97,6 +97,7 @@
     
     
         
     
@@ -15,13 +15,15 @@
 #if $db_opts.db_opts_selector == "db":
   -db "${db_opts.database.fields.path}"
 #elif $db_opts.db_opts_selector == "histdb":
-  -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
+  -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}"
 #end if
 -evalue $evalue_cutoff
 @BLAST_OUTPUT@
 @THREADS@
 #if $adv_opts.adv_opts_selector=="advanced":
-@ADVANCED_OPTIONS@
+@ADV_FILTER_QUERY@
+@ADV_MAX_HITS@
+@ADV_QCOV_HSP_PERC@
 ## End of advanced options:
 #end if
     
@@ -41,8 +43,8 @@
             
             
             
-            
             
+            
         
     
     
@@ -52,6 +54,16 @@
 
         
     
+    
+        
+            
+            
+            
+            
+            
+            
+        
+    
     
     
 @SEARCH_TIME_WARNING@
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     Search protein domain database (PSSMs) with translated nucleotide query sequence(s)
     
     
@@ -15,14 +15,16 @@
 #if $db_opts.db_opts_selector == "db":
   -db "${db_opts.database.fields.path}"
 #elif $db_opts.db_opts_selector == "histdb":
-  -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
+  -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}"
 #end if
 -evalue $evalue_cutoff
 @BLAST_OUTPUT@
 ## rpstblastn does not support multiple threads up to release 2.2.27+. Added in BLAST 2.2.28+.
 ##-num_threads 8
 #if $adv_opts.adv_opts_selector=="advanced":
-@ADVANCED_OPTIONS@
+@ADV_FILTER_QUERY@
+@ADV_MAX_HITS@
+@ADV_QCOV_HSP_PERC@
 ## End of advanced options:
 #end if
     
@@ -41,8 +43,8 @@
             
             
             
-            
             
+            
         
     
     
@@ -50,6 +52,16 @@
             
         
     
+    
+        
+            
+            
+            
+            
+            
+            
+        
+    
     
     
 @SEARCH_TIME_WARNING@
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     low-complexity regions in protein sequences
     
         segmasker
@@ -12,7 +12,7 @@
 #if $db_opts.db_opts_selector == "db":
   -in "${db_opts.database.fields.path}" -infmt blastdb
 #elif $db_opts.db_opts_selector == "histdb":
-  -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb
+  -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb
 #else:
   -in "$subject" -infmt fasta
 #end if
@@ -94,7 +94,7 @@
 **References**
 
 If you use this Galaxy tool in work leading to a scientific publication please
-cite the following papers (a more specific paper covering this wrapper is planned):
+cite the following papers:
 
 @REFERENCES@
     
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     Search translated nucleotide database with protein query sequence(s)
     
     
@@ -13,16 +13,20 @@
 tblastn
 -query "$query"
 @BLAST_DB_SUBJECT@
+-task $blast_type
 -evalue $evalue_cutoff
 @BLAST_OUTPUT@
 @THREADS@
 #if $adv_opts.adv_opts_selector=="advanced":
 -db_gencode $adv_opts.db_gencode
 -matrix $adv_opts.matrix
-@ADVANCED_OPTIONS@
+@ADV_FILTER_QUERY@
+@ADV_MAX_HITS@
+@ADV_WORD_SIZE@
 ##Ungapped disabled for now - see comments below
 ##$adv_opts.ungapped
 @ADV_ID_LIST_FILTER@
+@ADV_QCOV_HSP_PERC@
 ## End of advanced options:
 #end if
     
@@ -33,8 +37,12 @@
          
 
         
+        
+            
+            
+        
+        
         
-        
         
             
 
@@ -51,6 +59,7 @@
             -->
             
             
+            
         
     
     
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
-
+
     Search translated nucleotide database with translated nucleotide query sequence(s)
     
     
@@ -21,10 +21,11 @@
 -db_gencode $adv_opts.db_gencode
 $adv_opts.strand
 -matrix $adv_opts.matrix
-## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
-## Note -max_target_seqs overrides -num_descriptions and -num_alignments
-@ADVANCED_OPTIONS@
+@ADV_FILTER_QUERY@
+@ADV_MAX_HITS@
+@ADV_WORD_SIZE@
 @ADV_ID_LIST_FILTER@
+@ADV_QCOV_HSP_PERC@
 ## End of advanced options:
 #end if
     
@@ -51,6 +52,7 @@
             
             
             
+            
         
     
     
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/repository_dependencies.xml
--- a/tools/ncbi_blast_plus/repository_dependencies.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/repository_dependencies.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,4 +1,4 @@
 
 
-    
+    
 
diff -r d0de6862cda1 -r b19b6addd05c tools/ncbi_blast_plus/tool_dependencies.xml
--- a/tools/ncbi_blast_plus/tool_dependencies.xml	Fri Oct 31 11:43:23 2014 -0400
+++ b/tools/ncbi_blast_plus/tool_dependencies.xml	Tue Jan 27 06:06:18 2015 -0500
@@ -1,6 +1,6 @@
 
 
-    
-        
+    
+