[Swift-commit] r7219 - SwiftApps/Swift-MapRed/blast
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Wed Oct 23 22:06:29 CDT 2013
Author: ketan
Date: 2013-10-23 22:06:29 -0500 (Wed, 23 Oct 2013)
New Revision: 7219
Modified:
SwiftApps/Swift-MapRed/blast/blast.swift
SwiftApps/Swift-MapRed/blast/run.sh
SwiftApps/Swift-MapRed/blast/sequence.seq
SwiftApps/Swift-MapRed/blast/sites.xml
Log:
Modified: SwiftApps/Swift-MapRed/blast/blast.swift
===================================================================
--- SwiftApps/Swift-MapRed/blast/blast.swift 2013-10-23 21:47:41 UTC (rev 7218)
+++ SwiftApps/Swift-MapRed/blast/blast.swift 2013-10-24 03:06:29 UTC (rev 7219)
@@ -1,3 +1,4 @@
+
type fastaseq;
type headerfile;
type indexfile;
@@ -11,46 +12,48 @@
seqfile psq;
}
-string num_partitions=@arg("n", "8");
+string num_partitions = arg("n", "50");
-string program_name=@arg("p", "blastp");
+string program_name = arg("p", "blastp");
-fastaseq dbin <single_file_mapper;file=@arg("d", "nr")>;
+fastaseq dbin <single_file_mapper;file = arg("d", "nr")>;
-query query_file <single_file_mapper;file=@arg("i", "sequence.seq")>;
+query query_file <single_file_mapper;file = arg("i", "sequence.seq")>;
-string expectation_value=@arg("e", "0.1");
+string expectation_value = arg("e", "0.1");
-output blast_output_file <single_file_mapper;file=@arg("o", "output.html")>;
+output blast_output_file <single_file_mapper;file = arg("o", "output.html")>;
-string filter_query_sequence=@arg("F", "F");
+string filter_query_sequence = arg("F", "F");
-fastaseq partition[] <ext;exec="splitmapper.sh",n=num_partitions>;
+fastaseq partition[] <ext;exec = "splitmapper.sh", n = num_partitions>;
-database formatdbout[] <ext; exec="formatdbmapper.sh",n=num_partitions>;
-output out[] <ext; exec="outputmapper.sh",n=num_partitions>;
+database formatdbout[] <ext; exec = "formatdbmapper.sh", n = num_partitions>;
+output out[] <ext; exec = "outputmapper.sh", n = num_partitions>;
+
app (fastaseq out[]) split_database (fastaseq d, string n){
- fastasplitn @filename(d) n;
+ fastasplitn filename(d) n;
}
app (database out) formatdb (fastaseq i){
- formatdb "-i" @filename(i);
+ formatdb "-i" filename(i);
}
app (output o) blastapp(query i, fastaseq d, string p, string e, string f, database db){
- blastall "-p" p "-i" @filename(i) "-d" @filename(d) "-o" @filename(o) "-e" e "-T" "-F" f;
+ blastall "-p" p "-i" filename(i) "-d" filename(d) "-o" filename(o) "-e" e "-T" "-F" f;
}
app (output o) blastmerge(output o_frags[]){
- blastmerge @filename(o) @filenames(o_frags);
+ blastmerge filename(o) filenames(o_frags);
}
+
partition=split_database(dbin, num_partitions);
foreach part,i in partition {
formatdbout[i] = formatdb(part);
- out[i]=blastapp(query_file, part, program_name, expectation_value, filter_query_sequence, formatdbout[i]);
+ out[i] = blastapp(query_file, part, program_name, expectation_value, filter_query_sequence, formatdbout[i]);
}
-blast_output_file=blastmerge(out);
+blast_output_file = blastmerge(out);
Modified: SwiftApps/Swift-MapRed/blast/run.sh
===================================================================
--- SwiftApps/Swift-MapRed/blast/run.sh 2013-10-23 21:47:41 UTC (rev 7218)
+++ SwiftApps/Swift-MapRed/blast/run.sh 2013-10-24 03:06:29 UTC (rev 7219)
@@ -1,3 +1 @@
-#!/bin/bash
-
swift -sites.file sites.xml -config cf tc.file tc.data blast.swift
Modified: SwiftApps/Swift-MapRed/blast/sequence.seq
===================================================================
--- SwiftApps/Swift-MapRed/blast/sequence.seq 2013-10-23 21:47:41 UTC (rev 7218)
+++ SwiftApps/Swift-MapRed/blast/sequence.seq 2013-10-24 03:06:29 UTC (rev 7219)
@@ -1,4 +1,106 @@
->seq1
-AACGCGTATATACACAGGG
->seq2
-CGTATAGATACA
+>gnl|md5|e0785fc0b8720a5c4d78be370ef19af0
+MEVLESGEQGVLQWDRKLSELSEPGDGEALMYHTHFSELLDEFSQNVLGQLLNDPFLSEK
+SVSMEVEPSPTSPAPLIQAEHSYSLCEEPRAQSPFTHITSDSFNDDEVESEKWYLSTDFP
+STSIKTEPITDEPPPGLVPSVTLTITAISTPLEKEEPPLEMNTGVDSSCQTIIPKIKLEP
+HEVDQFLNFSPKEAPVDHLHLPPTPPSSHGSDSEGSLSPNPRLHPFSLPQTHSPSRAAPR
+APSALSSSPLLTAPHKLQGSGPLVLTEEEKRTLIAEGYPIPTKLPLSKSEEKALKKIRRK
+IKNKISAQESRRKKKEYMDSLEKKVESCSTENLELRKKVEVLENTNRTLLQQLQKLQTLV
+MGKVSRTCKLAGTQTGTCLMVVVLCFAVAFGSFFQGYGPYPSATKMALPSQHSLQEPYTA
+SVVRSRNLLIYEEHSPPEESSSPGSAGELGGWDRGSSLLRVSGLESRPDVDLPHFIISNE
+TSLEKSVLLELQQHLVSAKLEGNETLKVVELDRRVNTTF
+>gnl|md5|f67549f249c59ecd0b48ff02ca209442
+MAEETRQSKLAIAKEKLKEYWQRNSLGVPAGVKRNRKTSGSSPETATSGGCHSPEDSATG
+IHGEGPTSSATLKDLESPCQELAVVLDSRSIKISQLNNTIKSLVIMANILVFVFPKCIVI
+DLNRNVDTEISKMSMG
+>gnl|md5|cd0de5548a14c880425dc87f8486310c
+MNSGAMRIHSKGHFQGGIQVKNEKNRPSLKSLKTDNRPEKSKCKPLWGKVFYLDLPSVTI
+SEKLQKDIKDLGGRVEEFLSKDISYLISNKKEAKFAQTLGRISPVPSPESAYTAETTSPH
+PSHDGSSFKSPDTVCLSRGKLLVEKAIKDHDFIPSNSILSNALSWGVKILHIDDIRYYIE
+QKKKELYLLKKSSTSVRDGGKRVGSGAQKTRTGRLKKPFVKVEDMSQLYRPFYLQLTNMP
+FINYSIQKPCSPFDVDKPSSMQKQTQVKLRIQTDGDKYGGTSIQLQLKEKKKKGYCECCL
+QKYEDLETHLLSEQHRNFAQSNQYQVVDDIVSKLVFDFVEYEKDTPKKKRIKYSVGSLSP
+VSASVLKKTEQKEKVELQHISQKDCQEDDTTVKEQNFLYKETQETEKKLLFISEPIPHPS
+NELRGLNEKMSNKCSMLSTAEDDIRQNFTQLPLHKNKQECILDISEHTLSENDLEELRVD
+HYKCNIQASVHVSDFSTDNSGSQPKQKSDTVLFPAKDLKEKDLHSIFTHDSGLITINSSQ
+EHLTVQAKAPFHTPPEEPNECDFKNMDSLPSGKIHRKVKILLGQNRKENLEPNAEFDKRT
+EFITQEENRICSSPVQSLPDLFQTSEEKSEFLGFTSYTEKSGICNVLDIWEEENSDNLLT
+AFFSSPSTSTFTGF
+>gnl|md5|c243d77c83c27dff598d70af18d8ed42
+MGAEQIRLEDRAQCAARQVLGGAGDGEGGVVHQRVDAPQGQRGFGAARHAVLAAQFQVQR
+VEALGAAGLDILGLAAGGDDAPAARPHVPRRVQPDARGTAGDQNGLHARLLAAGVLRQGR
+ALRKPRISGWTGAACGPIHRNMSDDPNVPDPTPPDPSQDQTTSEPLSRAIGERYLTYALS
+TIMNRALPDARDGLKPVHRRILFAMRELRLSPTGAFRKSAKISGDVMGNYHPHGDAAIYD
+AMARLAQPFAMRYPLVDGQGNFGNIDGDNPAASRYTEARLTAAAEALMEGLAENAVDFRP
+NYDGTLEEPIVLPAAFPNLLCNGASGIAVGMATNVPPHNLHEVIDACLHLIKAPDARDDT
+LVSIVPGPDFPTGGVLVESRETIAEAYRTGRGSLRLRARWSVEDLGRGQWQIVVTEIPYQ
+VQKSKLIERLAEVIQLKKVPILADVRDESAEDIRIVLEPRTRAVDAEQLMAALFRVSDLE
+VRFGLNMNVLIDGRVPKVCSLKEVLRAFLDHRREVLVRRSNHRLDKIAARLEVLEGYMIA
+FLNLDRVIEIIRHEDDPKAVMIAEFKLSDVQVEAILNMRLRALRRLEEIELRAEHENLTR
+EREGLAAMLADEGAQWARIAEELRETRAKFGKSASGGQRRTEIGEAGEVAEIDMDAMIER
+EPITVILSKMGWIRAMKGHQPLDAEVKFKDGDGPFMALHAETTDKLMVFAANGRFYTLPA
+NNLPGGRGMGEPLRLMIDLPNDAAVIDMFPWRDGERYLVASKAGDGFVVAGADILAQTRA
+GKQVLNGEAALCRRVTGDHVAVVGQNRKLLVFPLSELPEMARGKGVRLQKYKDGGLSDAV
+CITLAEGLRWQETGGRTRSEPDLTEWLGKRAGAGYMAPRGFPRDNRFN
+>gnl|md5|ccc28dbc1a3ca81c8dd929af669b1173
+MDRAERIGFWVSGFAHAGLLGAALVGGALFRPQPLEAVRMAEVATMSEAEFQSLAAAAAG
+RGPVSDVAATTPAQPRPPADENRLGEVEAVSPPAPDAQAAELSTPSDRPEARPDLSDFQT
+PNRPVAVATDAPRPAEPENTVELAAL
+>gnl|md5|9d3da0729b348bbcaba8c65c444b6fee
+MAGPAHGRAHRGAALMLEVAFRHRFPGLSLEVAFQAPGGVTALFGPSGCGKSTAINAIAG
+LLRPDQGRIALDGRVLFDGATNLSPQARRIGCVFQDARLFPHMTVAANLRYPSRWRRGAA
+RDFDRITEMLALGPLLHRRPGTLSGGERQRVAIGRALLSDPALLVMDEPLAALDEARKAE
+IMPWLERLRDQIRLPILYVSHSVPEVLRLATTVVLMRQGRVTHSGALADILADPELAPQL
+GAREAGALIRATVEAREADGLTRVATAGGPMLLPELDLAPGRVLRLRILAHEVILAREAP
+RGLSALNALPVAVTRIEGGLVQLALGHGAQHERMLAQVTPRSVKALELQPGTACHAIVKS
+VSVLPS
+>gnl|md5|4276fd81078276b607fce4cf16581984
+MPRRRSSCCPRSLAGRPVPRNTRQPSRGSTLPGSPRRWKSPRPHGRSISEGLARPGKGRT
+FIGRPSPSLNIWPGIAGIMPPLAVGSWVAAVEQTYAADAGMRRDEAIRSATPGAAFPIFA
+AQAHGLASCPMVGFDAERLAREFALAADEIPVLLVAVGHAAEGNRPQKPRLPVAQILTTL
+QQPEVDMPKPSDILLTALAPAVWGSTYIVATELLPGAPPLSVAAIRALPTGLILLLLVRQ
+LPKGDWLWRSFVLGALNFTVFWALLFVAAYRLPGGIAATVGAVQPLIVVFAASAVLGTRI
+RVLSVLAAVMGMAGVALLVLQDGAVPDMPGIAAALGGAFSMAFGTVLTRKWRPPVSALVL
+TAWQLTAGGLLLLPLALLLDPPMPPLDAANAAGMGYLVLFTALTYILWFRGVARLEPAAV
+SSLGFLSPLTAILLGWAILGQALSASQMIGAAVVVASIWLSQRATPSRQVHAR
+>gnl|md5|6803c5e1ab1272ec69688700d3c02e0e
+MKVYLANQPVDFRKGPDSQLSLVRDAGSDPFSFELEILAAHVLGEILKGPRVFADETGLP
+TLAPGTGTVNKAWLWAYARDDSTFGGSGPPMVPYRFEDSRSGECVHRHLGGYGGILQVDG
+YAAYNQLVRKDGGNAGPSLAECWAHSRRRFYELHTAGTVRSPPPRSSGWPISGSSNPRFV
+AKTPTFAPPRGRPSPPPPSPDCSPSGNRPCRASRANRSWPRPSAMPSPGATSSSDS
+>gnl|md5|c63587eb43399c568f1164527fc27358
+PFWATPFALAACTPEAPPPPEPETVSVDPCGAARYSHLIGQTSPTISVPEGQMYRIARED
+RPMTMEMIQDRLTFIVDSRGKLLSVSCS
+>gnl|md5|3f0af0be21624a9da7db4d62141deca1
+MSRHRGAKRCRRYGLLGIISLLSPAYLLSVERWPFHSGPPDHYGRLSSLLDLSVLQSGWL
+LPLHSTSDFRPL
+>gnl|md5|bfd0bd685d4ee94a015cd061816ab82d
+RHIRRDALEASVLNGLKKHLMEPELFREFCAEFTREVNRLRMERGADLEVARRELDKIGR
+QISQIIEAITDGMYHPSMKEKMTKLEARKAEATEKLANADEPPPLLHPNMAALYAQRITE
+LSENLQHEDSRAQAAEILRSLVDQVTLLPEEGELAIVLRGDLGAILRFAAGKKDPDFLSE
+AEALDNLLGQMAVSRKPGRTKAKTSALNATEVSQLSLVAGVGFEPTTFRL
+>gnl|md5|458f535dc6b3a85dbf0b50bf0ffae312
+MMMPTARSMTLPRAMNSLNSLNMGLPFPACCACSGRGCHITLTPCNMRQDMTGNDMTALS
+EFPITRRWPPRRPDVIQLYTLNTPNGIKTSVMLEECGLDYDAHRISIGDPEDQFTPEFLS
+LNPNNKIPAMIDPNGPDGKPMGLFETGAMLVYLGDKTGKFLPASGAARYHTIQWLMWQMG
+GVGPMFGQVGYFHRYKGSEIEDARPRTRYYNEARRLLGVLDRQLEGRDWITGEYSIADMA
+VGPWLRTVRVNYEAEKETGMDGFANVQAYLDRFLARPAVQRGIEVGAE
+>gnl|md5|f53520edd5c9ba7e5bed2fd08cb44ad7
+MPSWRRNWAAATRIRPAVRFWPRSGWTDAAGPMRPDPRPAACAAAPAGAEPRHRCTEEPA
+LTESRKINPWLKAALEFGPLILFFLVFMRFRDQTVSLAGRDYSGFILATLAFVPVLALST
+LALWRLTGRLSPMQVATLVLVVVFGGLSVWLNDPKFFKMKPTIIYLIFAALLGTSLALRR
+NWLELVMSEALPMNAEGWRILTLRMALLFLGLAAANEAVWRLMSETAWVNFKTFGLPAIM
+VAFFIANSRLFERHAQPRDGE
+>gnl|md5|68631421ddc36a3fd81617d12227b1dd
+MILHRPDDDSTARRLEIELRNGPALEAKLVDKIGGAWVELNARHERLVRQEVGARLDAER
+DRKAEVILDLLYEEAAEGRLYTSTQFASNFENRAGLGSQHTIQDRLNVLATKGFIKYQRN
+GALYGLPLVRSRFGYMCVEGMRFGRVEQVDPETGEITGQGLAVLPSHYRCASSGAALEVE
+NPSVWVWPEVVDV
+>gnl|md5|04b3fad17b0d40e02b489a48c451ecc3
+MPVACCRPCGAADGGADLGRSGGEGWLHLFPVLLGAGQARTHEALRRQGRIARRTAGTPR
+PWFIVIITAGLLARRSLPLPAFPMPCGTSGVIRRRLAAYSCGGSAGLAPKGAPASLFAFG
+SDRPERTVMPTYRDDEAISVKMLYWPATLCPREEVSPLTTTGAEDLKQADTVLYMQFFRL
+R
+>gnl|md5|0fab0da718e659ed5fb9c7a5f6a3d18e
+MAEHLPFLAHCSPAPRGLARAWGFGRRPGSNDRGNDTLTHNVLRFASGLWRGQPGRVILY
+TIHYKAFTMTASTTMTIRVSPETKQKLERIAGETRRSKSFLAAEAVSAYVERELEIIDGI
+RRGMADAAAGRVVSHEDAMAEIHAVIDAAEATRAGKA
Modified: SwiftApps/Swift-MapRed/blast/sites.xml
===================================================================
--- SwiftApps/Swift-MapRed/blast/sites.xml 2013-10-23 21:47:41 UTC (rev 7218)
+++ SwiftApps/Swift-MapRed/blast/sites.xml 2013-10-24 03:06:29 UTC (rev 7219)
@@ -2,10 +2,10 @@
<config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
<pool handle="localhost">
<execution provider="local" />
- <profile namespace="karajan" key="jobThrottle">0</profile>
+ <profile namespace="karajan" key="jobThrottle">0.06</profile>
<profile namespace="karajan" key="initialScore">10000</profile>
<filesystem provider="local"/>
- <workdirectory>/tmp/swift.work</workdirectory>
+ <workdirectory>swift.work</workdirectory>
<profile namespace="swift" key="stagingMethod">local</profile>
</pool>
</config>
More information about the Swift-commit
mailing list