| Next changeset 1:4351ee79c942 (2016-11-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 |
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added:
TODO.md macros.xml nhmmscan.xml readme.rst test-data/MADE1.hmm test-data/MADE1.out test-data/MADE1.out.domtblout test-data/MADE1.out.pfamtblout test-data/MADE1.out.tblout test-data/MADE1.sto test-data/dna_target.fa test-data/fn3.hmm test-data/fn3.keys test-data/fn3.out test-data/fn3.sto test-data/globins-45-align.sto test-data/globins-masked.sto test-data/globins.domtblout test-data/globins.pfamtblout test-data/globins.tblout test-data/globins4-emit-1.sto test-data/globins4-emit.sto test-data/globins4.hmm test-data/globins4.hmm.bin test-data/globins4.hmm2 test-data/globins4.out test-data/globins4.sto test-data/globins45.fa test-data/jackhmmer.domtblout test-data/jackhmmer.out test-data/jackhmmer.tblout test-data/nhmmer.out test-data/phmmer.domtblout test-data/phmmer.out test-data/phmmer.pfamtblout test-data/phmmer.tblout test-data/uniprot_globins_match.out test-data/uniprot_matches.fasta tool_dependencies.xml |
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| diff -r 000000000000 -r a6098dd0cb46 TODO.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TODO.md Sat Jun 25 15:07:32 2016 -0400 |
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| @@ -0,0 +1,39 @@ +# Necessary + +- output names on `$(grep tblout *.xml)` +- Help text +- HmmPress datatypes +- Publicly available hmm databases? data manager needed? Locally installed, etc? +- Use hmmpress databases in History/Locally Cached/etc + +# Programs + +- hmmstat +- hmmsim +- hmmc2 +- hmmlogo +skylign + +Easel toolkit + +- esl-afetch +- esl-alimanip +- esl-alimap +- esl-alimask +- esl-alimerge +- esl-alipid +- esl-alistat +- esl-cluster +- esl-compalign +- esl-compstruct +- esl-construct +- esl-histplot +- esl-mask +- esl-reformat +- esl-selectn +- esl-seqrange +- esl-seqstat +- esl-sfetch +- esl-shuffle +- esl-ssdraw +- esl-stranslate +- esl-weight |
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| diff -r 000000000000 -r a6098dd0cb46 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Jun 25 15:07:32 2016 -0400 |
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| b'@@ -0,0 +1,1072 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="3.1b2">hmmer</requirement>\n+ <yield/>\n+ </requirements>\n+ </xml>\n+ <token name="@WRAPPER_VERSION@">0.1</token>\n+ <xml name="stdio">\n+ <stdio>\n+ <!-- Anything other than zero is an error -->\n+ <exit_code range="1:"/>\n+ <exit_code range=":-1"/>\n+ <!-- In case the return code has not been set propery check stderr too -->\n+ <regex match="Error:"/>\n+ <regex match="Exception:"/>\n+ </stdio>\n+ </xml>\n+ <token name="@THRESHOLDS@">\n+-E $E\n+--domE $domE\n+\n+#if $T:\n+-T $T\n+#end if\n+\n+#if $domT:\n+--domT $domT\n+#end if\n+\n+#if $incE:\n+--incE $incE\n+#end if\n+\n+#if $incT:\n+--incT $incT\n+#end if\n+\n+#if $incdomE:\n+--incdomE $incdomE\n+#end if\n+\n+#if $incdomT:\n+--incdomT $incdomT\n+#end if\n+ </token>\n+ <xml name="thresholds_xml">\n+ <!-- Options controlling reporting thresholds -->\n+ <param name="E" label="report sequences <= this E-Value threshold in output" help="(-E)" value="10.0" type="float" min="0"/>\n+ <param name="domE" label="report domains <= this E-Value threshold in output" help="(--domE)" value="10.0" type="float" min="0"/>\n+ <param name="T" label="report sequences >= this score threshold in output" help="(-T)" type="float" optional="True"/>\n+ <param name="domT" label="report domains >= this score threshold in output" help="(--domT)" type="float" optional="True"/>\n+ <!-- Options controlling inclusion (significance) thresholds -->\n+ <param name="incE" label="consider sequences <= this E-Value threshold as significant" help="(--incE)" type="float" optional="True"/>\n+ <param name="incdomE" label="consider domains <= this E-Value threshold as significant" help="(--incdomE)" type="float" optional="True"/>\n+ <param name="incT" label="consider sequences >= this score threshold as significant" help="(--incT)" type="float" optional="True"/>\n+ <param name="incdomT" label="consider domains >= this score threshold as significant" help="(--incdomT)" type="float" optional="True"/>\n+ </xml>\n+ <token name="@THRESHOLDS_NODOM@">\n+-E $E\n+\n+#if $T:\n+-T $T\n+#end if\n+\n+#if $incE:\n+--incE $incE\n+#end if\n+\n+#if $incT:\n+--incT $incT\n+#end if\n+ </token>\n+ <xml name="thresholds_nodom">\n+ <!-- Options controlling reporting thresholds -->\n+ <param name="E" label="report sequences <= this E-Value threshold in output" help="(-E)" value="10.0" type="float" min="0"/>\n+ <param name="T" label="report sequences >= this score threshold in output" help="(-T)" type="float" optional="True"/>\n+ <!-- Options controlling inclusion (significance) thresholds -->\n+ <param name="incE" label="consider sequences <= this E-Value threshold as significant" help="(--incE)" type="float" optional="True"/>\n+ <param name="incT" label="consider sequences >= this score threshold as significant" help="(--incT)" type="float" optional="True"/>\n+ </xml>\n+ <token name="@ACCEL_HEUR@">\n+$max\n+--F1 $F1\n+--F2 $F2\n+--F3 $F3\n+$nobias\n+\n+ </token>\n+ <xml name="accel_heur_xml">\n+ <!-- Options controlling acceleration heuristics -->\n+ <param name="max" type="boolean" truevalue="--max" label="Turn all heuristic filters off (less speed, more power)" help="(--max)" falsevalue=""/>\n+ <param name="F1" type="float" label="Stage 1 (MSV) threshold: promote hits w/ P <= F1" help="(--F1)" value="0.02"/>\n+ <param name="F2" type="float" label="Stage 2 (Vit) threshold: promote hits w/ P <= F2" help="(--F2)" value="1e-3"/>\n+ <param name="F3" type="float" label="Stage 3 (Fwd) threshold: promote hits w/ P <= F3" help="(--F3)" value="1e-5"/>\n+ <param name="nobias" type="boolean" truevalue="--nobias" label="Turn off composition bias filter" help="(--nobias)" falsevalue=""/>\n+ </xml>\n+ <token name="@EVAL_CALIB@">\n+--EmL $EmL\n+--EmN $EmN\n+--EvL $EvL\n+--EvN $EvN\n+--EfL $EfL\n+--EfN $EfN\n+--Eft $Eft\n+ </token>\n+ <xml '..b'omain output.\n+\n+**E-value of per target inclusion threshold**\n+\n+Use an E-value of <= <x> as the per-target inclusion threshold. The default is\n+0.01, meaning that on average, about 1 false positive would be expected in\n+every 100 searches with different query sequences.\n+\n+**Bit score of per target inclusion threshold**\n+\n+Instead of using E-values for setting the inclusion threshold, instead use a\n+bit score of >= <x> as the per-target inclusion threshold. It would be unusual\n+to use bit score thresholds with hmmscan, because you don\xe2\x80\x99t expect a single\n+score threshold to work for different profiles; different profiles have\n+slightly different expected score distributions.\n+\n+**domain E-value per target inclusion treshold**\n+\n+Use a conditional E-value of <= <x> as the per-domain inclusion threshold, in\n+targets that have already satisfied the overall per-target inclusion threshold.\n+\n+**domain Bit score per target inclusion treshold**\n+\n+Instead of using E-values, instead use a bit score of >= <x> as the per-domain\n+inclusion threshold. As with --incT above, it would be unusual to use a single\n+bit score threshold in hmmscan.\n+\n+]]></token>\n+ <token name="@THRESHOLDS_NODOM_HELP@"><![CDATA[\n+Options for Reporting Thresholds\n+--------------------------------\n+\n+Reporting thresholds control which hits are reported in output files (the main\n+output, --tblout, and --domtblout).\n+\n+**E-value (-E)**\n+\n+In the per-target output, report target profiles with an E-value of <= <x>. The\n+default is 10.0, meaning that on average, about 10 false positives will be\n+reported per query, so you can see the top of the noise and decide for yourself\n+if it\xe2\x80\x99s really noise.\n+\n+**Bit score (-T)**\n+\n+Instead of thresholding per-profile output on E-value, instead report target profiles\n+with a bit score of >= <x>.\n+\n+Options for Inclusion Thresholds\n+--------------------------------\n+\n+Inclusion thresholds are stricter than reporting thresholds. Inclusion\n+thresholds control which hits are considered to be reliable enough to be\n+included in an output alignment or a subsequent search round. In hmmscan, which\n+does not have any alignment output (like hmmsearch or phmmer) nor any iterative\n+search steps (like jackhmmer), inclusion thresholds have little effect. They\n+only affect what domains get marked as significant (!) or questionable (?) in\n+domain output.\n+\n+**E-value of per target inclusion threshold**\n+\n+Use an E-value of <= <x> as the per-target inclusion threshold. The default is\n+0.01, meaning that on average, about 1 false positive would be expected in\n+every 100 searches with different query sequences.\n+\n+**Bit score of per target inclusion threshold**\n+\n+Instead of using E-values for setting the inclusion threshold, instead use a\n+bit score of >= <x> as the per-target inclusion threshold. It would be unusual\n+to use bit score thresholds with hmmscan, because you don\xe2\x80\x99t expect a single\n+score threshold to work for different profiles; different profiles have\n+slightly different expected score distributions.\n+\n+]]></token>\n+ <token name="@ATTRIBUTION@"><![CDATA[\n+\n+Attribution\n+-----------\n+\n+This Galaxy tool relies on HMMER3_ from http://hmmer.janelia.org/\n+Internally the software is cited as:\n+\n+::\n+\n+ # hmmscan :: search sequence(s) against a profile database\n+ # HMMER 3.1 (February 2013); http://hmmer.org/\n+ # Copyright (C) 2011 Howard Hughes Medical Institute.\n+ # Freely distributed under the GNU General Public License (GPLv3).\n+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n+\n+The wrappers were written by Eric Rasche and is licensed under Apache2_. The\n+documentation is copied from the HMMER3 documentation.\n+\n+.. _Apache2: http://www.apache.org/licenses/LICENSE-2.0\n+.. _HMMER3: http://hmmer.janelia.org/\n+\n+\n+ ]]></token>\n+ <token name="@HELP_PRE@"><![CDATA[\n+\n+What it does\n+============\n+ ]]></token>\n+ <token name="@HELP_PRE_OTH@"><![CDATA[\n+Options\n+=======\n+ ]]></token>\n+</macros>\n' |
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| diff -r 000000000000 -r a6098dd0cb46 nhmmscan.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nhmmscan.xml Sat Jun 25 15:07:32 2016 -0400 |
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| @@ -0,0 +1,101 @@ +<?xml version="1.0"?> +<tool id="hmmer_nhmmscan" name="nhmmscan" version="@WRAPPER_VERSION@.0"> + <description>search DNA sequence(s) against a DNA profile database</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ +hmmpress $hmmfile; + +nhmmscan + +@OFORMAT_WITH_OPTS_N@ +@THRESHOLDS_NODOM@ +@CUT@ +@ACCEL_HEUR@ +--B1 $B1 +--B2 $B2 +--B3 $B3 + +@ADV_OPTS@ +@LENGTHS@ +@CPU@ +@SEED@ + +$hmmfile +$seqfile +> $output + ]]></command> + <inputs> + <expand macro="input_hmm" /> + <!-- todo use Galaxy features like data libraries/data tables/??? --> + <param name="seqfile" type="data" format="fasta" label="Sequence file"/> + <expand macro="oformat_with_opts_n"/> + <expand macro="thresholds_nodom"/> + <expand macro="cut"/> + <expand macro="accel_heur_xml"/> + + <param name="B1" type="integer" label="window length for biased-composition modifier (MSV)" help="(--B1)" value="110"/> + <param name="B2" type="integer" label="window length for biased-composition modifier (Vit)" help="(--B2)" value="240"/> + <param name="B3" type="integer" label="window length for biased-composition modifier (Fwd)" help="(--B3)" value="1000"/> + + <expand macro="adv_opts"/> + <expand macro="lengths"/> + <expand macro="seed"/> + </inputs> + <outputs> + <data format="txt" name="output" label="HMM matches of $seqfile.name in $hmmfile.name"/> + + <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name"> + <filter>'tblout' in str(oformat)</filter> + </data> + <data format="txt" name="dfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name"> + <filter>'pfamtblout' in str(oformat)</filter> + </data> + <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name"> + <filter>'aliscoresout' in str(oformat)</filter> + </data> + </outputs> + <tests> + <test> + <param name="hmmfile" value="MADE1.hmm"/> + <param name="seqfile" value="dna_target.fa"/> + <expand macro="oformat_test" /> + <expand macro="seed_test" /> + <output name="output" file="MADE1.out" lines_diff="140"/> + <output name="tblout" file="MADE1.out.tblout" lines_diff="30"/> + <output name="domtblout" file="MADE1.out.domtblout" lines_diff="30"/> + <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="36"/> + </test> + </tests> + <help><![CDATA[ +@HELP_PRE@ + +nhmmscan is used to search nucleotide sequences against collections of +nucleotide profiles. For each sequence in <seqfile>, use that query sequence to +search the target database of profiles in <hmmfile>, and output ranked lists of +the profiles with the most significant matches to the sequence. + +The <seqfile> may contain more than one query sequence. It can be in FASTA +format, or several other common sequence file formats (genbank, embl, and +uniprot, among others), or in alignment file formats (stockholm, aligned fasta, +and others). See the --qformat option for a complete list. + +@HELP_PRE_OTH@ + +@OFORMAT_WITH_OPTS_N_HELP@ +@THRESHOLDS_NODOM_HELP@ +@CUT_HELP@ +@ACCEL_HEUR_HELP@ +@BIAS_COMP_HELP@ +@ADV_OPTS_HELP@ +@LENGTHS_HELP@ +@SEED_HELP@ + + +@ATTRIBUTION@ +]]></help> + <expand macro="citation"/> +</tool> |
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| diff -r 000000000000 -r a6098dd0cb46 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Sat Jun 25 15:07:32 2016 -0400 |
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| @@ -0,0 +1,54 @@ +Galaxy wrapper for HMMER3 +========================= + +This wrapper is copyright 2015 by Eric Rasche + +HMMER is used for searching sequence databases for homologs of protein +sequences, and for making protein sequence alignments. It implements methods +using probabilistic models called profile hidden Markov models (profile HMMs). + +Compared to BLAST, FASTA, and other sequence alignment and database search +tools based on older scoring methodology, HMMER aims to be significantly more +accurate and more able to detect remote homologs because of the strength of its +underlying mathematical models. In the past, this strength came at significant +computational expense, but in the new HMMER3 project, HMMER is now essentially +as fast as BLAST. + +http://hmmer.janelia.org/ +http://hmmer.janelia.org/about + + +Installation +============ + +The recommended installation is by means of the toolshed_. + +.. _toolshed: http://toolshed.g2.bx.psu.edu/view/iuc/hmmer3 + + +History +======= + +* v0.1 - Initial public release + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. |
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| diff -r 000000000000 -r a6098dd0cb46 test-data/MADE1.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MADE1.hmm Sat Jun 25 15:07:32 2016 -0400 |
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| b'@@ -0,0 +1,265 @@\n+HMMER3/f [3.1b2 | February 2015]\n+NAME MADE1\n+ACC DF0000629.2\n+DESC MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+LENG 80\n+MAXL 425\n+ALPH DNA\n+RF yes\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Sat Jun 25 17:24:24 2016\n+NSEQ 1997\n+EFFN 3.911818\n+CKSUM 3015610723\n+STATS LOCAL MSV -8.5408 0.71858\n+STATS LOCAL VITERBI -9.6224 0.71858\n+STATS LOCAL FORWARD -3.4150 0.71858\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.24533 1.59094 1.62722 1.16493\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.21058 4.11281 1.75146 1.46634 0.26236 0.00000 *\n+ 1 2.69765 2.44396 2.81521 0.24089 1 t x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03960 3.94183 3.94183 1.46634 0.26236 1.10301 0.40327\n+ 2 2.72939 2.37873 2.85832 0.24244 2 t x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03725 4.00179 4.00179 1.46634 0.26236 1.21367 0.35255\n+ 3 0.16099 3.16370 2.87328 2.99734 3 a x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03604 4.03416 4.03416 1.46634 0.26236 1.32877 0.30762\n+ 4 1.98862 2.42132 0.42649 2.10770 4 g x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03539 4.05203 4.05203 1.46634 0.26236 1.35213 0.29933\n+ 5 1.96369 2.69532 0.36534 2.32099 5 g x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03764 4.06427 3.92372 1.46634 0.26236 1.00259 0.45717\n+ 6 2.56994 2.11239 2.71946 0.30571 6 t x - -\n+ 1.37159 1.41129 1.39124 1.37159\n+ 0.03806 3.89715 4.07214 1.50442 0.25122 1.12269 0.39364\n+ 7 2.58388 2.10353 2.64646 0.31253 12 t x - -\n+ 1.38764 1.38524 1.38764 1.38465\n+ 0.03494 4.03864 4.09125 1.40070 0.28293 1.44046 0.27026\n+ 8 2.18552 2.70201 0.28821 2.64645 14 g x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03628 4.09157 3.96779 1.46634 0.26236 1.26997 0.32967\n+ 9 2.16916 2.82142 0.28427 2.60854 15 g x - -\n+ 1.38091 1.39033 1.38365 1.39033\n+ 0.03566 4.00237 4.08886 1.38021 0.28972 1.26961 0.32981\n+ 10 2.45517 2.15232 2.42886 0.34277 18 t x - -\n+ 1.39065 1.39065 1.39065 1.37335\n+ 0.03536 4.01212 4.09576 1.39554 0.28462 1.25024 0.33748\n+ 11 2.10260 2.95484 0.28160 2.64222 21 g x - -\n+ 1.36740 1.40555 1.40555 1.36740\n+ 0.03843 3.92069 4.02468 1.44733 0.26814 1.15789 0.37709\n+ 12 2.54740 0.30185 2.61355 2.21647 26 c x - -\n+ 1.38748 1.38276 1.38748 1.38748\n+ 0.03457 4.05446 4.09623 1.40847 0.28040 1.17686 0.36852\n+ 13 0.28443 2.72003 2.32214 2.48149 28 a x - -\n+ 1.38740 1.38740 1.38298 1.38740\n+ 0.03441 4.05976 4.10001 1.41198 0.27926 0.97690 0.47237\n+ 14 0.29412 2.55413 2.49679 2.35701 30 a x - -\n+ 1.38194 1.39067 1.38194 1.39067\n+ 0.03505 4.02482 4.10005 1.39522 0.28473 1.16906 0.37202\n+ 15 0.18837 2.99710 2.82270 2.77556 33 a x - -\n+ 1.39015 1.39472 1.37503 1.38539\n+ 0.03725 3.97815 4.02618 1.37955 0.28994 1.16870 0.37218\n+ 16 0.50816 2.05151 2.22111 1.82407 37 a x - -\n+ 1.36727 1.38730 1.39683 1.39405\n+ 0.04830 3.89881 3.61610 1.29026 0.32186 1.08301 0.41336\n+ 17 2.11260 2.73141 0.29747 2.64152 41 g x - -\n+ 1.36913 1.40376 1.40376 1.36913\n+ 0.03705 3.93681 4.08299 1.44872 0.26771 1.09472 0.40742\n+ 18 2.24459 1.90539 2.34054 0.43234 46 t x - -\n+ 1.33632 1.42493 1.39937 1.38665\n+ 0.04427 3.64574 4.06297 1.70501 0.20061 1.19872 0.35894\n+ 19 0.44322 2.17202 2.18055'..b'2.20911 0.11631 1.00864 0.45368\n+ 59 0.41659 2.44509 1.93972 2.20507 1034 a x - -\n+ 1.38198 1.38198 1.39194 1.38932\n+ 0.03641 3.98130 4.06929 1.35873 0.29704 1.31330 0.31325\n+ 60 0.41612 2.39160 1.97116 2.21075 1037 a x - -\n+ 1.03649 1.46430 1.57421 1.57557\n+ 0.04787 3.52599 4.05584 2.32461 0.10294 0.84329 0.56263\n+ 61 2.66264 2.12302 2.82746 0.28581 1056 t x - -\n+ 1.36925 1.39635 1.38930 1.39048\n+ 0.04103 3.97406 3.84419 1.39433 0.28502 1.12555 0.39227\n+ 62 2.26510 2.13196 2.42551 0.37231 1060 t x - -\n+ 1.37965 1.39147 1.39147 1.38264\n+ 0.04136 3.91664 3.88204 1.24613 0.33914 0.95630 0.48501\n+ 63 0.41244 2.25761 2.16787 2.12907 1062 a x - -\n+ 1.34515 1.41203 1.41203 1.37753\n+ 0.04086 3.77867 4.06371 1.30483 0.31638 1.13245 0.38897\n+ 64 2.51464 0.37905 2.62296 1.82008 1068 c x - -\n+ 1.39543 1.38753 1.39233 1.37008\n+ 0.03884 3.90614 4.01884 1.36573 0.29463 1.15716 0.37743\n+ 65 2.16380 2.11332 2.18714 0.42765 1073 t x - -\n+ 1.38764 1.38471 1.38519 1.38764\n+ 0.03603 4.05405 4.01529 1.40080 0.28289 1.06383 0.42332\n+ 66 2.79349 2.39141 2.87271 0.23478 1075 t x - -\n+ 1.37227 1.39101 1.39101 1.39101\n+ 0.03884 4.01734 3.90722 1.39017 0.28639 1.09574 0.40690\n+ 67 2.82488 2.47749 2.93179 0.21887 1078 t x - -\n+ 1.38141 1.39112 1.38915 1.38353\n+ 0.03675 3.99492 4.03549 1.35958 0.29675 1.21867 0.35044\n+ 68 2.77679 2.30433 2.90694 0.24425 1081 t x - -\n+ 1.37593 1.38989 1.45520 1.32825\n+ 0.04566 3.68855 3.93098 1.76176 0.18843 1.07133 0.41939\n+ 69 2.47698 3.17398 0.19595 2.95437 1093 g x - -\n+ 1.38264 1.38264 1.39734 1.38264\n+ 0.05482 3.96677 3.36946 1.40348 0.28202 1.13963 0.38557\n+ 70 2.84327 0.27906 2.97336 2.00890 1097 c x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03475 4.08873 4.05197 1.46634 0.26236 0.79234 0.60291\n+ 71 0.21870 2.83638 2.69251 2.65798 1098 a x - -\n+ 1.37446 1.37942 1.39640 1.39509\n+ 0.04066 3.94379 3.88865 1.41905 0.27700 1.24551 0.33939\n+ 72 2.35233 0.46085 2.23804 1.78715 1103 c x - -\n+ 1.38536 1.38781 1.38781 1.38421\n+ 0.03885 4.04214 3.88532 1.39310 0.28542 1.30851 0.31501\n+ 73 2.57111 0.32543 2.74124 1.98892 1105 c x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03403 4.09710 4.08422 1.46634 0.26236 1.37004 0.29316\n+ 74 0.27014 2.61416 2.53262 2.47636 1106 a x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03889 4.09695 3.83874 1.46634 0.26236 1.37489 0.29151\n+ 75 0.52873 2.16549 1.91736 1.90409 1107 a x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04237 4.09207 3.69758 1.46634 0.26236 1.41112 0.27954\n+ 76 2.33134 0.38082 2.65861 1.90055 1108 c x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04659 4.08459 3.55121 1.46634 0.26236 1.54765 0.23921\n+ 77 2.20588 0.45134 2.35553 1.84373 1109 c x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05904 4.07266 3.21140 1.46634 0.26236 1.68734 0.20458\n+ 78 2.69018 2.22054 2.82311 0.26898 1110 t x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.08061 4.04912 2.81320 1.46634 0.26236 1.91269 0.15980\n+ 79 0.16248 3.15867 2.86159 2.98963 1111 a x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.12592 4.00561 2.30158 1.46634 0.26236 2.22059 0.11490\n+ 80 0.17484 3.04770 2.86638 2.88183 1112 a x - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02045 3.90014 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/MADE1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MADE1.out Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| @@ -0,0 +1,87 @@ +# hmmscan :: search sequence(s) against a profile database +# HMMER 3.1b2 (February 2015); http://hmmer.org/ +# Copyright (C) 2015 Howard Hughes Medical Institute. +# Freely distributed under the GNU General Public License (GPLv3). +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# query sequence file: /tmp/tmpYWzicI/files/000/dataset_20.dat +# target HMM database: /tmp/tmpYWzicI/files/000/dataset_19.dat +# per-seq hits tabular output: /tmp/tmpYWzicI/files/000/dataset_22.dat +# per-dom hits tabular output: /tmp/tmpYWzicI/files/000/dataset_23.dat +# pfam-style tabular hit output: /tmp/tmpYWzicI/files/000/dataset_24.dat +# max ASCII text line length: unlimited +# Vit filter P threshold: <= 0.001 +# Fwd filter P threshold: <= 1e-05 +# random number seed set to: 4 +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +Query: humanchr1/239220001-239550000 [L=330000] +Scores for complete sequence (score includes all domains): + --- full sequence --- --- best 1 domain --- -#dom- + E-value score bias E-value score bias exp N Model Description + ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- + 1e-17 51.0 28.5 2.7e-12 33.7 0.7 9.6 5 MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon + + +Domain annotation for each model (and alignments): +>> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon + # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc + --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- + 1 ? -4.2 0.1 1 1 30 54 .. 80044 80068 .. 80030 80073 .. 0.80 + 2 ? -6.6 3.3 1 1 13 71 .. 154012 154072 .. 154011 154076 .. 0.75 + 3 ! 27.4 0.7 2.4e-10 2.4e-10 1 44 [. 174456 174514 .. 174456 174577 .. 0.62 + 4 ! 33.7 0.7 2.7e-12 2.7e-12 2 80 .] 302388 302466 .. 302387 302466 .. 0.86 + 5 ? 2.9 0.7 0.011 0.011 27 75 .. 304060 304107 .. 304021 304109 .. 0.61 + + Alignments for each domain: + == domain 1 score: -4.2 bits; conditional E-value: 1 + xxxxxxxxxxxxxxxxxxxxxxxxx RF + MADE1 30 ttgccattacttttaatggcaaaaa 54 + t g catt ttt aatggcaaa a + humanchr1/239220001-239550000 80044 TAGTCATTCATTTCAATGGCAAATA 80068 + 45789****************9966 PP + + == domain 2 score: -6.6 bits; conditional E-value: 1 + xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF + MADE1 13 aaaagtaattgcggtttttgccatt......acttttaatggcaaaaaccgcaattacttttgca 71 + aaaagta tt + ttttgc att a tttaa gcaaa a + tta tttgca + humanchr1/239220001-239550000 154012 AAAAGTAGTTTTCAATTTTGCAATTtgaccaATATTTAAATGCAAATATT----TTATATTTGCA 154072 + 78999999999999999999999984444444457777777899998876....77777888876 PP + + == domain 3 score: 27.4 bits; conditional E-value: 2.4e-10 + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............x RF + MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt...............a 44 + ttaggtt gtgcaaaagtaattg+ggtttttg cattactttt a + humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTTctgcatgctagaagtA 174514 + 79***************************************964443333333333330 PP + + == domain 4 score: 33.7 bits; conditional E-value: 2.7e-12 + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF + MADE1 2 taggttggtgcaaaagtaattgcggtttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaacctaa 80 + t ggt ggtgcaaaa aattg+ggtttttgccatt cttttaat gc a + a t ctttt caccaa ctaa + humanchr1/239220001-239550000 302388 TTGGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCTTTTAAAAGTAATGCTTTTACACCAATCTAA 302466 + 56899******************************************963333233345578**************996 PP + + == domain 5 score: 2.9 bits; conditional E-value: 0.011 + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF + MADE1 27 tttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaa 75 + tttt g c ta tt a tgg aaaaa ++ca tta ttttgca aa + humanchr1/239220001-239550000 304060 TTTTAGACTATA-GTTAAGTGGGAAAAAATACACTTATTTTTGCATTAA 304107 + 222222222222.3455779************************98765 PP + + + +Internal pipeline statistics summary: +------------------------------------- +Query sequence(s): 1 (330000 residues searched) +Target model(s): 1 (80 nodes) +Passed MSV filter: 1 (1); expected 0.0 (0.02) +Passed bias filter: 1 (1); expected 0.0 (0.02) +Passed Vit filter: 1 (1); expected 0.0 (0.001) +Passed Fwd filter: 1 (1); expected 0.0 (1e-05) +Initial search space (Z): 1 [actual number of targets] +Domain search space (domZ): 1 [number of targets reported over threshold] +# CPU time: 0.15u 0.00s 00:00:00.15 Elapsed: 00:00:00.16 +# Mc/sec: 165.00 +// +[ok] |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/MADE1.out.domtblout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MADE1.out.domtblout Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| @@ -0,0 +1,18 @@ +# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord +# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target +#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 1e-17 51.0 28.5 1 5 1 1 -4.2 0.1 30 54 80044 80068 80030 80073 0.80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 1e-17 51.0 28.5 2 5 1 1 -6.6 3.3 13 71 154012 154072 154011 154076 0.75 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 1e-17 51.0 28.5 3 5 2.4e-10 2.4e-10 27.4 0.7 1 44 174456 174514 174456 174577 0.62 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 1e-17 51.0 28.5 4 5 2.7e-12 2.7e-12 33.7 0.7 2 80 302388 302466 302387 302466 0.86 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 1e-17 51.0 28.5 5 5 0.011 0.011 2.9 0.7 27 75 304060 304107 304021 304109 0.61 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +# +# Program: hmmscan +# Version: 3.1b2 (February 2015) +# Pipeline mode: SCAN +# Query file: /tmp/tmpYWzicI/files/000/dataset_2.dat +# Target file: /tmp/tmpYWzicI/files/000/dataset_1.dat +# Option settings: hmmscan --tblout /tmp/tmpYWzicI/files/000/dataset_4.dat --domtblout /tmp/tmpYWzicI/files/000/dataset_5.dat --pfamtblout /tmp/tmpYWzicI/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpYWzicI/files/000/dataset_1.dat /tmp/tmpYWzicI/files/000/dataset_2.dat +# Current dir: /tmp/tmpYWzicI/job_working_directory/000/3 +# Date: Sat Jun 25 19:05:15 2016 +# [ok] |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/MADE1.out.pfamtblout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MADE1.out.pfamtblout Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| @@ -0,0 +1,27 @@ +# Sequence scores +# --------------- +# +# name bits E-value n exp bias description +# ------------------- ------ --------- --- ----- ----- --------------------- +MADE1 51.0 1e-17 5 9.6 28.5 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon + +# Domain scores +# ------------- +# +# name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description +# ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ --------------------- +MADE1 33.7 2.7e-12 4 0.7 302387 302466 302388 302466 2 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 27.4 2.4e-10 3 0.7 174456 174577 174456 174514 1 44 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 2.9 0.011 5 0.7 304021 304109 304060 304107 27 75 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 -4.2 1 1 0.1 80030 80073 80044 80068 30 54 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 -6.6 1 2 3.3 154011 154076 154012 154072 13 71 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +# +# Program: hmmscan +# Version: 3.1b2 (February 2015) +# Pipeline mode: SEARCH +# Query file: /tmp/tmpYWzicI/files/000/dataset_2.dat +# Target file: /tmp/tmpYWzicI/files/000/dataset_1.dat +# Option settings: hmmscan --tblout /tmp/tmpYWzicI/files/000/dataset_4.dat --domtblout /tmp/tmpYWzicI/files/000/dataset_5.dat --pfamtblout /tmp/tmpYWzicI/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpYWzicI/files/000/dataset_1.dat /tmp/tmpYWzicI/files/000/dataset_2.dat +# Current dir: /tmp/tmpYWzicI/job_working_directory/000/3 +# Date: Sat Jun 25 19:05:15 2016 +# [ok] |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/MADE1.out.tblout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MADE1.out.tblout Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| @@ -0,0 +1,14 @@ +# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- +# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target +#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 7.1e-18 51.5 28.5 2e-12 34.0 0.7 9.6 5 0 0 5 5 5 2 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +# +# Program: hmmscan +# Version: 3.1b1 (May 2013) +# Pipeline mode: SCAN +# Query file: test-data/dna_target.fa +# Target file: test-data/MADE1.hmm +# Option settings: hmmscan --tblout tblout --domtblout domtblout --pfamtblout pfamtblout test-data/MADE1.hmm test-data/dna_target.fa +# Current dir: /home/users/cpt/cpt/esr/Projects/galaxy/tools-iuc/tools/hmmer +# Date: Tue Feb 10 14:40:35 2015 +# [ok] |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/MADE1.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MADE1.sto Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,4021 @@\n+# STOCKHOLM 1.0\n+#=GF ID MADE1\n+#=GF AC DF0000629.2\n+#=GF DE MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+#=GF AU Finn RD, Hubley R, Jones T, Jurka J, Smit A, Wheeler T\n+#=GF SE Repbase\n+#=GF GA 15.98;\n+#=GF TC 32.00;\n+#=GF NC 15.90;\n+#=GF BM hmmbuild --hand --maxinsertlen 10 HMM.ann SEED.ann\n+#=GF SM nhmmer -Z 3102 --dfamtblout DFAMOUT -E 100 --noali HMM.ann\n+#=GF SM dfamseq\n+#=GF CT Type; DNA Transposon;\n+#=GF CT Class; Cut and Paste;\n+#=GF CT Superfamily; TcMar-Mariner;\n+#=GF MS TaxId:9606 TaxName:Homo sapiens\n+#=GF RN [1]\n+#=GF RM 8643651\n+#=GF RT Tiggers and DNA transposon fossils in the human genome.\n+#=GF RA Smit AF, Riggs AD;\n+#=GF RL Proc Natl Acad Sci U S A 1996;93:1443-1448\n+#=GF DR Repbase; MADE1;\n+#=GF CC Resembles an internal deletion product of Mariner1; has 37 bp\n+#=GF CC TIRs and a TA target site.\n+#=GF SQ 1997\n+#=GS H.sapiens_13.1/49567006-49566901 DE 13 dna:chromosome chromosome:GRCh37:13:1:115169878:1\n+#=GS H.sapiens_8.1/107923792-107923714 DE 8 dna:chromosome chromosome:GRCh37:8:1:146364022:1\n+#=GS H.sapiens_6.1/35544547-35544476 DE 6 dna:chromosome chromosome:GRCh37:6:1:171115067:1\n+#=GS H.sapiens_8.1/33053357-33053450 DE 8 dna:chromosome chromosome:GRCh37:8:1:146364022:1\n+#=GS H.sapiens_7.1/137095299-137095226 DE 7 dna:chromosome chromosome:GRCh37:7:1:159138663:1\n+#=GS H.sapiens_19.1/19100550-19100497 DE 19 dna:chromosome chromosome:GRCh37:19:1:59128983:1\n+#=GS H.sapiens_1.1/164701792-164701870 DE 1 dna:chromosome chromosome:GRCh37:1:1:249250621:1\n+#=GS H.sapiens_3.1/68038940-68038866 DE 3 dna:chromosome chromosome:GRCh37:3:1:198022430:1\n+#=GS H.sapiens_Y.1/16255032-16255111 DE Y dna:chromosome chromosome:GRCh37:Y:1:10000:1\n+#=GS H.sapiens_11.1/78684849-78684770 DE 11 dna:chromosome chromosome:GRCh37:11:1:135006516:1\n+#=GS H.sapiens_9.1/102803629-102803549 DE 9 dna:chromosome chromosome:GRCh37:9:1:141213431:1\n+#=GS H.sapiens_7.1/70331740-70331819 DE 7 dna:chromosome chromosome:GRCh37:7:1:159138663:1\n+#=GS H.sapiens_12.1/65806432-65806356 DE 12 dna:chromosome chromosome:GRCh37:12:1:133851895:1\n+#=GS H.sapiens_4.1/140063757-140063828 DE 4 dna:chromosome chromosome:GRCh37:4:1:191154276:1\n+#=GS H.sapiens_2.1/145673253-145673319 DE 2 dna:chromosome chromosome:GRCh37:2:1:243199373:1\n+#=GS H.sapiens_8.1/75316483-75316561 DE 8 dna:chromosome chromosome:GRCh37:8:1:146364022:1\n+#=GS H.sapiens_10.1/58241727-58241653 DE 10 dna:chromosome chromosome:GRCh37:10:1:135534747:1\n+#=GS H.sapiens_10.1/9215317-9215239 DE 10 dna:chromosome chromosome:GRCh37:10:1:135534747:1\n+#=GS H.sapiens_3.1/5959133-5959195 DE 3 dna:chromosome chromosome:GRCh37:3:1:198022430:1\n+#=GS H.sapiens_5.1/123101247-123101157 DE 5 dna:chromosome chromosome:GRCh37:5:1:180915260:1\n+#=GS H.sapiens_X.1/35165291-35165214 DE X dna:chromosome chromosome:GRCh37:X:1:155270560:1\n+#=GS H.sapiens_1.1/178351842-178351911 DE 1 dna:chromosome chromosome:GRCh37:1:1:249250621:1\n+#=GS H.sapiens_5.1/109325838-109325779 DE 5 dna:chromosome chromosome:GRCh37:5:1:180915260:1\n+#=GS H.sapiens_3.1/108039241-108039320 DE 3 dna:chromosome chromosome:GRCh37:3:1:198022430:1\n+#=GS H.sapiens_3.1/11149279-11149387 DE 3 dna:chromosome chromosome:GRCh37:3:1:198022430:1\n+#=GS H.sapiens_9.1/76348944-76348881 DE 9 dna:chromosome chromosome:GRCh37:9:1:141213431:1\n+#=GS H.sapiens_4.1/13679946-13679866 DE 4 dna:chromosome chromosome:GRCh37:4:1:191154276:1\n+#=GS H.sapiens_3.1/50865115-50865038 DE 3 dna:chromosome chromosome:GRCh37:3:1:198022430:1\n+#=GS H.sapiens_3.1/142708263-142708322 DE 3 dna:chromosome chromosome:GRCh37:3:1:198022430:1\n+#=GS H.sapiens_14.1/99520157-99520073 DE 14 dna:chromosome chromosome:GRCh37:14:1:107349540:1\n+#=GS H.sapiens_8.1/49894414-49894352 DE 8 dna:chromosome chromosome:GRCh37:8:1:146364022:1\n+#=GS H.sapiens_22.1/33739050-33738973 DE 22 dna'..b'......T.............T................T....................................T............................A.........................A......................AT......................................G...........................G...............................C........A...................A.............................A...........................A......................A.........................C......................T...............G.................C................A..A..................C...T.A.....C....T.T..T..T...........G...CA....T.CAACCTA.\n+H.sapiens_Y.1/15779845-15779925 TTAGGT.....T.AG..T..G....C.G.A..T...A...G....T..........A........A.......T.........T...G.T...............G........................G...................T..................T.......................T....................T................................T...............................G....................................C.............................C........................................A..................................................T.........................T..............................................A.....................................C...........................T.............T................T....................................C............................A........................TA.......................T......................................G...........................G...............................C........A...................A.............................A...........................A......................A.........................G......................C...............A.................C................A..A..................T...T.A.....C....T.T..T..T...........G...CA....C.CAAGCTAA\n+H.sapiens_14.1/99179197-99179121 .TAGGT.....T.GG..T..G....C.A.A..A...A...G....T..........A........A.......T.........C...G.T...............G........................A...................T..................T.......................T....................T................................................................G....................................C.............................C........................................A..................................................T.........................T....................................................................................C...........................T.............T................T....................................T............................A.........................A.......................T......................................G...........................G...............................T........G...................A.............................A...........................A......................A.........................C......................C...............A.................C................A..A..................T...T.A.....C....T.T..T..T...........G...CA....C.CAACCTAA\n+#=GC RF xxxxxx.....x.xx..x..x....x.x.x..x...x...x....x..........x........x.......x.........x...x.x...............x........................x...................x..................x.......................x....................x................................x...............................x....................................x.............................x........................................x..................................................x.........................x..............................................x.....................................x...........................x.............x................x....................................x............................x.........................x.......................x......................................x...........................x...............................x........x...................x.............................x...........................x......................x.........................x......................x...............x.................x................x..x..................x...x.x.....x....x.x..x..x...........x...xx....x.xxxxxxxx\n+//\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/dna_target.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_target.fa Sat Jun 25 15:07:32 2016 -0400 |
| b |
| b'@@ -0,0 +1,5501 @@\n+>humanchr1/239220001-239550000 \n+CCAAAAATACGAAAAAGTAGCCAGGCATAATGGCACACATGTGTGGTCCCGCTGCTTGGG\n+AGGCCGAGGTGGGAGGATCGCTTGAGCTCGGAAGGCAGAGATTGCAGTGAGCTGAAATCC\n+CACCACTGCACTCCAGCATGGGTGACAAAGCAAGACTCTGTCTCACCAAAAAAAAAAAAA\n+AAAAGAAGGAACTGGCAGAGTCCCAACTGACAGGTATATTTTCTGTTGACCAAAATACGG\n+TTCTTACTGATATTTGATACTGACTCATAGTCACAACTGCCATATGAAAAGAGAGAGATC\n+ATTTTTTTTTCCTGGCAATATGTGATGGTGGAAGATACTTAGTGTGGTGTCCTGATAAGA\n+TAAGTAAGCAACAATGAGGAGGGAACCCCAGGGAGGGAGGACCATTGTTCCGAGAGAACA\n+GCTAATCACAGACAACCTGTTGGCAGGACATCCTGTTCCCAAATGCCTTGCTTGGCAAGT\n+AGGCCCAGCAGCAGGACCTCATTGTGCAGGTGGCCCCCTCCAGCATGATCCTATAAAACT\n+TCCCTCCAGCCCCCGCCTCTTGGCGGACAGACTTCTCTCTGCTGCACTGCCCATTGCTTT\n+CTTGCAATCTTTGTACTTTCCCTAATAAATCTGCCTTTCCTTACCCATGACTGTCTGTCT\n+TGGTAAATTCTTTTACCTCCCACGACACCAGCCACAGCCAGTTGCACTCACAGCACTTAG\n+GAAAATAAAAAAAATCAAGGCTGACACTCTGGATACCAATATGTAATGAAGTGTTCTTCT\n+TACAAGAGCTTATGAGATAAATAGAAACGTAACAACAATTTTTATTAAGCAAGATATAAA\n+AACTTCACCATAGGCTGATCCTGTTTTCATTCATGGAAGATAAATACTATCCCTCACTTA\n+AGAGCTTTTTGTGTAGGAATTCTTCTTCCTTATTTTTTCACGAATAAAGATAGGGATGTC\n+CTTAGCATCCAAAATCAGTCAAAAAAAAATTGACATTTCATGTCCTGGTTAGACTACTCT\n+GGCAGCTTGCTGGAATGGTCACTTGCTTCTCCCAACTGGATCTCAAGTCCAGACCCCTTT\n+GTTGTCGGCCCCCCTCCTGGCCACCCCCACCACAATCACTTAATAAGAAATACCAGCTGT\n+AGAGCTCAGAACTGCTATGACAATTAAAGCTTCCCACCTTCATGAAAACTGTTGAAAATG\n+GGGCAGAACAAAAAGTAGTGTGACAGAATTTCTCTATACTGTCTGATGCATTGCTTCCAA\n+TGTAGGGAGACCTTTAATTGGTTCTCTGGCTTTTGGTTCCATCCTATTGTAAACAAAGAA\n+TCAAAGTATAGTAAGGTTCAAAGAAGTAGGGAGTGCTGAATTTGGCAGATGGCACAAGAC\n+ATGGTTAGAAAGAAAGCATCCTCAGAGGAGATGAGAATGATGCTGAGCCTTGGCAAATTG\n+CAAGGAATGCGTAGTTAAGCAGAGCAACTTTTCACAGTCAGATTTAGAGTATAACTAACT\n+CTGGAATGACGAGACACACAAAAAGATAAATGCTATTTATCACCACTGCTCACAATGAGG\n+AATCAGTAAGCAGCCATAACAGATGCTGCGCTGCCCAGATCCCCTCCTTAGGACTGAGGT\n+GCTCACTTGCCAGCTGCAAAGACTCGTGCCTGAGTCTCTCTCCAGGCAATGTTCTCAGGT\n+CAAAAGGCAGCTGCCCTGCTGGAGGTTATAGCTCCATCCAGCGGCATGCAGAATCCATTG\n+ATTAGCAGATGTGGGCATATGAAGACAATGTCTTGGCTCAAATTAGAACGGTTCTAAAAT\n+TGCTGCGACCCTGGCTAGAATTACATTGCAGGTGAGCTTCTTCCTCCATCCAGTCCTGTT\n+TCTCTCACTCCATTACAGTTGTGATTCCCAAGAGCACTTCACAATAAACCTCCAGCACAC\n+AGTCTCCTTCTCTGAGTCTCTTTCTAGGAAAGCCTGACCTAAGACAACAGCCTCCCTATG\n+GCAAAAATGTCCAAATTAATAGCTTCTTTATATAGGGGGCAAAACCACCAGCAACCAAAA\n+CTTTTATTTAAAAAAATGACAATTGTATGACTAATCAGCGTACATTTAACTTCAGGATTG\n+AAAATGTTGCATCCTGAGCTTAATTTCCTTGATTTTACTTTGAACACTCTTTGAGTTGTG\n+TTTCTATTTTTAGACCACAGAATTTAAGATAAATGTGCATAATTTAGAGAGGTTTCAAAG\n+AAAGGCAAGTCAAGTGATTAAATAATGAGAATAAAATTAGTATAAAAAGTGCCAGGAACA\n+TTTGGTCTTTTGAAAGGAAGGGCAAGGGGGCCATTTTAATAACAGCCTTCACATACATGC\n+CTACTTATTCAGATAGACGGTTGTGAGGTCAAGCTGGAGGGGCAGATAGGGATCCGATCA\n+CTATAGACCCAGATTCCTGCGGTAGCTTCCTACATTATCTCCCAGCTTTCACCCTCCTGG\n+CAACATCCAGAGTGATCCTTGAGAAACCATAACAAATCACATCGCTCTTCACCTCCAATC\n+CACCTCTTCACTCTCCATCAGTCCTTCTTATGAACTACACACACTCTGTGATCAAGCCCT\n+GGCTGCCTCTAGGGATTGTCTCCTCCCATTCACCACTACAAAACTTCTTCCTCGAAGGTG\n+TCCAGCAGGCCAAGCCACGCTGGACTCAGGGATCTCCCCACGGCTGTGTTCTTCCCATAG\n+TACCACAAACCCTCCACTCCATTCACTTATCTGCTCAATGGCACCTCCTGTGAAAGGATT\n+TAAAGTAGCCCTCCTCGTGATGTTTTATTCCCTTACTTTGCTTTACAAGCCATCAGAGCA\n+TTTATTACTTCTTGATATTCTAATTCTAATATGCTAACGTTATATTTTCTATATATACCA\n+TTAAATATGGAGAGAATGGATAGATATAGATTTAGATAGCTGATACAGGTAAATATAGAC\n+AGAGGTAAAAATATAGATAGAGACTCTTTCATTTAGTCCTACGTGCCCATCAAAATGTAA\n+GCTCCGTAAGGGTAGGATCTTTGTCTCTTAGTTAACTCCTCTATGGTGGAGGAGATGTGA\n+GACAACCAGAAATTTCTGTCTAAAAAAAAAAATCACACACTCGATCACACACTCGATAGG\n+TGTTCAATCAATATTTGGTGACTGAATGAATGGATGAATGTGATCCCTTTAAATCTGTAT\n+CCTCACTATACAAACTTCCTTAAATATCTATTAGGTAATTTAGCTAAACTTTTCTTACTC\n+GCTCCAGTGTGGTGTGTGTTTGTCTTTTCTTCCTCCTTGACCTATAACTATTGACAGTTA\n+TACAATATGGTGGTTCCACAGCCACCAGCCTCCTTTTCCTATTCTCTAGAAAGAACGAGG\n+ATGAGCTATAAAATTCATCTAACCCTATCATCTTTTTAAGGGGTATAATATTAAGTGGAA\n+ATTCTTTACAAATTTAAAGTTATATTCAATTTGTAAATAAGAATAATTATTATTGCCTGT\n+AACTTTTGAACTTGGCCCATCTCGTTTCTGCCTTCTTGAAATTCGGTATTTTTTATTAGA\n+GCTTTCAGAGTCAGCTTTTGATTTTATTGATCTTTTTTGTTTTGTTTTTATTTATGTTCT\n+TGTCTTTTTAACTTACATTGTGTGTGTATTCTTATTTATGTTCTTGTCTTTTTAACTTAG\n+ATTTTTGTATGTATTCTTTTCTTTATTTCTACCTCCTACAATGGAATACCCAGTTATTTT\n+TTATATATATGATATATATATGGCATATATATGACATATATGTATGTCTTTCTTACTTAT\n+ATTTTTAAGTCTTTACTTCTAACTTCTAGAATGGAATATA'..b'CTTGTGCAGGGAAATTCCCATTATTAAAAC\n+CATCAGATCTCATGAGACTTATTCACTGTCATGAGAACAGTACGGGAAAGACCTACATGA\n+TTCAATTATCTCCCTCCCACAACATGTGGGAATTATGGGAGCTACAAGATGAGATTTCGA\n+TGTGGACAAAGCCAAACCATATCAATACCTTTCGAGTTCTTCACCATGATTTTTTCAAAT\n+GTTGTTTCTGCTAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTCTTTCTGC\n+TCTCTCTGGATATTTTCTATTGATTTCTATATGAGACCATCAGTTTATTTGTGTAGTATC\n+CAGGTGGTTTTTAAACCTATGTAATTACTTCTTGATTTAGCAATTCAACAAAGTTCATTT\n+TATTATTTTTATGAAACCTAATATCCTGCTGAAATGCTCTGTTTTTTAATCCATTTTGCC\n+CATCTCCACGGTAGTTCATGGTTATTTAAAAGCCCTTGCCTATTAGTTCCAAAATCTGTG\n+TCATTTCTTGAGCTCTATTGACTGTATTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT\n+TTCTTTCTTTCTTTCTTTCTCTCTTTCTTTCTTTCTTTTTTTGCCATCAGGTACTCTTTT\n+CTGCTTCTTTGCATGTCTGGTAAGTTTTGATTGCATGCAGCATTTGTAGAAATTTTAGCT\n+TATGTTTTCTTCCTCTCATAAACTTTGAGTTGTGTTCTAGCAGGTGGTTAAATCATTGGT\n+AGATCACCCTAACCCTACAGAAGCCTAGTTTTTGCTTCGTTCAGTCAAATCTATTTCAGT\n+TTATTCTTTCTCTTAGGACATCATCCTTCTATCTAAGGAGTATCCTTCAAGGGTTTCATC\n+CTAATGCCTGAGGTGTTCACCAAAGTCTTTCCATTCTGACTGGAACCGAACTCCAACATC\n+TCCTCAGAATTGTGTGATCTCTAAAATGTCCACTCAAATTTCAGCCTCTCTGCCACTGCA\n+CTGTATCTGTCAGGTCTCTAGAATAATGCCTCTGGACACATGCAGCCTAGCAATTCAGCT\n+AACGAACTGAGAGGAATTGCCACACAGACTTCCGGTGCTGCCTCTTGGTACTCACCTCTC\n+TGTCACCTTGCTTACCTCCAGAAACCTTAGTTACTTTATATAGCTCCAAGCTCTTGAGCT\n+ATATGCCCTCTGCTCAGTGAAACTGCAGCTCTCTGCTTATTCTCAACCTCCCAAAACTTC\n+TGCTGAAAAAAATATCCCCTGAGGAAAAATAATCCATGGGAATGGGCTCATTCCATGTGC\n+CTCCAGTTACCCCAAATTGCAGCACTATGTTGGTTATGGTTCAGAAGTAAAAAATGTTTG\n+ATATAGTTTTTCCAGGTTTTATAGCTATTTTATGGTAGAAAGGCAAGTGAGTGCTATTAG\n+CTAATTGTCCAGAACCAGAGTCTCATTTCATAACTGCATAAATCCTTTGCTTATCTTGTG\n+TATTTTTTTAAACAAACCTAAAATGCAGGATTTCTAAGTATTTTCCAGTTCTAGCTGATT\n+TCCTTCATTTTAGATGAAAATCCAAAGGTAAATACTCTTTGGTTTCTGATTTTTGGCATC\n+TTGTAAATAAGCATTGCCTCCAGTTTGGTTCATTCTCAGATCTATTAAGTATCCCATTTA\n+TATTTTCCTCTGAAATATAATTTGATAAATCTGCTGAATGATCGGGCACCAAGGTCAGGA\n+CCAATACCTTATTCAAGCCCAGCATGAATCCACTTACCAAGAAACTGGAGGCAACTCTGT\n+CTAAACTGTAATTTGTTTGATACAAACATGCCATCTACATTTACCTTGTCCATAATGATA\n+ATGGGAAGGTTAGCTGAAATCAGGAAATACTGTATTATGAGTTTAGTGACTATTTACAAG\n+TGGAAATGAATTTAATCTGGTATGATTTATTTTACTAAATTGTAGTTGCTTCCTTTTCTT\n+TTCTCACTAGTCACAAATGATTTATTTCAGTATCTTCTCCAGAACATTGCCAGAGGCCAG\n+TCTCAAACTTAACCATTGTATACATACCAGAATATTTTCATTAAAAATTAATAACTTTTG\n+TCTTTCTCTGAAAACTACATAATCACTACTTGTCCATTCTTTTGGTCCTTGCCTGTTCTT\n+TATGGATCAATATTATCAAAGCTACTCCTGTTTCCACAGGCAAATAACAATTCTATGTAA\n+TGGGAAAGATATTAAATCCGAATTCATGTTCCTCTTACTAGCTATATAATGGACAATTAA\n+ATTATTCCTTTAAATTCCTTTCTCCTTTAGTACACAAGGATAAAATACTCATTTGATTGT\n+TTTAAAGATTAAAGAAGTATCTGAAAGTAACTGTTATATTTTCTTCTGAGAGGTATCCCA\n+ATAAAAAGGCTACAATATTGTTATTATTATTACTATTCTAGTATCCTGGATGCAATTTAC\n+CTAAGCCTAGATATTTTAATTAATTTAAGTAGCCACATGCTTTCTCACTAGCTATTTTCC\n+CAGCATGATCTCAATCTTTTCTACGCAAAGTTTAGTCTCTTCTCTCCTAAAGATTGTTCT\n+ACCTAGAGAAGAATATAGGTTCAGAAAGGAATTCATATACTGGTGTTTCTCTAATCTCTT\n+AGAATTACTTAATTTTTCAAAGAGCTCTATCTTTTCCTATTTATCTTCTTGTTCCAAATA\n+GAATTAAAATCATTTGCTGCCTTTAATATTGTTAAATATTTCATTTCATACTATGCTTCA\n+ATTTCTTGCTTTTTTCTTCTTTTTATCTTCCTCCTTCCTTCCTTTTTCTTTCTTTTCTTC\n+TTTTTCAGTTATCATTGTTATGCTTGTCCTTTCTTGTGAGATTCCTCTGTTATCTTTCCT\n+TATGTGCTTTTTAAACAAAACCTCGAGAGTGCCGTGGGACAGCCTCATTGGTATCTTTTC\n+AAATTTGGTATCTCTCCACTTTTTCCTTACATAGTTAGCTGGCAGTAGTACATAATAACC\n+TTTTCTGTCTCTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTA\n+GATTTTCATTCCTCTTGAGCTTTAAAAGACTGGCTAGCAATGTTATATCTTTCATTTTAT\n+TTTCTGATTTAAAAAAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT\n+ACGCGCGCGCGCGCGCGCGTGCACGTCAGTGTCTTCTTCATGGATGCTTGTCTTATTTTC\n+TCCCAAGGTGTAACTGTCCAGGGAGGGAAAAGTCAAGTCGTCCTCTATTACACTGCTCTG\n+CAGAAACAGACTCACTAAATGTCAAAAAGTAGATGCATCAGACTGTTCCTTAGAGAAAGG\n+TTTGCCATGGAGTCGTATATTGTAACTGAGCTGAAGTTCACTCATCGATAAGTTGTGCCC\n+AAGGAATCGAATTCCTTCCAGTCCTTCTAAGCAGTCCAGGGAAACCAATTTAAAAGCGAA\n+CACAACAAAACTAACAGACCGGCAAAATCTATCTTTGAAGCGCCGCGGGAGGCACAATTT\n+GGGAACAGGTGAGGCCATGCTGGGTGGGTGAGGCCCCCCTCTCTCCTGCTTGGTGTTCCG\n+CTTTCAGCCAACCCACCCCAGGAGTACCCTGGGATCTCCTCGCCCCCTGCCAGGCGGAGA\n+ACGCGGAGCCCAGCGGGCACGCGGGAATGGAGCTAGGCGCCGGCAGGGCAACTGGGCATG\n+CTCAGAAGCCGGGCAGGTTTTGGTCTCAAGCACGCAGCCTGTGCATTACACCAGCTCTCT\n+CAGTCCGGGGAGGAGGAGGAGCAGGAGGAACGCGAGGAGGAAGGAGAGGAGGAGCGGCCA\n+GCAGTAGCCACGACCGCCACCACCAGGCAGAGGAAGAGTTCGTGGGGAGGAAAAGACCTC\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/fn3.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fn3.hmm Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,285 @@\n+HMMER3/f [3.1 | February 2013]\n+NAME fn3\n+ACC PF00041.13\n+DESC Fibronectin type III domain\n+LENG 86\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS yes\n+MAP yes\n+DATE Fri Feb 15 06:04:13 2013\n+NSEQ 106\n+EFFN 11.415833\n+CKSUM 3564431818\n+GA 8.00 7.20\n+TC 8.00 7.20\n+NC 7.90 7.90\n+STATS LOCAL MSV -9.4043 0.71847\n+STATS LOCAL VITERBI -9.7737 0.71847\n+STATS LOCAL FORWARD -3.8341 0.71847\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.70330 4.91262 3.03272 2.64079 3.60307 2.84344 3.74204 3.07942 2.79841 2.65364 4.14864 2.95826 2.87120 3.02176 2.96125 2.44783 2.59757 2.57680 4.02726 3.21526\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.00000 *\n+ 1 3.16986 5.21447 4.52134 3.29953 4.34285 4.18764 4.30886 3.35801 3.70246 2.11675 4.32057 4.32984 0.76706 3.91880 4.22437 3.23552 3.21670 2.88223 5.80355 3.93889 1 p - - -\n+ 2.68629 4.42236 2.77530 2.73088 3.46365 2.40512 3.72505 3.29365 2.67737 2.69316 4.24701 2.90358 2.73734 3.18157 2.89812 2.37898 2.77517 2.98515 4.58488 3.61514\n+ 0.09796 2.38361 6.81068 0.10064 2.34607 0.48576 0.95510\n+ 2 2.70230 5.97353 2.24744 2.62947 5.31433 2.60356 4.43584 4.79731 3.17221 2.95090 5.01531 3.26630 2.09873 3.30219 3.34190 1.45782 3.14099 3.57507 6.40877 4.25623 3 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510\n+ 3 1.38116 5.98285 3.50784 2.54546 5.32790 3.48945 4.43311 4.81385 2.38773 3.98773 5.02352 3.27895 1.92260 2.69012 2.96119 2.64228 3.29228 3.29618 6.41555 4.20553 4 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510\n+ 4 3.32856 5.10403 4.47046 4.60386 4.23079 4.75438 5.09647 2.69918 4.46632 2.97102 4.23502 4.77984 0.63388 4.68581 3.76781 4.05413 3.46306 2.04533 5.75329 4.56372 5 P - - -\n+ 2.68616 4.42236 2.77530 2.73134 3.46365 2.40523 3.72505 3.29295 2.67751 2.69303 4.24634 2.90357 2.73739 3.18157 2.89783 2.37897 2.77530 2.98529 4.58488 3.61514\n+ 0.09682 2.39494 6.81068 0.10162 2.33687 0.48576 0.95510\n+ 5 2.95325 4.65976 3.57762 2.20709 3.14816 2.51487 3.41109 4.78902 2.65862 3.19599 4.41042 3.45032 3.44719 2.43205 2.26492 2.25400 2.23196 3.66828 4.80003 4.52485 7 e - - C\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01246 6.08833 4.59386 0.61958 0.77255 0.48576 0.95510\n+ 6 2.74215 5.97618 2.19482 2.69150 4.58171 2.33553 3.83525 3.28222 2.95080 3.32698 5.01691 1.45822 3.52462 2.79670 2.90942 3.13467 3.27956 4.36668 6.40902 3.92307 8 n - - E\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00341 6.07928 6.80162 0.61958 0.77255 0.44282 1.02784\n+ 7 3.32507 4.98102 3.78072 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00992 6.08833 4.87890 0.61958 0.77255 0.48576 0.95510\n+ 79 2.39836 4.69624 2.57939 2.56364 4.72011 1.55094 3.74815 4.26504 2.61409 4.28517 5.02018 2.82673 4.26340 2.69971 2.87382 2.73983 2.53993 3.07568 6.41202 5.00074 110 g - - T\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00340 6.08180 6.80415 0.61958 0.77255 0.45398 1.00812\n+ 80 2.22211 4.94595 2.69424 2.44928 4.84552 2.32005 3.06335 2.95704 2.33976 3.55821 4.09648 2.87488 4.09930 2.85656 2.97877 3.08279 3.07714 2.39346 6.40553 4.01548 111 a - - T\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.38398 6.08833 1.15015 0.61958 0.77255 0.48576 0.95510\n+ 81 2.96920 5.43248 3.46409 2.76236 3.93019 1.02513 4.29951 4.07917 3.10833 3.39330 4.50784 3.40559 4.48149 3.45547 3.56956 2.50552 2.39680 3.76237 5.94228 3.01765 112 g - - E\n+ 2.68652 4.42259 2.77488 2.73144 3.46170 2.40466 3.72529 3.29388 2.67703 2.69373 4.24724 2.90335 2.73774 3.18162 2.89801 2.37895 2.77529 2.98552 4.58511 3.61537\n+ 0.29928 1.35852 6.43163 0.48724 0.95274 1.77816 0.18506\n+ 82 2.84273 4.18992 3.05053 2.12883 3.36284 2.75189 4.25559 3.03507 2.66396 2.65563 4.59024 2.63081 3.84786 2.76844 3.19058 2.84597 2.82776 2.89016 3.06821 3.41272 117 e - - E\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00494 5.70928 6.43163 0.61958 0.77255 1.56406 0.23482\n+ 83 3.37920 5.61493 3.74277 3.20384 4.92800 1.01625 3.96683 4.35082 2.94708 2.91738 4.72998 3.71516 3.70329 3.52945 3.00683 1.61777 3.61882 4.00263 6.13360 4.80162 118 g - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00481 5.73459 6.45693 0.61958 0.77255 0.30535 1.33510\n+ 84 2.58463 5.93784 3.04102 2.09605 4.57465 2.51630 3.24109 4.26208 2.60545 3.44607 3.62705 3.20484 1.89678 2.68661 2.74662 2.97880 3.02092 3.23569 6.37074 4.50367 119 p - - E\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00361 6.02233 6.74467 0.61958 0.77255 0.28862 1.38348\n+ 85 2.48488 5.72055 3.87501 1.97538 3.04853 3.48010 4.51877 3.51898 2.88839 2.73568 4.42660 3.64380 2.08811 3.48814 2.70856 2.40769 2.92982 4.05679 2.77386 3.43366 120 e - - B\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510\n+ 86 3.03720 5.94099 3.75455 2.96917 5.26587 2.91682 3.66571 4.11840 2.98472 4.23738 4.98891 3.74380 4.66031 3.40955 3.12788 0.72443 2.46104 4.32115 6.38683 4.99111 121 s - - E\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00227 6.08723 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/fn3.keys --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fn3.keys Sat Jun 25 15:07:32 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +fn3 |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/fn3.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fn3.out Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| @@ -0,0 +1,119 @@ +# hmmsearch :: search profile(s) against a sequence database +# HMMER 3.1 (February 2013); http://hmmer.org/ +# Copyright (C) 2011 Howard Hughes Medical Institute. +# Freely distributed under the GNU General Public License (GPLv3). +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# query HMM file: fn3.hmm +# target sequence database: 7LESS_DROME +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +Query: fn3 [M=86] +Accession: PF00041.13 +Description: Fibronectin type III domain +Scores for complete sequences (score includes all domains): + --- full sequence --- --- best 1 domain --- -#dom- + E-value score bias E-value score bias exp N Sequence Description + ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- + 1.9e-57 178.0 0.4 1.2e-16 47.2 0.9 9.4 9 7LESS_DROME RecName: Full=Protein sevenless; EC=2.7 + + +Domain annotation for each sequence (and alignments): +>> 7LESS_DROME RecName: Full=Protein sevenless; EC=2.7.10.1; + # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc + --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- + 1 ? -1.3 0.0 0.17 0.17 61 74 .. 396 409 .. 395 411 .. 0.85 + 2 ! 40.7 0.0 1.3e-14 1.3e-14 2 84 .. 439 520 .. 437 521 .. 0.95 + 3 ! 14.4 0.0 2e-06 2e-06 13 85 .. 836 913 .. 826 914 .. 0.73 + 4 ! 5.1 0.0 0.0016 0.0016 10 36 .. 1209 1235 .. 1203 1259 .. 0.82 + 5 ! 24.3 0.0 1.7e-09 1.7e-09 14 80 .. 1313 1380 .. 1304 1386 .. 0.82 + 6 ? 0.0 0.0 0.063 0.063 58 72 .. 1754 1768 .. 1739 1769 .. 0.89 + 7 ! 47.2 0.9 1.2e-16 1.2e-16 1 85 [. 1799 1890 .. 1799 1891 .. 0.91 + 8 ! 17.8 0.0 1.8e-07 1.8e-07 6 74 .. 1904 1966 .. 1901 1976 .. 0.90 + 9 ! 12.8 0.0 6.6e-06 6.6e-06 1 86 [] 1993 2107 .. 1993 2107 .. 0.89 + + Alignments for each domain: + == domain 1 score: -1.3 bits; conditional E-value: 0.17 + EES--TT-EEEEEE CS + fn3 61 ltgLepgteYefrV 74 + l+ L p+t+Y+fr + 7LESS_DROME 396 LEALIPYTQYRFRF 409 + 67899*******95 PP + + == domain 2 score: 40.7 bits; conditional E-value: 1.3e-14 + ---CEEEEEEECTTEEEEEEE--S--SS--SEEEEEEEETTTCCGCEEEEEETTTSEEEEES--TT-EEEEEEEEEETTEE-E CS + fn3 2 saPenlsvsevtstsltlsWsppkdgggpitgYeveyqekgegeewqevtvprtttsvtltgLepgteYefrVqavngagegp 84 + saP ++ + ++ l ++W p + +gpi+gY++++++++++ + e+ vp+ s+ +++L++gt+Y++ + +n++gegp + 7LESS_DROME 439 SAPVIEHLMGLDDSHLAVHWHPGRFTNGPIEGYRLRLSSSEGNA-TSEQLVPAGRGSYIFSQLQAGTNYTLALSMINKQGEGP 520 + 78999999999*****************************9998.**********************************9997 PP + + == domain 3 score: 14.4 bits; conditional E-value: 2e-06 + CTTEEEEEEE--S.--SS--S.....EEEEEEEETTTCCGCEEEEEETTTSEEEEES--TT-EEEEEEEEEETTE.E-EB CS + fn3 13 tstsltlsWsppk.dgggpit.....gYeveyqekgegeewqevtvprtttsvtltgLepgteYefrVqavngag.egpe 85 + ++ + +sW++p+ ++ + + +Ye+e+ ++ ++++ +++ ++ + l+ L+p+ Y++rV+a+n +g g++ + 7LESS_DROME 836 GAQAAKISWKEPErNPYQSADaarswSYELEVLDVASQSAFSIRNIRGPI--FGLQRLQPDNLYQLRVRAINVDGePGEW 913 + 56677889999987443333223333899999999999955555566666..**********************965655 PP + + == domain 4 score: 5.1 bits; conditional E-value: 0.0016 + EEECTTEEEEEEE--S--SS--SEEEE CS + fn3 10 sevtstsltlsWsppkdgggpitgYev 36 + ++ + ++++W+p+++gg + ++Y++ + 7LESS_DROME 1209 DDGHWDDFHVRWQPSTSGGNHSVSYRL 1235 + 555678999*******99999999997 PP + + == domain 5 score: 24.3 bits; conditional E-value: 1.7e-09 + TTEEEEEEE--S...--SS--SEEEEEEEETTTCCGCEEEEEETTTSEEEEES--TT-EEEEEEEEEETT CS + fn3 14 stsltlsWsppk...dgggpitgYeveyqekgegeewqevtvprtttsvtltgLepgteYefrVqavnga 80 + + s++l+W++p+ + + + Y + ++ ++ + e ++ ++ ++ +++L+p+++Y+f+V+a+ +a + 7LESS_DROME 1313 NVSAVLRWDAPEqgqEAPMQALEYHISCWVG-SEL-HEELRLNQSALEARVEHLQPDQTYHFQVEARVAA 1380 + 5689********76556667899******55.665.688888888888*****************98665 PP + + == domain 6 score: 0.0 bits; conditional E-value: 0.063 + EEEEES--TT-EEEE CS + fn3 58 svtltgLepgteYef 72 + s++lt+L p t+Y++ + 7LESS_DROME 1754 SLNLTDLLPFTRYRV 1768 + 799**********98 PP + + == domain 7 score: 47.2 bits; conditional E-value: 1.2e-16 + ----CEEEEEEECTTEEEEEEE--S--SS--SEEEEEEEETTTCC.......GCEEEEEETTTSEEEEES--TT-EEEEEEEEEETTEE-EB CS + fn3 1 psaPenlsvsevtstsltlsWsppkdgggpitgYeveyqekgege.......ewqevtvprtttsvtltgLepgteYefrVqavngagegpe 85 + ps+P+n+sv+ ++++l++sW pp++ +++ ++Y++++q++ +ge ++ + ++ +t+ ++ ltg++pg+ Y+++Vqa+ + +++ + + 7LESS_DROME 1799 PSPPRNFSVRVLSPRELEVSWLPPEQLRSESVYYTLHWQQELDGEnvqdrreWEAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTKSNS 1890 + 9*************************************99989998****97777777777777*******************988776665 PP + + == domain 8 score: 17.8 bits; conditional E-value: 1.8e-07 + EEEEEEECTTEEEEEEE--S--SS--SEEEEEEEETTTCCGCEEEEEETTTSEEEEES--TT-EEEEEE CS + fn3 6 nlsvsevtstsltlsWsppkdgggpitgYeveyqekgegeewqevtvprtttsvtltgLepgteYefrV 74 + +l++ e ++ sl+l+W +p+ + ++e++++ e+ +++v +++t ++++ L+p t+Y+ r+ + 7LESS_DROME 1904 ELQLLELGPYSLSLTWAGT---PDPLGSLQLECRSSAEQ---LRRNVAGNHTKMVVEPLQPRTRYQCRL 1966 + 5788899************...8***********88555...79**********************986 PP + + == domain 9 score: 12.8 bits; conditional E-value: 6.6e-06 + ----CEEEEEEECTTEEEEEEE--S--SS--SEEEEEEEETTTCC...........................GCEEEEEETTTS.EEEEES--TT- CS + fn3 1 psaPenlsvsevtstsltlsWsppkdgggpitgYeveyqekgege...........................ewqevtvprttt.svtltgLepgt 68 + ps+P+ ++++ + + ++++W++ + +g+pi Y++e + ++ e+q+ + +tt+ s+ ++ L ++ + 7LESS_DROME 1993 PSQPGKPQLEHIAEEVFRVTWTAARGNGAPIALYNLEALQARSDIrrrrrrrrrnsggsleqlpwaeepvvvEDQWLDFCNTTElSCIVKSLHSSR 2088 + 89***********************9************7775554799999999999999999999999999999999999999999999999999 PP + + EEEEEEEEEETTE.E-EBE CS + fn3 69 eYefrVqavngag.egpes 86 + frV+a++ + +gp+s + 7LESS_DROME 2089 LLLFRVRARSLEHgWGPYS 2107 + 9999999999554488876 PP + + + +Internal pipeline statistics summary: +------------------------------------- +Query model(s): 1 (86 nodes) +Target sequences: 1 (2554 residues searched) +Passed MSV filter: 1 (1); expected 0.0 (0.02) +Passed bias filter: 1 (1); expected 0.0 (0.02) +Passed Vit filter: 1 (1); expected 0.0 (0.001) +Passed Fwd filter: 1 (1); expected 0.0 (1e-05) +Initial search space (Z): 1 [actual number of targets] +Domain search space (domZ): 1 [number of targets reported over threshold] +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 21.96 +// +[ok] |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/fn3.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fn3.sto Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,497 @@\n+# STOCKHOLM 1.0\n+#=GF ID fn3\n+#=GF AC PF00041.13\n+#=GF DE Fibronectin type III domain\n+#=GF AU Sonnhammer ELL\n+#=GF GA 8.0 7.2\n+#=GF NC 7.9 7.9\n+#=GF TC 8.0 7.2\n+#=GF SE Swissprot_feature_table\n+#=GF TP Domain\n+#=GF BM hmmbuild -FHMM_ls.ann SEED.ann\n+#=GF BM hmmcalibrate --seed 0 HMM_ls\n+#=GF BM hmmbuild -f -FHMM_fs.ann SEED.ann\n+#=GF BM hmmcalibrate --seed 0 HMM_fs\n+#=GF AM byscore\n+#=GF RN [1]\n+#=GF RM 2169613\n+#=GF RT Structural design and molecular evolution of a cytokine receptor\n+#=GF RT superfamily. \n+#=GF RA Bazan JF; \n+#=GF RL PNAS USA 1990;87:6934-6938.\n+#=GF RN [2]\n+#=GF RM 7528812\n+#=GF RT Tracing the spread of fibronectin type III domains in bacterial\n+#=GF RT glycohydrolases. \n+#=GF RA Little E, Bork P, Doolittle R; \n+#=GF RL J Mol Evol 1994;39:631-643.\n+#=GF RC Definition of fibronectin domains \n+#=GF RN [3]\n+#=GF RM 2992939\n+#=GF RT Primary structure of human fibronectin: differential splicing\n+#=GF RT may generate at least 10 polypeptides from a single gene. \n+#=GF RA Kornblihtt AR, Umezawa K, Vibe-Pedersen K, Baralle FE; \n+#=GF RL EMBO J 1985;4:1755-1759.\n+#=GF DR INTERPRO; IPR003961;\n+#=GF DR HOMSTRAD; fn3;\n+#=GF DR SMART; FN3;\n+#=GF DR SCOP; 1ttf; sf;\n+#=GF DR PRINTS; PR00014;\n+#=GF DR PROSITE; PDOC00214;\n+#=GF SQ 106\n+\n+#=GS TIE1_HUMAN/644-729 AC P35590.1\n+#=GS NCAM1_BOVIN/509-597 AC P31836.1\n+#=GS LAR_DROME/417-503 AC P16621.2\n+#=GS NGCA_CHICK/700-794 AC Q03696.2\n+#=GS MPSF_CHICK/499-585 AC Q02173.1\n+#=GS MPSF_CHICK/371-457 AC Q02173.1\n+#=GS MPSF_CHICK/600-684 AC Q02173.1\n+#=GS NRCAM_CHICK/623-709 AC P35331.1\n+#=GS MYPC2_CHICK/631-717 AC P16419.3\n+#=GS MYLK_CHICK/1318-1403 AC P11799.2\n+#=GS CNTN2_CHICK/602-692 AC P28685.1\n+#=GS MPSF_CHICK/699-785 AC Q02173.1\n+#=GS MPSF_CHICK/801-887 AC Q02173.1\n+#=GS MYPC2_CHICK/924-1006 AC P16419.3\n+#=GS LAR_DROME/322-404 AC P16621.2\n+#=GS FAS2_SCHAM/530-616 AC P22648.2\n+#=GS PTP69_DROME/332-425 AC P16620.2\n+#=GS TENA_CHICK/1227-1306 AC P10039.2\n+#=GS TENA_CHICK/1136-1215 AC P10039.2\n+#=GS TENA_HUMAN/1529-1608 AC P24821.2\n+#=GS TENA_CHICK/1045-1124 AC P10039.2\n+#=GS TENA_HUMAN/1255-1335 AC P24821.2\n+#=GS PTPRB_HUMAN/22-103 AC P23467.1\n+#=GS TIE2_HUMAN/639-724 AC Q02763.1\n+#=GS LAR_DROME/515-598 AC P16621.2\n+#=GS FINC_BOVIN/577-660 AC P07589.3\n+#=GS TIE1_HUMAN/446-533 AC P35590.1\n+#=GS PTPRK_MOUSE/290-376 AC P35822.1\n+#=GS TIE2_HUMAN/444-529 AC Q02763.1\n+#=GS TIE2_HUMAN/543-626 AC Q02763.1\n+#=GS 7LESS_DROVI/1917-1997 AC P20806.1\n+#=GS PTPRZ_HUMAN/312-401 AC P23471.3\n+#=GS FAS2_SCHAM/642-735 AC P22648.2\n+#=GS NCAM1_BOVIN/610-691 AC P31836.1\n+#=GS ITB4_HUMAN/1127-1208 AC P16144.4\n+#=GS UFO_HUMAN/327-411 AC P30530.2\n+#=GS KALM_CHICK/543-641 AC P33005.2\n+#=GS PTP10_DROME/958-1044 AC P35992.3\n+#=GS PTP69_DROME/236-321 AC P16620.2\n+#=GS NRG_DROME/917-1007 AC P20241.2\n+#=GS FINC_BOVIN/689-768 AC P07589.3\n+#=GS FINC_BOVIN/780-858 AC P07589.3\n+#=GS IL7RA_HUMAN/129-221 AC P16871.1\n+#=GS PTP10_DROME/405-485 AC P35992.3\n+#=GS FINC_BOVIN/1417-1499 AC P07589.3\n+#=GS FINC_RAT/1266-1346 AC P04937.2\n+#=GS FINC_BOVIN/1327-1406 AC P07589.3\n+#=GS TENA_CHICK/1317-1395 AC P10039.2\n+#=GS FINC_BOVIN/875-955 AC P07589.3\n+#=GS FINC_BOVIN/1511-1590 AC P07589.3\n+#=GS TENA_CHICK/864-945 AC P10039.2\n+#=GS TENA_CHICK/593-671 AC P10039.2\n+#=GS FINC_BOVIN/1142-1225 AC P07589.3\n+#=GS FINC_BOVIN/1693-1771 AC P07589.3\n+#=GS FINC_BOVIN/1236-1316 AC P07589.3\n+#=GS FINC_BOVIN/1601-1680 AC P07589.3\n+#=GS TENA_CHICK/1494-1571 AC P10039.2\n+#=GS TENA_CHICK/956-1033 AC P10039.2\n+#=GS TENA_CHICK/682-767 AC P10039.2\n+#=GS TENA_CHICK/774-853 AC P10039.2\n+#=GS TENA_CHICK/1406-1483 AC P10039.2\n+#=GS FINC_BOVIN/1782-1861 AC P07589.3\n+#=GS PTPRB_HUMAN/1085-1162 AC P23467.1\n+#=GS PTPRB_HUMAN/1173-1250 AC P23467.1\n+#=GS PTPRB_HUMAN/554-632 AC P23467.1\n+#=GS PTPRB_HUMAN/643-725 AC P23467.1\n+#=GS PTPRB_HUMAN/731-808 AC P23467.1\n+#=GS PTPRB_HUMAN/995-1074 AC P23467.1\n'..b'EEE.EEETTE....E----\n+UFO_HUMAN/327-411 TVCVA.AYTAAG....DGPWS\n+KALM_CHICK/543-641 RLEVQ.VLTTGG....EGPAT\n+PTP10_DROME/958-1044 VFKIQ.AKTAIG....FGPER\n+PTP69_DROME/236-321 FLRIV.GKNSIG....NGQPT\n+NRG_DROME/917-1007 RISIT.ATTKMG....EGSEH\n+FINC_BOVIN/689-768 TVNVY.EISEE.......GEQ\n+FINC_BOVIN/780-858 NITIY.AVEEN.......QES\n+IL7RA_HUMAN/129-221 EIKVR.SIPDHYFKGFWSEWS\n+PTP10_DROME/405-485 SLSVQ.AVSKK.......MES\n+FINC_BOVIN/1417-1499 TITVY.AVTGRG....DSPAS\n+FINC_RAT/1266-1346 DISVI.TLING.......GES\n+FINC_BOVIN/1327-1406 VVSIV.ALNSK.......EES\n+TENA_CHICK/1317-1395 NVNII.SVKGF.......EES\n+#=GR TENA_CHICK/1317-1395 SS EEEEE.EEETT.......EE-\n+FINC_BOVIN/875-955 HFKVF.AVNQG.......RES\n+FINC_BOVIN/1511-1590 VVSVY.AQNQN.......GES\n+TENA_CHICK/864-945 GIGVT.AVRQD.......RES\n+TENA_CHICK/593-671 FIRVF.AILKN.......KKS\n+FINC_BOVIN/1142-1225 NVSVY.TVKDD.......KES\n+FINC_BOVIN/1693-1771 KIHLY.TLNDN.......ARS\n+FINC_BOVIN/1236-1316 LVSVS.SVYEQ.......HES\n+FINC_BOVIN/1601-1680 EVSVY.ALKDT.......LTS\n+TENA_CHICK/1494-1571 TVKLQ.ALSRS.......MRS\n+TENA_CHICK/956-1033 TISLV.AEKGR.......HKS\n+TENA_CHICK/682-767 NVSLH.IVKNNTR...GPGLS\n+TENA_CHICK/774-853 EVTLI.SRRGD.......MES\n+TENA_CHICK/1406-1483 TLRVH.AVKDA.......QKS\n+FINC_BOVIN/1782-1861 TIQVI.ALKNN.......QKS\n+PTPRB_HUMAN/1085-1162 KMVIV.THSGE........LS\n+PTPRB_HUMAN/1173-1250 VLWVV.THSGD........LS\n+PTPRB_HUMAN/554-632 SVVVT.TVSGG.......ISS\n+PTPRB_HUMAN/643-725 TVTIT.TRSGKYE...NHSFS\n+PTPRB_HUMAN/731-808 SVTVT.TKSGQ........YE\n+PTPRB_HUMAN/995-1074 KIQIL.TVSGG.......LFS\n+PTPRB_HUMAN/467-543 MATVT.SISGD........LK\n+PTPRB_HUMAN/907-984 QIMIA.SVSGS........LK\n+PTPRB_HUMAN/112-192 NIAIT.AVSGG.......KRS\n+PTPRB_HUMAN/1355-1434 LVSIK.VQSAG.......MTS\n+PTP10_DROME/583-661 TIQVN.TVSFG.......VES\n+PTP10_DROME/312-394 NVIVK.TVSGK.......VTS\n+PTP10_DROME/217-301 NISVQ.TMSED.......EIS\n+PTP10_DROME/123-205 QVQAY.TIYDG.......KES\n+EPHA2_HUMAN/329-420 TFTVE.ARNGV........SG\n+EPHA1_HUMAN/333-431 TFNVE.AQNGVS....GLGSS\n+EPHB2_CHICK/326-422 TFEIQ.AVNGVTD...QSPFS\n+EPHA3_CHICK/325-421 TFEID.AVNGVSD...LSTLS\n+PTP10_DROME/864-944 TFTVV.VRSGTES..SVLRSS\n+PTPRB_HUMAN/1261-1344 QFNVK.TVSGDS....WKTYS\n+TIE1_HUMAN/545-632 QLDVQ.LYHCTL....LGPAS\n+7LESS_DROME/1799-1891 SLWVQ.AHATPT....KSNSS\n+PHB_ALCFA/344-418 SYTVT.AVDPTAG...ESQPS\n+APU_THETY/928-1009 VYAVT.AVDNDGN...ESALS\n+CHIT_STRLI/142-219 SYSVK.ARDTADQ...TGPAS\n+CHIA1_BACCI/465-542 TFTIK.AKDAAGN...LSAAS\n+GUNB_CELFI/651-733 SYVVK.AKDVAGN...VSAAS\n+CHIX_STROI/169-240 AFQVA.AVNGA.......GES\n+APU_THETY/1165-1248 YYKVV.AVDTSY....NRTAS\n+KALM_CHICK/177-269 QFRVA.AVNVHG....TRGFT\n+CNTN1_CHICK/799-884 HIDVS.AFNSAG....YGPPS\n+CNTN2_CHICK/807-896 HVSVR.AYNRAG....AGPPS\n+NRG_DROME/815-905 YARIL.AYNGRF....NGPPS\n+L1CAM_HUMAN/812-907 HLEVQ.AFNGRG....SGPAS\n+LAR_DROME/709-800 SIQVA.ALTRKG....DGDRS\n+PTP99_DROME/171-259 RVIVK.AFTTKN....EGEPS\n+EPHA2_HUMAN/436-519 LVQVQ.ALTQEG....QGAGS\n+LAR_DROME/909-995 IFRVR.AYTKQG....AGPFS\n+NRCAM_CHICK/928-1014 KFYFN.AQTSV......GSGS\n+EPHB2_CHICK/437-521 VFQVR.ARTVAG....YGRYS\n+EPHA4_MOUSE/441-525 VFHVR.ARTAAG....YGDFS\n+ITB4_HUMAN/1220-1310 RYTVK.ARNGAG....WGPER\n+#=GR ITB4_HUMAN/1220-1310 SS EEEEE.EEETTE....E--BE\n+ITB4_HUMAN/1641-1728 KFKVQ.ARTTEG....FGPER\n+ITB4_HUMAN/1528-1612 VFRVR.AQSQEG....WGRER\n+#=GC SS_cons EEEEE.EEETTE....E-EBE\n+#=GC seq_cons phpVt.Ahsst.......t.S\n+//\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins-45-align.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/globins-45-align.sto Sat Jun 25 15:07:32 2016 -0400 |
| b |
| b'@@ -0,0 +1,95 @@\n+# STOCKHOLM 1.0\n+\n+MYG_ESCGI .-VLSDAEWQLVLNIWAKVEADVAGHGQDILIRLFKGHPETLEKFDKFKHLKTEAEMKASEDLKKHGNTVLTALGGILKK-KGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRHPGDFGADAQAAMNKALELFRKDIAAKYKelgfqg\n+#=GR MYG_ESCGI PP ..69****************************************************************************.99******************************************************************7******\n+MYG_HORSE g--LSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKK-KGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGNFGADAQGAMTKALELFRNDIAAKYKelgfqg\n+#=GR MYG_HORSE PP 8..89***************************************************************************.99******************************************************************7******\n+MYG_PROGU g--LSDGEWQLVLNVWGKVEGDLSGHGQEVLIRLFKGHPETLEKFDKFKHLKAEDEMRASEELKKHGTTVLTALGGILKK-KGQHAAELAPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDIAAKYKelgfqg\n+#=GR MYG_PROGU PP 8..89***************************************************************************.99******************************************************************7******\n+MYG_SAISC g--LSDGEWQLVLNIWGKVEADIPSHGQEVLISLFKGHPETLEKFDKFKHLKSEDEMKASEELKKHGTTVLTALGGILKK-KGQHEAELKPLAQSHATKHKIPVKYLELISDAIVHVLQKKHPGDFGADAQGAMKKALELFRNDMAAKYKelgfqg\n+#=GR MYG_SAISC PP 8..89***************************************************************************.99******************************************************************7******\n+MYG_LYCPI g--LSDGEWQIVLNIWGKVETDLAGHGQEVLIRLFKNHPETLDKFDKFKHLKTEDEMKGSEDLKKHGNTVLTALGGILKK-KGHHEAELKPLAQSHATKHKIPVKYLEFISDAIIQVLQNKHSGDFHADTEAAMKKALELFRNDIAAKYKelgfqg\n+#=GR MYG_LYCPI PP 8..89***************************************************************************.99******************************************************************7******\n+MYG_MOUSE g--LSDGEWQLVLNVWGKVEADLAGHGQEVLIGLFKTHPETLDKFDKFKNLKSEEDMKGSEDLKKHGCTVLTALGTILKK-KGQHAAEIQPLAQSHATKHKIPVKYLEFISEIIIEVLKKRHSGDFGADAQGAMSKALELFRNDIAAKYKelgfqg\n+#=GR MYG_MOUSE PP 8..89***************************************************************************.99******************************************************************7******\n+MYG_MUSAN v------DWEKVNSVWSAVESDLTAIGQNILLRLFEQYPESQNHFPKFKNKS-LGELKDTADIKAQADTVLSALGNIVKK-KGSHSQPVKALAATHITTHKIPPHYFTKITTIAVDVLSEMYPSEMNAQVQAAFSGAFKIICSDIEKEYKaanfqg\n+#=GR MYG_MUSAN PP 7......89***************************************9877.89*************************.99****************************************************************997******\n+HBA_AILME .-VLSPADKTNVKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHF-DLS-----PGSAQVKAHGKKVADALTTAVGHLD-DLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPAEFTPAVHASLDKFFSAVSTVLTSKYR......\n+#=GR HBA_AILME PP ..69********************************************.9**.....9***********************9.******************************************************************7......\n+HBA_PROLO .-VLSPADKANIKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHF-DLS-----PGSAQVKAHGKKVADALTLAVGHLD-DLPGALSALSDLHAYKLRVDPVNFKLLSHCLLVTLACHHPAEFTPAVHASLDKFFTSVSTVLTSKYR......\n+#=GR HBA_PROLO PP ..69********************************************.9**.....9***********************9.******************************************************************7......\n+HBA_PAGLA .-VLSSADKNNIKATWDKIGSHAGEYGAEALERTFISFPTTKTYFPHF-DLS-----HGSAQVKAHGKKVADALTLAVGHLE-DLPNALSALSDLHAYKLRVDPVNFKLLSHCLLVTLACHHPAEFTPAVHSALDKFFSAVSTVLTSKYR......\n+#=GR HBA_PAGLA PP ..69********************************************.***.....***********************98.9*****************************************************************7......\n+HBA_MACFA .-VLSPADKTNVKAAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALTLAVGHVD-DMPQALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR......\n+#=GR HBA_MACFA PP ..69********************************************.***.....************************9.******************************************************************7......\n+HBA_MACSI .-VLSPADKTNVKDAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHF-'..b'**************************.******************************************************************7......\n+HBB_URSMA .VHLTGEEKSLVTGLWGKV--NVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSADAIMNNPKVKAHGKKVLNSFSDGLKNLD-NLKGTFAKLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH......\n+#=GR HBB_URSMA PP .689***************..*************************************************************.******************************************************************7......\n+HBB_RABIT .VHLSSEEKSAVTALWGKV--NVEEVGGEALGRLLVVYPWTQRFFESFGDLSSANAVMNNPKVKAHGKKVLAAFSEGLSHLD-NLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH......\n+#=GR HBB_RABIT PP .69****************..*************************************************************.******************************************************************7......\n+HBB_TUPGL .VHLSGEEKAAVTGLWGKV--DLEKVGGQSLGSLLIVYPWTQRFFDSFGDLSSPSAVMSNPKVKAHGKKVLTSFSDGLNHLD-NLKGTFAKLSELHCDKLHVDPENFRLLGNVLVRVLACNFGPEFTPQVQAAFQKVVAGVANALAHKYH......\n+#=GR HBB_TUPGL PP .69****************..*************************************************************.******************************************************************7......\n+HBB_TRIIN .VHLTPEEKALVIGLWAKV--NVKEYGGEALGRLLVVYPWTQRFFEHFGDLSSASAIMNNPKVKAHGEKVFTSFGDGLKHLE-DLKGAFAELSELHCDKLHVDPENFRLLGNVLVCVLARHFGKEFSPEAQAAYQKVVAGVANALAHKYH......\n+#=GR HBB_TRIIN PP .69****************..***********************************************************98.9*****************************************************************7......\n+HBB_COLLI v-HWSAEEKQLITSIWGKV--NVADCGAEALARLLIVYPWTQRFFSSFGNLSSATAISGNPNVKAHGKKVLTSFGDAVKNLD-NIKGTFAQLSELHCDKLHVDPENFRLLGDILVIILAAHFGKDFTPECQAAWQKLVRVVAHALARKYH......\n+#=GR HBB_COLLI PP 5.779**************..*************************************************************.******************************************************************7......\n+HBB_LARRI v-HWSAEEKQLITGLWGKV--NVADCGAEALARLLIVYPWTQRFFASFGNLSSPTAINGNPMVRAHGKKVLTSFGEAVKNLD-NIKNTFAQLSELHCDKLHVDPENFRLLGDILIIVLAAHFAKDFTPDSQAAWQKLVRVVAHALARKYH......\n+#=GR HBB_LARRI PP 5.779**************..*************************************************************.******************************************************************7......\n+HBB1_VAREX v-HWTAEEKQLICSLWGKI--DVGLIGGETLAGLLVIYPWTQRQFSHFGNLSSPTAIAGNPRVKAHGKKVLTSFGDAIKNLD-NIKDTFAKLSELHCDKLHVDPTNFKLLGNVLVIVLADHHGKEFTPAHHAAYQKLVNVVSHSLARRYH......\n+#=GR HBB1_VAREX PP 6.6799*************..*************************************************************.******************************************************************7......\n+HBB2_XENTR v-HWTAEEKATIASVWGKV--DIEQDGHDALSRLLVVYPWTQRYFSSFGNLSNVSAVSGNVKVKAHGNKVLSAVGSAIQHLD-DVKSHLKGLSKSHAEDLHVDPENFKRLADVLVIVLAAKLGSAFTPQVQAVWEKLNATLVAALSHGY-f.....\n+#=GR HBB2_XENTR PP 6.6799*************..************************************************************9.9*************************************************************9988.9.....\n+HBBL_RANCA v-HWTAEEKAVINSVWQKV--DVEQDGHEALTRLFIVYPWTQRYFSTFGDLSSPAAIAGNPKVHAHGKKILGAIDNAIHNLD-DVKGTLHDLSEEHANELHVDPENFRRLGEVLIVVLGAKLGKAFSPQVQHVWEKFIAVLVDALSHSYH......\n+#=GR HBBL_RANCA PP 6.6799*************..************************************************************9.9*****************************************************************7......\n+HBB2_TRICR .VHLTAEDRKEIAAILGKV--NVDSLGGQCLARLIVVNPWSRRYFHDFGDLSSCDAICRNPKVLAHGAKVMRSIVEATKHLD-NLREYYADLSVTHSLKFYVDPENFKLFSGIVIVCLALTLQTDFSCHKQLAFEKLMKGVSHALGHGY-......\n+#=GR HBB2_TRICR PP .69****************..*************************************************************.**************************************************************9988.......\n+#=GC PP_cons .679*****************************************************************************99******************************************************************7......\n+#=GC RF .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......\n+//\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins-masked.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/globins-masked.sto Sat Jun 25 15:07:32 2016 -0400 |
| b |
| @@ -0,0 +1,13 @@ +# STOCKHOLM 1.0 + +#=GS HBB_HUMAN WT 0.91 +#=GS HBA_HUMAN WT 0.82 +#=GS MYG_PHYCA WT 1.13 +#=GS GLB5_PETMA WT 1.14 + +HBB_HUMAN --------VHLTPEEKSAVTALWGKV----NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHL---D--NLKGTFATLSELHCDKL--HVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------ +HBA_HUMAN ---------VLSPADKTNVKAAWGKVGA--HAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALTNAVAHV---D--DMPNALSALSDLHAHKL--RVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------ +MYG_PHYCA ---------VLSEGEWQLVLHVWAKVEA--DVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKK----K-GHHEAELKPLAQSHATKH--KIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG +GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYS--TYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASM--DDTEKMSMKLRDLSGKHAKSF--QVDPQYFKVLAAVIADTVAAG---------DAGFEKLMSMICILLRSAY------- +#=GC MM .................mmmmmmmmmmm...........mmmmmmmmmmm......................................................................................................................... +// |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins.domtblout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/globins.domtblout Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| @@ -0,0 +1,15 @@ +# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord +# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target +#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- +sp|P02185|MYG_PHYCD - 154 globins4 - 149 1.8e-70 222.7 3.2 1 1 2e-70 2e-70 222.6 3.2 2 149 2 148 1 148 0.99 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 +sp|P02024|HBB_GORGO - 147 globins4 - 149 9.2e-69 217.2 0.1 1 1 1e-68 1e-68 217.0 0.1 1 149 2 147 2 147 0.99 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 +# +# Program: hmmsearch +# Version: 3.1b2 (February 2015) +# Pipeline mode: SEARCH +# Query file: /tmp/tmpJW6ntL/files/000/dataset_1.dat +# Target file: /tmp/tmpJW6ntL/files/000/dataset_2.dat +# Option settings: hmmsearch --tblout /tmp/tmpJW6ntL/files/000/dataset_4.dat --domtblout /tmp/tmpJW6ntL/files/000/dataset_5.dat --pfamtblout /tmp/tmpJW6ntL/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpJW6ntL/files/000/dataset_1.dat /tmp/tmpJW6ntL/files/000/dataset_2.dat +# Current dir: /tmp/tmpJW6ntL/job_working_directory/000/3 +# Date: Sat Jun 25 19:27:08 2016 +# [ok] |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins.pfamtblout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/globins.pfamtblout Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| @@ -0,0 +1,25 @@ +# Sequence scores +# --------------- +# +# name bits E-value n exp bias description +# ------------------- ------ --------- --- ----- ----- --------------------- +sp|P02185|MYG_PHYCD 222.7 1.8e-70 1 1.0 3.2 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 +sp|P02024|HBB_GORGO 217.2 9.2e-69 1 1.0 0.1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 + +# Domain scores +# ------------- +# +# name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description +# ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ --------------------- +sp|P02185|MYG_PHYCD 222.6 2e-70 1 3.2 1 148 2 148 2 149 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 +sp|P02024|HBB_GORGO 217.0 1e-68 1 0.1 2 147 2 147 1 149 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 +# +# Program: hmmsearch +# Version: 3.1b2 (February 2015) +# Pipeline mode: SEARCH +# Query file: /tmp/tmpJW6ntL/files/000/dataset_1.dat +# Target file: /tmp/tmpJW6ntL/files/000/dataset_2.dat +# Option settings: hmmsearch --tblout /tmp/tmpJW6ntL/files/000/dataset_4.dat --domtblout /tmp/tmpJW6ntL/files/000/dataset_5.dat --pfamtblout /tmp/tmpJW6ntL/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpJW6ntL/files/000/dataset_1.dat /tmp/tmpJW6ntL/files/000/dataset_2.dat +# Current dir: /tmp/tmpJW6ntL/job_working_directory/000/3 +# Date: Sat Jun 25 19:27:08 2016 +# [ok] |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins.tblout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/globins.tblout Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| @@ -0,0 +1,15 @@ +# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- +# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target +#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- +sp|P02185|MYG_PHYCD - globins4 - 1.8e-70 222.7 3.2 2e-70 222.6 3.2 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 +sp|P02024|HBB_GORGO - globins4 - 9.2e-69 217.2 0.1 1e-68 217.0 0.1 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 +# +# Program: hmmsearch +# Version: 3.1b2 (February 2015) +# Pipeline mode: SEARCH +# Query file: /tmp/tmpJW6ntL/files/000/dataset_1.dat +# Target file: /tmp/tmpJW6ntL/files/000/dataset_2.dat +# Option settings: hmmsearch --tblout /tmp/tmpJW6ntL/files/000/dataset_4.dat --domtblout /tmp/tmpJW6ntL/files/000/dataset_5.dat --pfamtblout /tmp/tmpJW6ntL/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpJW6ntL/files/000/dataset_1.dat /tmp/tmpJW6ntL/files/000/dataset_2.dat +# Current dir: /tmp/tmpJW6ntL/job_working_directory/000/3 +# Date: Sat Jun 25 19:27:08 2016 +# [ok] |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins4-emit-1.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/globins4-emit-1.sto Sat Jun 25 15:07:32 2016 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>globins4-sample1 +CLDDGAENDNVLTGVLDLNPDEPSEAEPLILILVQSAPTTKAHFQKFVLLTTNMQVEFDT +EIKAHTTMIIGASRAILSSIVQNRMNYYLLLLAKENHSGKERATRKKTDRECLHILGEVI +TITLKREFPMDSNPAHSSRDGTFDLLVSLYRKALRNLY |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins4-emit.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/globins4-emit.sto Sat Jun 25 15:07:32 2016 -0400 |
| b |
| @@ -0,0 +1,26 @@ +# STOCKHOLM 1.0 + +globins4-sample1 -.CLD.DgAENDNVL..TGV.LDLNPD...EPSEAEPLILILVQ.SAPTTK.AH...........FQKFVLLTTN.MQVEFDTEI..KAHT.T.MIIGASRAILSSI.VqNRMN.Y.YLLLLAkEnhsgkE.R..ATRKKTDRECLHILGEVITITL..KREFPMDSNPAHssrDGTFDLLVSLYRKALRNL.Y-..... +globins4-sample2 K.PLS.P.AQKKTIR..SAW.LLPGHS...KNDLGQEALVHLDL.AVPAMQ.TMishmlllylhkFPQFEHLSPNvKKLAYAELM..RVGA.I.TTL--LSKQWDTLeA.DATR.R.IPLEEN.D.....V.H..LQKYGLIRKKLQVISALVAKVI..LAGHPENFGPKV...SSAF----IVFYKG--EI.YK..... +globins4-sample3 S.MIS.K.RFKVLVE..NLW.LKV-AT...AGDIGSDQLVTFKA.VFTKIY.LT...........FDEFKGEKV-.---HREIAI..KLYTlS.AIAAILNPPLLNL.R.RIYN.H.ELSQLS.A.....L.H..CTQMQSNQEYFLV--NLTVDTI..YETKPTQYREKS...EASENKVTNLVSNALTAN.YR..... +globins4-sample4 IsTEC.L.EENEAAK..DVRqEHIVSEmglVDVYSQLLGVLMTT.SIPPTElNR...........MKEKRKLMTR.AGMTTSYAI..RMRG.NhVIHEALSSSAGR-.N.--NQcD.DVVQLS.Q.....K.Y..VTKIYVHPQKIEHITRVLVII-..PYE---THAAEE...DANMEKAVLSVRSRIVTK.FD..... +globins4-sample5 -.LIS.E.ASFPLVQnvEIW.VKVFNH...YAEAGNESLIKIVV.TYPDGS.KL...........NHCF-HGK-A.TTCQAANDW..KYDK.E.TFVSTLRKVLASR.K.TRFI.KgKILTVE.N.....E.H..KNSVSVALMRPKLGSNCT--TL..LEVIPSWAGPYE...ESAADKCIPLCASILTSE.YR..... +globins4-sample6 -.ALPgD.TGKQYSH..VCW.AN-HAR...--ESGLDILVRYYL.SLPQTL.NF...........FPKFVDITPK.PIMTNNARL..KEEG.A.AVLDA-MNSLLKI.V.QTIE.N.QFWALK.K.....S.F..AHALHVD-KIYKMLNELLIVIV..AAMEPEHDRPHA...DTAMYKVLQKLRKQLGEGrSLiygfp +globins4-sample7 P.KFH.N.STKGEVE..RSY.VKVVSK...VDNEGMEYLKDFLSfSRPHAQ.GK...........FGMLKSLQTL.PGLH-VESC..TTME.I.EVLQNLSTPVTGL.D.SQKG.N.EIKELC.R.....V.HldRRTAHVADETFKTYNNSTILRVaqKVHTMRRFDFAA...ADALESFLSYVPCLIEAQ.YQ..... +globins4-sample8 V.ALS.K.MEQTRVK..ALY.YQV---...SARSGAQALAEMLVrAHPDSR.ML...........FNQAEVIQTR.LTLAENAQI.qRGWG.K.MVVKADSKNMTRV.EgEKHG.M.EPKASA.R.....N.H..IPRENVINGFFKLSALKVVKTV..DVELARGITFSG...NAPVCPYFKGFAAVLSEP.YE..... +globins4-sample9 A.PLN.A.PGWQDVE..-IW.EYV---...-FHRTIRILRNLLK.EIPWER.RH...........FIKTSTVCLP.IICMGNAKLpwRDGG.T.QGRRALNPSVKQC.QfAKTS.G.SLRQCY.D.....R.QhvAIKDRVLINYFQIVGDLVVDYV..DVKLPQDFNPNL...EADIDRRLFISQRSLNCK.W-..... +globins4-sample10 -.TLE.M.QLRTDLS..NVA.VKSLAD...LE-VGLEKLMKLYN.SAKLLH.ALr.........cFEPTTKIVTA.SAPKGLRFV..KHQG.T.KVMTAINQAFADM.E.TNYE.Q.KYQSLR.E.....KyK..IEELSIDPRNFQLLAGRVVVRS..AKPLPILLSRQF...ERVLEEHLHLIGKDLQHK.Y-..... +#=GC RF x.xxx.x.xxxxxxx..xxx.xxxxxx...xxxxxxxxxxxxxx.xxxxxx.xx...........xxxxxxxxxx.xxxxxxxxx..xxxx.x.xxxxxxxxxxxxx.x.xxxx.x.xxxxxx.x.....x.x..xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx.xx..... + +globins4-sample1 ... +globins4-sample2 ... +globins4-sample3 ... +globins4-sample4 ... +globins4-sample5 ... +globins4-sample6 gmp +globins4-sample7 ... +globins4-sample8 ... +globins4-sample9 ... +globins4-sample10 ... +#=GC RF ... +// |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins4.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/globins4.hmm Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,469 @@\n+HMMER3/f [3.1b1 | May 2013]\n+NAME globins4\n+LENG 149\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Mon Feb 9 11:39:55 2015\n+NSEQ 4\n+EFFN 0.964844\n+CKSUM 2027839109\n+STATS LOCAL MSV -9.7726 0.70957\n+STATS LOCAL VITERBI -10.7883 0.70957\n+STATS LOCAL FORWARD -4.5789 0.70957\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.36553 4.52577 2.96709 2.70473 3.20818 3.02239 3.41069 2.90041 2.55332 2.35210 3.67329 3.19812 3.45595 3.16091 3.07934 2.66722 2.85475 2.56965 4.55393 3.62921\n+ 2.68640 4.42247 2.77497 2.73145 3.46376 2.40504 3.72516 3.29302 2.67763 2.69377 4.24712 2.90369 2.73719 3.18168 2.89823 2.37879 2.77497 2.98431 4.58499 3.61525\n+ 0.57544 1.78073 1.31293 1.75577 0.18968 0.00000 *\n+ 1 1.70038 4.17733 3.76164 3.36686 3.72281 3.29583 4.27570 2.40482 3.29230 2.54324 3.63799 3.55099 3.93183 3.61602 3.56580 2.71897 2.84104 1.67328 5.32720 4.10031 9 v - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03156 3.86736 4.58970 0.61958 0.77255 0.34406 1.23405\n+ 2 2.62748 4.47174 3.31917 2.82619 3.63815 3.49607 2.75382 3.03401 2.75280 2.74783 3.65114 3.24714 2.62341 3.12082 3.11124 2.79244 2.89355 1.88003 5.06315 3.77128 10 v - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 3 3.50771 4.88753 4.66754 4.31907 3.27776 4.35743 4.88268 2.50779 4.08449 0.57907 3.22569 4.56607 4.74802 4.37991 4.20749 3.97946 3.79191 2.62059 5.25407 4.04279 11 L - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 4 2.34080 4.28719 3.51550 3.22063 4.37406 3.06195 4.29366 3.74891 3.24370 3.47337 4.31943 3.39310 3.80273 3.56072 3.55390 1.08280 2.00280 3.23325 5.72380 4.49519 12 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 5 2.04218 4.87966 2.77126 1.92448 4.32563 3.33660 3.78415 3.73388 2.61886 3.34029 4.16568 2.96714 2.18012 2.94561 3.07633 2.70238 2.96803 3.36068 5.56791 4.21854 13 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 6 1.67844 4.79514 2.78469 2.00544 4.34945 2.26719 3.85010 3.76260 2.72087 3.37961 4.20641 2.99947 3.85561 3.02442 3.17766 2.68798 2.96575 3.36703 5.60901 4.27005 14 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 7 3.05756 5.63998 1.78612 1.06702 4.93093 3.31407 3.86695 4.45859 2.89031 3.95237 4.80915 2.77798 3.94091 3.03432 3.489'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 142 2.65037 4.69800 3.11777 2.58559 3.93396 3.48363 3.71066 2.49275 2.05906 2.95516 3.80693 2.50024 3.88815 2.89605 2.88872 2.72907 2.42763 2.99850 5.24239 3.94877 158 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 143 2.21701 4.52657 2.45380 2.75014 3.73535 3.53805 3.84294 2.86807 2.75770 2.17002 3.64455 3.21159 3.95457 3.08148 3.16791 2.80094 2.89608 2.24528 5.16549 3.89225 159 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 144 3.41438 4.70993 5.04893 4.51836 3.21871 4.71073 5.05993 1.60681 4.34794 0.90468 3.01922 4.76098 4.89446 4.48359 4.45935 4.09339 3.64659 2.14279 5.32906 4.22624 160 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 145 1.66341 4.55765 3.29747 2.78822 4.09563 3.34088 3.86205 3.44543 2.60980 3.11452 3.96692 3.19039 3.87148 3.05878 2.16675 2.67137 2.29043 3.09965 5.38848 4.12438 161 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 146 1.96741 4.60402 3.09101 2.67267 4.09875 3.30287 2.64764 3.55483 2.68845 3.18630 4.02165 3.11035 3.84730 3.04694 3.09548 1.72418 2.88008 3.18467 5.41006 4.09565 162 s - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 147 2.02427 4.88556 3.14956 2.70898 4.40362 3.45865 3.80224 3.73109 1.30907 3.34916 4.21424 3.15279 3.95761 2.96243 2.65527 2.83485 3.06573 3.38348 5.54009 4.27566 163 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02321 4.17053 4.89288 0.61958 0.77255 0.48576 0.95510\n+ 148 3.70647 5.07328 4.29292 4.08736 2.37118 4.18885 3.80078 3.67800 3.93734 3.05218 4.32316 4.11065 4.65987 4.16910 4.05541 3.80923 3.99693 3.56378 4.02310 0.58497 164 Y - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.19360 4.17053 1.82902 0.61958 0.77255 0.48576 0.95510\n+ 149 2.92198 5.11574 3.28049 2.65489 4.47826 3.59727 2.51142 3.88373 1.57593 3.35205 4.19259 3.10178 3.96579 2.72398 1.84611 2.91372 3.10363 3.55066 5.42147 4.18835 165 k - - -\n+ 2.68634 4.42241 2.77536 2.73098 3.46370 2.40469 3.72511 3.29370 2.67757 2.69331 4.24706 2.90363 2.73756 3.18097 2.89817 2.37903 2.77536 2.98535 4.58493 3.61418\n+ 0.22163 1.61553 * 1.50361 0.25145 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins4.hmm.bin |
| b |
| Binary file test-data/globins4.hmm.bin has changed |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins4.hmm2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/globins4.hmm2 Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,463 @@\n+HMMER2.0 [converted from 3.1b2]\n+NAME globins4\n+LENG 149\n+ALPH Amino\n+RF no\n+CS no\n+MAP yes\n+NSEQ 4\n+DATE Mon Feb 9 11:39:55 2015\n+XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n+NULT -4 -8455\n+NULE 656 -1722 98 419 -333 475 -1125 239 250 947 -1073 -271 -50 -338 114 451 113 430 -2131 -717\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d b->m m->e\n+ -452 * -1894\n+ 1 1213 17 -1203 -954 -716 -908 -721 613 -677 -294 146 -530 -1300 -557 -936 -51 110 1478 -1232 -876 9\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -46 -5579 -6622 -894 -1115 -496 -1780 -830 *\n+ 2 -125 -408 -565 -174 -594 -1197 1474 -294 101 -589 127 -92 587 157 -280 -157 35 1180 -851 -402 10\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 3 -1395 -1008 -2510 -2328 -74 -2440 -1597 465 -1820 2540 741 -1995 -2478 -1659 -1862 -1870 -1262 112 -1127 -793 11\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 4 289 -142 -848 -743 -1656 -571 -747 -1326 -607 -1636 -837 -302 -1114 -477 -919 2309 1320 -772 -1805 -1446 12\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 5 720 -996 226 1127 -1586 -967 -12 -1304 294 -1444 -615 312 1227 410 -230 -28 -73 -956 -1580 -1047 13\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 6 1244 -874 206 1010 -1620 576 -107 -1345 147 -1501 -674 266 -1190 296 -376 -7 -70 -965 -1639 -1121 14\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 7 -745 -2093 1647 2364 -2459 -934 -132 -2349 -97 -2327 -1544 585 -1313 282 -826 -363 -621 -1916 -2339 -1579 15\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 8 -635 -1057 -831 -298 -776 -1494 33 -1068 2270 -1126 -444 -200 -1534 331 530 -531 -393 -888 2804 -311 16\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 9 -76 -729 -155 138 -1389 -965 -43 -1111 336 -1268 -448 162 -1188 1474 -109 774 1544 -773 -1416 -944 17\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -89'..b' -307 155\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 140 -786 -314 -2766 -2294 1397 -2470 -1388 1811 -1947 564 740 -1826 -2354 -1591 -1983 -1500 -590 1931 -993 -645 156\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 141 737 2273 -756 -307 -898 -955 -210 -561 15 -824 -50 -131 -1206 75 919 739 140 -296 -1087 -707 157\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 142 -158 -734 -274 173 -1021 -1179 94 487 1102 -888 -98 986 -1237 482 41 -66 707 -434 -1110 -658 158\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 143 467 -487 684 -64 -734 -1258 -97 -55 94 245 137 -40 -1333 214 -362 -170 31 653 -999 -576 159\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 144 -1260 -751 -3060 -2615 11 -2949 -1853 1765 -2200 2070 1039 -2276 -2689 -1809 -2225 -2034 -1052 801 -1235 -1058 160\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 145 1266 -532 -534 -119 -1254 -973 -124 -888 307 -1118 -328 -10 -1213 247 1082 17 905 -579 -1321 -911 161\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 146 827 -599 -236 48 -1259 -918 1628 -1046 194 -1222 -407 106 -1178 264 -258 1384 54 -702 -1352 -870 162\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 147 745 -1005 -320 -5 -1699 -1143 -38 -1300 2184 -1457 -685 44 -1338 386 378 -219 -214 -989 -1540 -1129 163\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -33 -6017 -7059 -894 -1115 -701 -1378 * *\n+ 148 -1682 -1276 -1970 -1993 1234 -2197 -36 -1223 -1608 -1028 -842 -1338 -2351 -1355 -1642 -1624 -1557 -1249 649 4195 164\n+ - -210 -336 220 -37 -342 377 73 -669 210 -511 -732 404 423 70 27 439 205 -414 -161 -176\n+ - -279 -6017 -2639 -894 -1115 -701 -1378 * *\n+ 149 -550 -1337 -509 73 -1806 -1343 1824 -1520 1799 -1461 -654 118 -1349 730 1545 -332 -269 -1230 -1368 -1003 165\n+ - * * * * * * * * * * * * * * * * * * * *\n+ - * * * * * * * * 0\n+//\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins4.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/globins4.out Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,19847 @@\n+# hmmsearch :: search profile(s) against a sequence database\n+# HMMER 3.1 (February 2013); http://hmmer.org/\n+# Copyright (C) 2011 Howard Hughes Medical Institute.\n+# Freely distributed under the GNU General Public License (GPLv3).\n+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n+# query HMM file: globins4.hmm\n+# target sequence database: uniprot_sprot.fasta\n+# per-seq hits tabular output: globins4.tbl\n+# per-dom hits tabular output: globins4.domtbl\n+# number of worker threads: 2\n+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n+\n+Query: globins4 [M=149]\n+Scores for complete sequences (score includes all domains):\n+ --- full sequence --- --- best 1 domain --- -#dom-\n+ E-value score bias E-value score bias exp N Sequence Description\n+ ------- ------ ----- ------- ------ ----- ---- -- -------- -----------\n+ 6.5e-65 222.7 3.2 7.2e-65 222.6 3.2 1.0 1 sp|P02185|MYG_PHYMC Myoglobin OS=Physeter macrocephalus GN\n+ 3.3e-63 217.2 0.1 3.7e-63 217.0 0.1 1.0 1 sp|P02024|HBB_GORGO Hemoglobin subunit beta OS=Gorilla gor\n+ 4.9e-63 216.6 0.0 5.4e-63 216.5 0.0 1.0 1 sp|P68871|HBB_HUMAN Hemoglobin subunit beta OS=Homo sapien\n+ 4.9e-63 216.6 0.0 5.4e-63 216.5 0.0 1.0 1 sp|P68872|HBB_PANPA Hemoglobin subunit beta OS=Pan paniscu\n+ 4.9e-63 216.6 0.0 5.4e-63 216.5 0.0 1.0 1 sp|P68873|HBB_PANTR Hemoglobin subunit beta OS=Pan troglod\n+ 7e-63 216.1 3.0 7.7e-63 216.0 3.0 1.0 1 sp|P02177|MYG_ESCGI Myoglobin OS=Eschrichtius gibbosus GN=\n+ 7e-63 216.1 3.0 7.7e-63 216.0 3.0 1.0 1 sp|Q0KIY1|MYG_BALBO Myoglobin OS=Balaenoptera borealis GN=\n+ 7e-63 216.1 3.0 7.7e-63 216.0 3.0 1.0 1 sp|Q0KIY2|MYG_BALED Myoglobin OS=Balaenoptera edeni GN=MB \n+ 7.6e-63 216.0 0.1 8.4e-63 215.9 0.1 1.0 1 sp|P02025|HBB_HYLLA Hemoglobin subunit beta OS=Hylobates l\n+ 1.1e-62 215.6 0.2 1.2e-62 215.4 0.2 1.0 1 sp|P02033|HBB_PILBA Hemoglobin subunit beta OS=Piliocolobu\n+ 1.1e-62 215.5 3.7 1.2e-62 215.3 3.7 1.0 1 sp|P02178|MYG_MEGNO Myoglobin OS=Megaptera novaeangliae GN\n+ 2.3e-62 214.4 1.8 2.6e-62 214.3 1.8 1.0 1 sp|P02174|MYG_GLOME Myoglobin OS=Globicephala melas GN=MB \n+ 4.2e-62 213.6 1.8 4.6e-62 213.5 1.8 1.0 1 sp|P02173|MYG_ORCOR Myoglobin OS=Orcinus orca GN=MB PE=1 S\n+ 4.6e-62 213.5 4.2 5.1e-62 213.3 4.2 1.0 1 sp|P02179|MYG_BALAC Myoglobin OS=Balaenoptera acutorostrat\n+ 4.9e-62 213.4 1.3 5.5e-62 213.2 1.3 1.0 1 sp|P02181|MYG_INIGE Myoglobin OS=Inia geoffrensis GN=MB PE\n+ 5.3e-62 213.3 0.1 5.9e-62 213.1 0.1 1.0 1 sp|P02028|HBB_CHLAE Hemoglobin subunit beta OS=Chlorocebus\n+ 5.6e-62 213.2 4.2 6.3e-62 213.0 4.2 1.0 1 sp|P02184|MYG_KOGSI Myoglobin OS=Kogia sima GN=MB PE=1 SV=\n+ 5.6e-62 213.2 4.2 6.3e-62 213.0 4.2 1.0 1 sp|Q0KIY5|MYG_KOGBR Myoglobin OS=Kogia breviceps GN=MB PE=\n+ 7.1e-62 212.9 0.2 7.9e-62 212.7 0.2 1.0 1 sp|P02040|HBB_CEBAL Hemoglobin subunit beta OS=Cebus albif\n+ 1e-61 212.3 1.8 1.2e-61 212.2 1.8 1.0 1 sp|Q0KIY3|MYG_PENEL Myoglobin OS=Peponocephala electra GN=\n+ 1.1e-61 212.3 0.1 1.2e-61 212.1 0.1 1.0 1 sp|Q6WN25|HBB_LAGLA Hemoglobin subunit beta OS=Lagothrix l\n+ 1.1e-61 212.3 2.0 1.2e-61 212.1 2.0 1.0 1 sp|P68276|MYG_DELDE Myoglobin OS=Delphinus delphis GN=MB P\n+ 1.1e-61 212.3 2.0 1.2e-61 212.1 2.0 1.0 1 sp|P68279|MYG_TURTR Myoglobin OS=Tursiops truncatus GN=MB \n+ 1.1e-61 212.3 2.0 1.2e-61 212.1 2.0 1.0 1 sp|Q0KIY7|MYG1_STEAT Myoglobin-1 OS=Stenella attenuata GN=M\n+ 1.1e-61 212.2 0.1 1.3e-61 212.1 0.1 1.'..b'-- --------- ------- ------- ------- ------- ------- ------- ----\n+ 1 ? 11.2 0.0 0.021 10 51 100 .. 50 98 .. 43 106 .. 0.92\n+\n+ Alignments for each domain:\n+ == domain 1 score: 11.2 bits; conditional E-value: 0.021\n+ globins4 51 stedelkksadvkkHgkkvldAlsdalakldekleaklkdLselHakklk 100\n+ +te++lk +dv H + + dA+++ +k+d ++ k++++ Ha++l \n+ sp|B0FZN9|SCML1_PONPY 50 NTEEQLKTVNDVLIHCQVIYDAMQNLDKKID-VIRRKVSKIQRFHARSLW 98 \n+ 79****************************9.99************9875 PP\n+\n+>> sp|Q9UN30|SCML1_HUMAN Sex comb on midleg-like protein 1 OS=Homo sapiens GN=SCML1 PE=1 SV=2\n+ # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc\n+ --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----\n+ 1 ? 11.8 0.1 0.013 6.3 51 100 .. 50 98 .. 44 117 .. 0.92\n+\n+ Alignments for each domain:\n+ == domain 1 score: 11.8 bits; conditional E-value: 0.013\n+ globins4 51 stedelkksadvkkHgkkvldAlsdalakldekleaklkdLselHakklk 100\n+ +te++lk +dv H + + dAl++ +k+d ++ k++++ Ha++l \n+ sp|Q9UN30|SCML1_HUMAN 50 NTEEQLKTVDDVLIHCQVIYDALQNLDKKID-VIRRKVSKIQRFHARSLW 98 \n+ 79****************************9.99************9985 PP\n+\n+>> sp|B8FUJ0|SYGB_DESHD Glycine--tRNA ligase beta subunit OS=Desulfitobacterium hafniense (strain DCB-2 / DSM 10664) GN\n+ # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc\n+ --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----\n+ 1 ? 9.1 0.0 0.091 44 86 134 .. 24 76 .. 13 81 .. 0.85\n+\n+ Alignments for each domain:\n+ == domain 1 score: 9.1 bits; conditional E-value: 0.091\n+ globins4 86 aklkdLselHakklkvdpkyfklls.....evlvdvlaarlpkeftadvqaale 134\n+ ++l++ +++++++l++d + +k+ + +vl++ la++ ++fta+v++ \n+ sp|B8FUJ0|SYGB_DESHD 24 NQLREQAQKYCQELRLDYQDLKVYTtprrfAVLIQGLAEK-QTDFTAEVKGPAV 76 \n+ 789999*****************984555569******99.99****9998655 PP\n+\n+>> sp|Q498L9|KI15B_XENLA Kinesin-like protein KIF15-B OS=Xenopus laevis GN=kif15-b PE=1 SV=1\n+ # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc\n+ --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----\n+ 1 ? 10.1 0.8 0.044 22 38 100 .. 600 661 .. 587 674 .. 0.86\n+\n+ Alignments for each domain:\n+ == domain 1 score: 10.1 bits; conditional E-value: 0.044\n+ globins4 38 PatqefFekFkdLstedelkksadvkkHgkkvldAlsdalakldekleaklkdLselHakklk 100\n+ ++++ +e+Fk+L+ + ++++ +++ k + l+++l ++e+ + ++++L Ha+ k\n+ sp|Q498L9|KI15B_XENLA 600 ATSKQEYEEFKELTKKKQVEQESELQSLMK-SNQHLENILDAIKENKRHEVSQLNRMHAETIK 661\n+ 467889*******************98765.57889999999999**************9765 PP\n+\n+\n+\n+Internal pipeline statistics summary:\n+-------------------------------------\n+Query model(s): 1 (149 nodes)\n+Target sequences: 539165 (191456931 residues searched)\n+Passed MSV filter: 20801 (0.03858); expected 10783.3 (0.02)\n+Passed bias filter: 17061 (0.0316434); expected 10783.3 (0.02)\n+Passed Vit filter: 2321 (0.0043048); expected 539.2 (0.001)\n+Passed Fwd filter: 1109 (0.00205688); expected 5.4 (1e-05)\n+Initial search space (Z): 539165 [actual number of targets]\n+Domain search space (domZ): 1108 [number of targets reported over threshold]\n+# CPU time: 6.50u 0.11s 00:00:06.61 Elapsed: 00:00:02.59\n+# Mc/sec: 11014.32\n+//\n+[ok]\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins4.sto --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/globins4.sto Sat Jun 25 15:07:32 2016 -0400 |
| b |
| @@ -0,0 +1,18 @@ +# STOCKHOLM 1.0 + +HBB_HUMAN ........VHLTPEEKSAVTALWGKV....NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVL +HBA_HUMAN .........VLSPADKTNVKAAWGKVGA..HAGEYGAEALERMFLSFPTTKTYFPHF.DLS.....HGSAQVKGHGKKVA +MYG_PHYCA .........VLSEGEWQLVLHVWAKVEA..DVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVL +GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYS..TYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERII + +HBB_HUMAN GAFSDGLAHL...D..NLKGTFATLSELHCDKL..HVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANAL +HBA_HUMAN DALTNAVAHV...D..DMPNALSALSDLHAHKL..RVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL +MYG_PHYCA TALGAILKK....K.GHHEAELKPLAQSHATKH..KIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDI +GLB5_PETMA NAVNDAVASM..DDTEKMSMKLRDLSGKHAKSF..QVDPQYFKVLAAVIADTVAAG.........DAGFEKLMSMICILL + +HBB_HUMAN AHKYH...... +HBA_HUMAN TSKYR...... +MYG_PHYCA AAKYKELGYQG +GLB5_PETMA RSAY....... +// + |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/globins45.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/globins45.fa Sat Jun 25 15:07:32 2016 -0400 |
| b |
| @@ -0,0 +1,186 @@ +>MYG_ESCGI +VLSDAEWQLVLNIWAKVEADVAGHGQDILIRLFKGHPETLEKFDKFKHLK +TEAEMKASEDLKKHGNTVLTALGGILKKKGHHEAELKPLAQSHATKHKIP +IKYLEFISDAIIHVLHSRHPGDFGADAQAAMNKALELFRKDIAAKYKELG +FQG +>MYG_HORSE +GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLK +TEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIP +IKYLEFISDAIIHVLHSKHPGNFGADAQGAMTKALELFRNDIAAKYKELG +FQG +>MYG_PROGU +GLSDGEWQLVLNVWGKVEGDLSGHGQEVLIRLFKGHPETLEKFDKFKHLK +AEDEMRASEELKKHGTTVLTALGGILKKKGQHAAELAPLAQSHATKHKIP +VKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDIAAKYKELG +FQG +>MYG_SAISC +GLSDGEWQLVLNIWGKVEADIPSHGQEVLISLFKGHPETLEKFDKFKHLK +SEDEMKASEELKKHGTTVLTALGGILKKKGQHEAELKPLAQSHATKHKIP +VKYLELISDAIVHVLQKKHPGDFGADAQGAMKKALELFRNDMAAKYKELG +FQG +>MYG_LYCPI +GLSDGEWQIVLNIWGKVETDLAGHGQEVLIRLFKNHPETLDKFDKFKHLK +TEDEMKGSEDLKKHGNTVLTALGGILKKKGHHEAELKPLAQSHATKHKIP +VKYLEFISDAIIQVLQNKHSGDFHADTEAAMKKALELFRNDIAAKYKELG +FQG +>MYG_MOUSE +GLSDGEWQLVLNVWGKVEADLAGHGQEVLIGLFKTHPETLDKFDKFKNLK +SEEDMKGSEDLKKHGCTVLTALGTILKKKGQHAAEIQPLAQSHATKHKIP +VKYLEFISEIIIEVLKKRHSGDFGADAQGAMSKALELFRNDIAAKYKELG +FQG +>MYG_MUSAN +VDWEKVNSVWSAVESDLTAIGQNILLRLFEQYPESQNHFPKFKNKSLGEL +KDTADIKAQADTVLSALGNIVKKKGSHSQPVKALAATHITTHKIPPHYFT +KITTIAVDVLSEMYPSEMNAQVQAAFSGAFKIICSDIEKEYKAANFQG +>HBA_AILME +VLSPADKTNVKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHFDLSP +GSAQVKAHGKKVADALTTAVGHLDDLPGALSALSDLHAHKLRVDPVNFKL +LSHCLLVTLASHHPAEFTPAVHASLDKFFSAVSTVLTSKYR +>HBA_PROLO +VLSPADKANIKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHFDLSP +GSAQVKAHGKKVADALTLAVGHLDDLPGALSALSDLHAYKLRVDPVNFKL +LSHCLLVTLACHHPAEFTPAVHASLDKFFTSVSTVLTSKYR +>HBA_PAGLA +VLSSADKNNIKATWDKIGSHAGEYGAEALERTFISFPTTKTYFPHFDLSH +GSAQVKAHGKKVADALTLAVGHLEDLPNALSALSDLHAYKLRVDPVNFKL +LSHCLLVTLACHHPAEFTPAVHSALDKFFSAVSTVLTSKYR +>HBA_MACFA +VLSPADKTNVKAAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHFDLSH +GSAQVKGHGKKVADALTLAVGHVDDMPQALSALSDLHAHKLRVDPVNFKL +LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR +>HBA_MACSI +VLSPADKTNVKDAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHFDLSH +GSAQVKGHGKKVADALTLAVGHVDDMPQALSALSDLHAHKLRVDPVNFKL +LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR +>HBA_PONPY +VLSPADKTNVKTAWGKVGAHAGDYGAEALERMFLSFPTTKTYFPHFDLSH +GSAQVKDHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL +LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR +>HBA2_GALCR +VLSPTDKSNVKAAWEKVGAHAGDYGAEALERMFLSFPTTKTYFPHFDLSH +GSTQVKGHGKKVADALTNAVLHVDDMPSALSALSDLHAHKLRVDPVNFKL +LRHCLLVTLACHHPAEFTPAVHASLDKFMASVSTVLTSKYR +>HBA_MESAU +VLSAKDKTNISEAWGKIGGHAGEYGAEALERMFFVYPTTKTYFPHFDVSH +GSAQVKGHGKKVADALTNAVGHLDDLPGALSALSDLHAHKLRVDPVNFKL +LSHCLLVTLANHHPADFTPAVHASLDKFFASVSTVLTSKYR +>HBA2_BOSMU +VLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSH +GSAQVKGHGAKVAAALTKAVGHLDDLPGALSELSDLHAHKLRVDPVNFKL +LSHSLLVTLASHLPSDFTPAVHASLDKFLANVSTVLTSKYR +>HBA_ERIEU +VLSATDKANVKTFWGKLGGHGGEYGGEALDRMFQAHPTTKTYFPHFDLNP +GSAQVKGHGKKVADALTTAVNNLDDVPGALSALSDLHAHKLRVDPVNFKL +LSHCLLVTLALHHPADFTPAVHASLDKFLATVATVLTSKYR +>HBA_FRAPO +VLSAADKNNVKGIFGKISSHAEDYGAEALERMFITYPSTKTYFPHFDLSH +GSAQVKGHGKKVVAALIEAANHIDDIAGTLSKLSDLHAHKLRVDPVNFKL +LGQCFLVVVAIHHPSALTPEVHASLDKFLCAVGNVLTAKYR +>HBA_PHACO +VLSAADKNNVKGIFTKIAGHAEEYGAEALERMFITYPSTKTYFPHFDLSH +GSAQIKGHGKKVVAALIEAVNHIDDITGTLSKLSDLHAHKLRVDPVNFKL +LGQCFLVVVAIHHPSALTPEVHASLDKFLCAVGTVLTAKYR +>HBA_TRIOC +VLSANDKTNVKTVFTKITGHAEDYGAETLERMFITYPPTKTYFPHFDLHH +GSAQIKAHGKKVVGALIEAVNHIDDIAGALSKLSDLHAQKLRVDPVNFKL +LGQCFLVVVAIHHPSVLTPEVHASLDKFLCAVGNVLSAKYR +>HBA_ANSSE +VLSAADKGNVKTVFGKIGGHAEEYGAETLQRMFQTFPQTKTYFPHFDLQP +GSAQIKAHGKKVAAALVEAANHIDDIAGALSKLSDLHAQKLRVDPVNFKF +LGHCFLVVLAIHHPSLLTPEVHASMDKFLCAVATVLTAKYR +>HBA_COLLI +VLSANDKSNVKAVFAKIGGQAGDLGGEALERLFITYPQTKTYFPHFDLSH +GSAQIKGHGKKVAEALVEAANHIDDIAGALSKLSDLHAQKLRVDPVNFKL +LGHCFLVVVAVHFPSLLTPEVHASLDKFVLAVGTVLTAKYR +>HBAD_CHLME +MLTADDKKLLTQLWEKVAGHQEEFGSEALQRMFLTYPQTKTYFPHFDLHP +GSEQVRGHGKKVAAALGNAVKSLDNLSQALSELSNLHAYNLRVDPANFKL +LAQCFQVVLATHLGKDYSPEMHAAFDKFLSAVAAVLAEKYR +>HBAD_PASMO +MLTAEDKKLIQQIWGKLGGAEEEIGADALWRMFHSYPSTKTYFPHFDLSQ +GSDQIRGHGKKVVAALSNAIKNLDNLSQALSELSNLHAYNLRVDPVNFKF +LSQCLQVSLATRLGKEYSPEVHSAVDKFMSAVASVLAEKYR +>HBAZ_HORSE +SLTKAERTMVVSIWGKISMQADAVGTEALQRLFSSYPQTKTYFPHFDLHE +GSPQLRAHGSKVAAAVGDAVKSIDNVAGALAKLSELHAYILRVDPVNFKF +LSHCLLVTLASRLPADFTADAHAAWDKFLSIVSSVLTEKYR +>HBA4_SALIR +SLSAKDKANVKAIWGKILPKSDEIGEQALSRMLVVYPQTKAYFSHWASVA +PGSAPVKKHGITIMNQIDDCVGHMDDLFGFLTKLSELHATKLRVDPTNFK +ILAHNLIVVIAAYFPAEFTPEIHLSVDKFLQQLALALAEKYR +>HBB_ORNAN +VHLSGGEKSAVTNLWGKVNINELGGEALGRLLVVYPWTQRFFEAFGDLSS +AGAVMGNPKVKAHGAKVLTSFGDALKNLDDLKGTFAKLSELHCDKLHVDP +ENFNRLGNVLIVVLARHFSKDFSPEVQAAWQKLVSGVAHALGHKYH +>HBB_TACAC +VHLSGSEKTAVTNLWGHVNVNELGGEALGRLLVVYPWTQRFFESFGDLSS +ADAVMGNAKVKAHGAKVLTSFGDALKNLDNLKGTFAKLSELHCDKLHVDP +ENFNRLGNVLVVVLARHFSKEFTPEAQAAWQKLVSGVSHALAHKYH +>HBE_PONPY +VHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSS +PSAILGNPKVKAHGKKVLTSFGDAIKNMDNLKTTFAKLSELHCDKLHVDP +ENFKLLGNVMVIILATHFGKEFTPEVQAAWQKLVSAVAIALAHKYH +>HBB_SPECI +VHLSDGEKNAISTAWGKVHAAEVGAEALGRLLVVYPWTQRFFDSFGDLSS +ASAVMGNAKVKAHGKKVIDSFSNGLKHLDNLKGTFASLSELHCDKLHVDP +ENFKLLGNMIVIVMAHHLGKDFTPEAQAAFQKVVAGVANALAHKYH +>HBB_SPETO +VHLTDGEKNAISTAWGKVNAAEIGAEALGRLLVVYPWTQRFFDSFGDLSS +ASAVMGNAKVKAHGKKVIDSFSNGLKHLDNLKGTFASLSELHCDKLHVDP +ENFKLLGNMIVIVMAHHLGKDFTPEAQAAFQKVVAGVANALSHKYH +>HBB_EQUHE +VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSN +PAAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAQLSELHCDKLHVDP +ENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH +>HBB_SUNMU +VHLSGEEKACVTGLWGKVNEDEVGAEALGRLLVVYPWTQRFFDSFGDLSS +ASAVMGNPKVKAHGKKVLHSLGEGVANLDNLKGTFAKLSELHCDKLHVDP +ENFRLLGNVLVVVLASKFGKEFTPPVQAAFQKVVAGVANALAHKYH +>HBB_CALAR +VHLTGEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLST +PDAVMNNPKVKAHGKKVLGAFSDGLTHLDNLKGTFAHLSELHCDKLHVDP +ENFRLLGNVLVCVLAHHFGKEFTPVVQAAYQKVVAGVANALAHKYH +>HBB_MANSP +VHLTPEEKTAVTTLWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSS +PDAVMGNPKVKAHGKKVLGAFSDGLNHLDNLKGTFAQLSELHCDKLHVDP +ENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH +>HBB_URSMA +VHLTGEEKSLVTGLWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSS +ADAIMNNPKVKAHGKKVLNSFSDGLKNLDNLKGTFAKLSELHCDKLHVDP +ENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH +>HBB_RABIT +VHLSSEEKSAVTALWGKVNVEEVGGEALGRLLVVYPWTQRFFESFGDLSS +ANAVMNNPKVKAHGKKVLAAFSEGLSHLDNLKGTFAKLSELHCDKLHVDP +ENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH +>HBB_TUPGL +VHLSGEEKAAVTGLWGKVDLEKVGGQSLGSLLIVYPWTQRFFDSFGDLSS +PSAVMSNPKVKAHGKKVLTSFSDGLNHLDNLKGTFAKLSELHCDKLHVDP +ENFRLLGNVLVRVLACNFGPEFTPQVQAAFQKVVAGVANALAHKYH +>HBB_TRIIN +VHLTPEEKALVIGLWAKVNVKEYGGEALGRLLVVYPWTQRFFEHFGDLSS +ASAIMNNPKVKAHGEKVFTSFGDGLKHLEDLKGAFAELSELHCDKLHVDP +ENFRLLGNVLVCVLARHFGKEFSPEAQAAYQKVVAGVANALAHKYH +>HBB_COLLI +VHWSAEEKQLITSIWGKVNVADCGAEALARLLIVYPWTQRFFSSFGNLSS +ATAISGNPNVKAHGKKVLTSFGDAVKNLDNIKGTFAQLSELHCDKLHVDP +ENFRLLGDILVIILAAHFGKDFTPECQAAWQKLVRVVAHALARKYH +>HBB_LARRI +VHWSAEEKQLITGLWGKVNVADCGAEALARLLIVYPWTQRFFASFGNLSS +PTAINGNPMVRAHGKKVLTSFGEAVKNLDNIKNTFAQLSELHCDKLHVDP +ENFRLLGDILIIVLAAHFAKDFTPDSQAAWQKLVRVVAHALARKYH +>HBB1_VAREX +VHWTAEEKQLICSLWGKIDVGLIGGETLAGLLVIYPWTQRQFSHFGNLSS +PTAIAGNPRVKAHGKKVLTSFGDAIKNLDNIKDTFAKLSELHCDKLHVDP +TNFKLLGNVLVIVLADHHGKEFTPAHHAAYQKLVNVVSHSLARRYH +>HBB2_XENTR +VHWTAEEKATIASVWGKVDIEQDGHDALSRLLVVYPWTQRYFSSFGNLSN +VSAVSGNVKVKAHGNKVLSAVGSAIQHLDDVKSHLKGLSKSHAEDLHVDP +ENFKRLADVLVIVLAAKLGSAFTPQVQAVWEKLNATLVAALSHGYF +>HBBL_RANCA +VHWTAEEKAVINSVWQKVDVEQDGHEALTRLFIVYPWTQRYFSTFGDLSS +PAAIAGNPKVHAHGKKILGAIDNAIHNLDDVKGTLHDLSEEHANELHVDP +ENFRRLGEVLIVVLGAKLGKAFSPQVQHVWEKFIAVLVDALSHSYH +>HBB2_TRICR +VHLTAEDRKEIAAILGKVNVDSLGGQCLARLIVVNPWSRRYFHDFGDLSS +CDAICRNPKVLAHGAKVMRSIVEATKHLDNLREYYADLSVTHSLKFYVDP +ENFKLFSGIVIVCLALTLQTDFSCHKQLAFEKLMKGVSHALGHGY |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/jackhmmer.domtblout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jackhmmer.domtblout Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,103 @@\n+# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord\n+# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target\n+#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------\n+HBB_MANSP - 146 sp|P02185|MYG_PHYCD - 142 7.7e-69 221.6 0.1 1 1 8.6e-69 8.6e-69 221.5 0.1 1 142 6 145 6 145 0.99 -\n+HBB_URSMA - 146 sp|P02185|MYG_PHYCD - 142 4.1e-68 219.3 0.2 1 1 4.5e-68 4.5e-68 219.1 0.2 1 142 6 145 6 145 0.99 -\n+HBB_RABIT - 146 sp|P02185|MYG_PHYCD - 142 5.6e-67 215.6 0.5 1 1 6.3e-67 6.3e-67 215.4 0.5 1 142 6 145 6 145 0.99 -\n+HBB_CALAR - 146 sp|P02185|MYG_PHYCD - 142 1.5e-66 214.2 0.1 1 1 1.7e-66 1.7e-66 214.0 0.1 1 142 6 145 6 145 0.99 -\n+HBB_TACAC - 146 sp|P02185|MYG_PHYCD - 142 5e-66 212.5 0.3 1 1 5.6e-66 5.6e-66 212.4 0.3 2 142 7 145 6 145 0.99 -\n+HBB_COLLI - 146 sp|P02185|MYG_PHYCD - 142 5.2e-66 212.5 0.0 1 1 5.7e-66 5.7e-66 212.3 0.0 1 142 6 145 6 145 0.99 -\n+HBE_PONPY - 146 sp|P02185|MYG_PHYCD - 142 6.6e-66 212.1 0.2 1 1 7.4e-66 7.4e-66 212.0 0.2 1 142 6 145 6 145 0.99 -\n+HBB_SUNMU - 146 sp|P02185|MYG_PHYCD - 142 7.2e-66 212.0 0.1 1 1 8e-66 8e-66 211.9 0.1 1 142 6 145 6 145 0.99 -\n+HBB_ORNAN - 146 sp|P02185|MYG_PHYCD - 142 1e-65 211.5 0.0 1 1 1.2e-65 1.2e-65 211.3 0.0 2 142 7 145 6 145 0.99 -\n+HBB_SPETO - 146 sp|P02185|MYG_PHYCD - 142 1.5e-65 211.0 0.4 1 1 1.7e-65 1.7e-65 210.8 0.4 2 142 7 145 6 145 0.99 -\n+HBB_EQUHE - 146 sp|P02185|MYG_PHYCD - 142 1.6e-65 210.9 0.2 1 1 1.8e-65 1.8e-65 210.7 0.2 1 142 6 145 6 145 0.99 -\n+HBB_SPECI - 146 sp|P02185|MYG_PHYCD - 142 2.3e-65 210.4 0.9 1 1 2.5e-65 2.5e-65 210.2 0.9 2 142 7 145 6 145 0.99 -\n+HBB_LARRI - 146 sp|P02185|MYG_PHYCD - 142 3e-65 210.0 0.0 1 1 3.4e-65 3.4e-65 209.8 0.0 1 142 6 145 6 145 0.99 -\n+HBB_TRIIN - 146 sp|P02185|MYG_PHYCD - 142 8e-65 208.6 0.1 1 1 8.9e-65 8.9e-65 208.5 0.1 1 142 6 145 6 145 0.99 -\n+HBB_TUPGL - 146 sp|P02185|MYG_PHYCD - 142 1.2e-62 201.6 0.0 1 1 1.3e-62 1.3e-62 201.5 0.0 1 142 6 145 6 145 0.99 -\n+HBA_MESAU - 141 sp|P02185|MYG_PHYCD - 142 1.5e-61 198.0 0.6 1 1 1.7e-61 1.7e-61 197.8 0.6 2 142 6 140 5 140 0.99 -\n+HBB1_VAREX - 146 sp|P02185|MYG_PHYCD - 142 3e-61 197.0 0.1 1 1 3.4e-61 3.4e-61 196.9 0.1 1 142 6 145 6 145 0.99 -\n+HBA_MACFA - 141 sp|P02185|MYG_PHYCD - 142 6e-61 196.1 1.1 1 1 6.6e-61 6.6e-61 195.9 1.1 2 142 6 140 5 140 0.99 -\n+HBA_MACSI - 141 sp|P02185|MYG_PHYCD - 142 9.7e-'..b'24|HBB_GORGO - 143 1e-59 191.9 0.1 1 1 1.1e-59 1.1e-59 191.8 0.1 1 143 2 140 2 140 0.98 -\n+HBA_PROLO - 141 sp|P02024|HBB_GORGO - 143 1.4e-59 191.5 0.0 1 1 1.5e-59 1.5e-59 191.4 0.0 1 143 2 140 2 140 0.99 -\n+HBA_ANSSE - 141 sp|P02024|HBB_GORGO - 143 1.6e-59 191.3 0.4 1 1 1.8e-59 1.8e-59 191.1 0.4 1 143 2 140 2 140 0.99 -\n+HBA_PAGLA - 141 sp|P02024|HBB_GORGO - 143 1.7e-59 191.2 0.5 1 1 1.9e-59 1.9e-59 191.1 0.5 1 143 2 140 2 140 0.99 -\n+HBA_TRIOC - 141 sp|P02024|HBB_GORGO - 143 1.1e-58 188.6 0.5 1 1 1.2e-58 1.2e-58 188.4 0.5 1 143 2 140 2 140 0.99 -\n+HBAD_CHLME - 141 sp|P02024|HBB_GORGO - 143 2.9e-58 187.2 0.6 1 1 3.2e-58 3.2e-58 187.1 0.6 1 143 2 140 2 140 0.98 -\n+HBAZ_HORSE - 141 sp|P02024|HBB_GORGO - 143 3.4e-58 187.0 0.1 1 1 3.8e-58 3.8e-58 186.9 0.1 1 143 2 140 2 140 0.98 -\n+HBA_COLLI - 141 sp|P02024|HBB_GORGO - 143 6.7e-58 186.1 0.2 1 1 7.4e-58 7.4e-58 185.9 0.2 1 143 2 140 2 140 0.98 -\n+HBAD_PASMO - 141 sp|P02024|HBB_GORGO - 143 8.9e-58 185.7 0.1 1 1 9.9e-58 9.9e-58 185.5 0.1 1 143 2 140 2 140 0.98 -\n+MYG_LYCPI - 153 sp|P02024|HBB_GORGO - 143 1.1e-56 182.1 1.9 1 1 1.3e-56 1.3e-56 181.9 1.9 1 143 2 146 2 146 0.97 -\n+MYG_SAISC - 153 sp|P02024|HBB_GORGO - 143 1.1e-56 182.1 1.1 1 1 1.3e-56 1.3e-56 181.9 1.1 1 143 2 146 2 146 0.98 -\n+MYG_ESCGI - 153 sp|P02024|HBB_GORGO - 143 2.5e-56 181.0 1.7 1 1 2.8e-56 2.8e-56 180.8 1.7 1 143 2 146 2 146 0.97 -\n+MYG_PROGU - 153 sp|P02024|HBB_GORGO - 143 3.2e-56 180.6 0.2 1 1 3.6e-56 3.6e-56 180.4 0.2 1 143 2 146 2 146 0.97 -\n+MYG_HORSE - 153 sp|P02024|HBB_GORGO - 143 9.5e-56 179.1 1.0 1 1 1.1e-55 1.1e-55 178.9 1.0 1 143 2 146 2 146 0.97 -\n+MYG_MOUSE - 153 sp|P02024|HBB_GORGO - 143 1.8e-55 178.2 0.3 1 1 2e-55 2e-55 178.0 0.3 1 143 2 146 2 146 0.97 -\n+HBA4_SALIR - 142 sp|P02024|HBB_GORGO - 143 3.4e-55 177.3 0.1 1 1 3.8e-55 3.8e-55 177.1 0.1 1 143 2 141 2 141 0.98 -\n+HBB2_TRICR - 145 sp|P02024|HBB_GORGO - 143 1.8e-53 171.7 0.0 1 1 2e-53 2e-53 171.6 0.0 1 143 3 145 3 145 0.99 -\n+MYG_MUSAN - 148 sp|P02024|HBB_GORGO - 143 1e-44 143.3 0.3 1 1 1.1e-44 1.1e-44 143.2 0.3 5 143 2 141 1 141 0.96 -\n+#\n+# Program: jackhmmer\n+# Version: 3.1b2 (February 2015)\n+# Pipeline mode: SEARCH\n+# Query file: /tmp/tmphb1nFG/files/000/dataset_1.dat\n+# Target file: /tmp/tmphb1nFG/files/000/dataset_2.dat\n+# Option settings: jackhmmer -N 5 --tblout /tmp/tmphb1nFG/files/000/dataset_4.dat --domtblout /tmp/tmphb1nFG/files/000/dataset_5.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --fast --hand --symfrac 0.5 --wpb --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmphb1nFG/files/000/dataset_1.dat /tmp/tmphb1nFG/files/000/dataset_2.dat \n+# Current dir: /tmp/tmphb1nFG/job_working_directory/000/3\n+# Date: Sat Jun 25 19:33:04 2016\n+# [ok]\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/jackhmmer.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jackhmmer.out Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,3225 @@\n+# jackhmmer :: iteratively search a protein sequence against a protein database\n+# HMMER 3.1b1 (May 2013); http://hmmer.org/\n+# Copyright (C) 2013 Howard Hughes Medical Institute.\n+# Freely distributed under the GNU General Public License (GPLv3).\n+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n+# query sequence file: /tmp/tmpwsYozTfiles/000/dataset_31.dat\n+# target sequence database: /tmp/tmpwsYozTfiles/000/dataset_32.dat\n+# per-seq hits tabular output: /tmp/tmpwsYozTfiles/000/dataset_34.dat\n+# per-dom hits tabular output: /tmp/tmpwsYozTfiles/000/dataset_35.dat\n+# max ASCII text line length: unlimited\n+# Vit filter P threshold: <= 0.001\n+# Fwd filter P threshold: <= 1e-05\n+# model architecture construction: fast/heuristic\n+# random number seed set to: 4\n+# number of worker threads: 2\n+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n+\n+Query: sp|P02185|MYG_PHYCD [L=154]\n+Description: Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+\n+Scores for complete sequences (score includes all domains):\n+ --- full sequence --- --- best 1 domain --- -#dom-\n+ E-value score bias E-value score bias exp N Sequence Description\n+ ------- ------ ----- ------- ------ ----- ---- -- -------- -----------\n++ 3.7e-96 310.8 5.1 4.1e-96 310.7 5.1 1.0 1 MYG_ESCGI \n++ 1.2e-91 296.2 4.6 1.4e-91 296.0 4.6 1.0 1 MYG_HORSE \n++ 1e-86 280.2 3.1 1.1e-86 280.0 3.1 1.0 1 MYG_PROGU \n++ 8.4e-86 277.2 4.7 9.3e-86 277.1 4.7 1.0 1 MYG_SAISC \n++ 1.4e-84 273.3 4.0 1.5e-84 273.1 4.0 1.0 1 MYG_LYCPI \n++ 7.4e-84 270.9 1.8 8.1e-84 270.8 1.8 1.0 1 MYG_MOUSE \n++ 2.3e-34 110.3 0.0 2.6e-34 110.2 0.0 1.0 1 MYG_MUSAN \n++ 6.6e-17 53.7 0.0 7.5e-17 53.5 0.0 1.0 1 HBAZ_HORSE \n++ 2.4e-14 45.4 0.0 2.8e-14 45.2 0.0 1.0 1 HBB_COLLI \n++ 1.3e-13 43.0 0.0 1.5e-13 42.7 0.0 1.0 1 HBB_LARRI \n++ 1.9e-12 39.2 0.1 2.3e-12 38.9 0.1 1.1 1 HBB2_XENTR \n++ 3.1e-12 38.5 0.1 3.3e-12 38.5 0.1 1.0 1 HBB_ORNAN \n++ 6.5e-12 37.5 0.3 6.9e-12 37.4 0.3 1.0 1 HBB_TRIIN \n++ 8.4e-12 37.1 0.1 9.5e-12 36.9 0.1 1.0 1 HBE_PONPY \n++ 1.1e-11 36.8 0.1 1.3e-11 36.6 0.1 1.0 1 HBB1_VAREX \n++ 2.2e-11 35.8 0.5 2.4e-11 35.6 0.5 1.0 1 HBB_SPECI \n++ 8.4e-11 33.9 0.2 8.9e-11 33.8 0.2 1.0 1 HBB_SPETO \n++ 1.1e-10 33.4 0.2 1.2e-10 33.3 0.2 1.0 1 HBB_TACAC \n++ 1.3e-10 33.3 0.0 1.4e-10 33.1 0.0 1.0 1 HBAD_PASMO \n++ 1.4e-10 33.1 0.1 1.5e-10 33.1 0.1 1.0 1 HBB_SUNMU \n++ 2.8e-10 32.2 0.1 3e-10 32.1 0.1 1.1 1 HBA_ERIEU \n++ 6e-10 31.1 0.6 6.7e-10 31.0 0.6 1.1 1 HBA2_BOSMU \n++ 6.1e-10 31.1 0.1 6.9e-10 30.9 0.1 1.1 1 HBAD_CHLME \n++ 6.6e-10 31.0 0.1 7e-10 30.9 0.1 1.0 1 HBB_URSMA \n++ 7.7e-10 30.7 0.2 9.5e-10 30.5 0.2 1.1 1 HBBL_RANCA \n++ 8.5e-10 30.6 0.2 9e-10 30.5 0.2 1.0 1 HBB_EQUHE \n++ 2.2e-09 29.3 0.2 2.4e-09 29.1 0.2 1.1 1 HBA_AILME \n++ 3.1e-09 28.8 0.0 3.3e-09 28.7 0.0 1.0 1 HBB_TUPGL \n++ 4.6e-09 28.2 0.1 5.4e-09 28.0 0.1 1.0 1 HBA4_SALIR \n++ 4.8e-09 28.2 0.2 5.4e-09 28.0 0.2 1.1 1 HBA2_GALCR \n++ 7.5e-09 27.6 0.4 8.2e-09 27.4 0.4 1.1 1 HBA_MESAU \n++ 9.2e-09 27.3 0.1 1.1e-08 27.1 0.1 1.0 1 HBB_MANSP \n++ 1.1e-08 27.0 0.3 1.2e-08 26.9 0.3 1.1 1 HBA_PONPY \n++ 1.1e-08 27.0 0.2 1.3e-08 26.8 0.2 1.1 1 HBA_PAGLA \n++ 1.2e-08 26.9 0.2 1.3e-08 26.7 0.2 1.1 1 HBA_ANSSE \n++ 2.5e-08 25.8 0.3 2.7e-08 '..b' ++de+G++aL+r+lvvyP+tk yF+++++++ gsa vk+hg +++++++++v ++ddl g l+kLselHatkl+vdp+nfk+l++ l+vv+aa fp+eftpe++ ++dk+l+++a ala+kY\n+ HBA4_SALIR 2 LSAKDKANVKAIWGKIlpKSDEIGEQALSRMLVVYPQTKAYFSHWASVA-----PGSAPVKKHGITIMNQIDDCVGHMDDLFGFLTKLSELHATKLRVDPTNFKILAHNLIVVIAAYFPAEFTPEIHLSVDKFLQQLALALAEKY 141\n+ 699*************999**************************7765.....9*****************************************************************************************9 PP\n+\n+>> HBB2_TRICR \n+ # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc\n+ --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----\n+ 1 ! 171.6 0.0 2e-53 2e-53 1 143 [] 3 145 .] 3 145 .] 0.99\n+\n+ Alignments for each domain:\n+ == domain 1 score: 171.6 bits; conditional E-value: 2e-53\n+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ sp|P02024|HBB_GORGO-i1 1 lsaeekalvkavwgkveadevGaeaLerllvvyPetkryFdkFkdlssedavkgsakvkahgkkvltalgeavkklddlkgalakLselHatklkvdpenfkllsevlvvvLaakfpkeftpevqaaldkllaavanalaakY 143\n+ l+ae++++++a++gkv++d++G+++L+rl+vv P+++ryF++F+dlss+da+++++kv ahg+kv++++ ea k+ld+l++ +a+Ls +H+ k+ vdpenfkl+s +++v+La +++++f+++ q a++kl+++v++al++ Y\n+ HBB2_TRICR 3 LTAEDRKEIAAILGKVNVDSLGGQCLARLIVVNPWSRRYFHDFGDLSSCDAICRNPKVLAHGAKVMRSIVEATKHLDNLREYYADLSVTHSLKFYVDPENFKLFSGIVIVCLALTLQTDFSCHKQLAFEKLMKGVSHALGHGY 145\n+ 79*******************************************************************************************************************************************99 PP\n+\n+>> MYG_MUSAN \n+ # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc\n+ --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----\n+ 1 ! 143.2 0.3 1.1e-44 1.1e-44 5 143 .] 2 141 .. 1 141 [. 0.96\n+\n+ Alignments for each domain:\n+ == domain 1 score: 143.2 bits; conditional E-value: 1.1e-44\n+ xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ sp|P02024|HBB_GORGO-i1 5 ekalvkavwgkvead..evGaeaLerllvvyPetkryFdkFkdlssedavkgsakvkahgkkvltalgeavkklddlkgalakLselHatklkvdpenfkllsevlvvvLaakfpkeftpevqaaldkllaavanalaakY 143\n+ ++++v++vw+ ve+d ++G+++L rl+++yPe++++F+kFk++s ++k++a++ka++++vl+alg++vkk++++++ +++L+++H+t++k++p++f+ ++++ v vL++++p+e++++vqaa++ +++ + +++ ++Y\n+ MYG_MUSAN 2 DWEKVNSVWSAVESDltAIGQNILLRLFEQYPESQNHFPKFKNKS-LGELKDTADIKAQADTVLSALGNIVKKKGSHSQPVKALAATHITTHKIPPHYFTKITTIAVDVLSEMYPSEMNAQVQAAFSGAFKIICSDIEKEY 141\n+ 7899********9886689**********************9998.667*************************************************************************************9999888 PP\n+\n+\n+\n+Internal pipeline statistics summary:\n+-------------------------------------\n+Query model(s): 1 (143 nodes)\n+Target sequences: 45 (6519 residues searched)\n+Passed MSV filter: 45 (1); expected 0.9 (0.02)\n+Passed bias filter: 45 (1); expected 0.9 (0.02)\n+Passed Vit filter: 45 (1); expected 0.0 (0.001)\n+Passed Fwd filter: 45 (1); expected 0.0 (1e-05)\n+Initial search space (Z): 45 [actual number of targets]\n+Domain search space (domZ): 45 [number of targets reported over threshold]\n+# CPU time: 0.34u 0.01s 00:00:00.35 Elapsed: 00:00:01.00\n+# Mc/sec: 0.93\n+\n+@@ New targets included: 0\n+@@ New alignment includes: 46 subseqs (was 46), including original query\n+@@\n+@@ CONVERGED (in 2 rounds). \n+@@\n+\n+//\n+[ok]\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/jackhmmer.tblout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jackhmmer.tblout Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,103 @@\n+# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----\n+# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target\n+#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------\n+HBB_MANSP - sp|P02185|MYG_PHYCD - 7.7e-69 221.6 0.1 8.6e-69 221.5 0.1 1.0 1 0 0 1 1 1 1 -\n+HBB_URSMA - sp|P02185|MYG_PHYCD - 4.1e-68 219.3 0.2 4.5e-68 219.1 0.2 1.0 1 0 0 1 1 1 1 -\n+HBB_RABIT - sp|P02185|MYG_PHYCD - 5.6e-67 215.6 0.5 6.3e-67 215.4 0.5 1.0 1 0 0 1 1 1 1 -\n+HBB_CALAR - sp|P02185|MYG_PHYCD - 1.5e-66 214.2 0.1 1.7e-66 214.0 0.1 1.0 1 0 0 1 1 1 1 -\n+HBB_TACAC - sp|P02185|MYG_PHYCD - 5e-66 212.5 0.3 5.6e-66 212.4 0.3 1.0 1 0 0 1 1 1 1 -\n+HBB_COLLI - sp|P02185|MYG_PHYCD - 5.2e-66 212.5 0.0 5.7e-66 212.3 0.0 1.0 1 0 0 1 1 1 1 -\n+HBE_PONPY - sp|P02185|MYG_PHYCD - 6.6e-66 212.1 0.2 7.4e-66 212.0 0.2 1.0 1 0 0 1 1 1 1 -\n+HBB_SUNMU - sp|P02185|MYG_PHYCD - 7.2e-66 212.0 0.1 8e-66 211.9 0.1 1.0 1 0 0 1 1 1 1 -\n+HBB_ORNAN - sp|P02185|MYG_PHYCD - 1e-65 211.5 0.0 1.2e-65 211.3 0.0 1.0 1 0 0 1 1 1 1 -\n+HBB_SPETO - sp|P02185|MYG_PHYCD - 1.5e-65 211.0 0.4 1.7e-65 210.8 0.4 1.0 1 0 0 1 1 1 1 -\n+HBB_EQUHE - sp|P02185|MYG_PHYCD - 1.6e-65 210.9 0.2 1.8e-65 210.7 0.2 1.0 1 0 0 1 1 1 1 -\n+HBB_SPECI - sp|P02185|MYG_PHYCD - 2.3e-65 210.4 0.9 2.5e-65 210.2 0.9 1.0 1 0 0 1 1 1 1 -\n+HBB_LARRI - sp|P02185|MYG_PHYCD - 3e-65 210.0 0.0 3.4e-65 209.8 0.0 1.0 1 0 0 1 1 1 1 -\n+HBB_TRIIN - sp|P02185|MYG_PHYCD - 8e-65 208.6 0.1 8.9e-65 208.5 0.1 1.0 1 0 0 1 1 1 1 -\n+HBB_TUPGL - sp|P02185|MYG_PHYCD - 1.2e-62 201.6 0.0 1.3e-62 201.5 0.0 1.0 1 0 0 1 1 1 1 -\n+HBA_MESAU - sp|P02185|MYG_PHYCD - 1.5e-61 198.0 0.6 1.7e-61 197.8 0.6 1.0 1 0 0 1 1 1 1 -\n+HBB1_VAREX - sp|P02185|MYG_PHYCD - 3e-61 197.0 0.1 3.4e-61 196.9 0.1 1.0 1 0 0 1 1 1 1 -\n+HBA_MACFA - sp|P02185|MYG_PHYCD - 6e-61 196.1 1.1 6.6e-61 195.9 1.1 1.0 1 0 0 1 1 1 1 -\n+HBA_MACSI - sp|P02185|MYG_PHYCD - 9.7e-61 195.4 1.0 1.1e-60 195.2 1.0 1.0 1 0 0 1 1 1 1 -\n+HBA2_BOSMU - sp|P02185|MYG_PHYCD - 3.2e-60 193.7 0.9 3.6e-60 193.6 0.9 1.0 1 0 0 1 1 1 1 -\n+HBA_PONPY - sp|P02185|MYG_PHYCD - 3.2e-60 193.7 2.0 3.6e-60 193.5 2.0 1.0 1 0 0 1 1 1 1 -\n+HBA2_GALCR - sp|P02185|MYG_PHYCD - 4.2e-60 193.3 1.5 4.7e-60 193.2 1.5 1.0 1 0 0 1 1 1 1 -\n+HBA_AILME - sp|P02185|MYG_PHYCD - 5.7e-60 192.9 0.5 6.3e-60 192.7 0.5 1.0 1 0 0 1 1 1 1 -\n+HBA_FRAPO - sp|P02185|MYG_PHYCD - 9.6e-60 192.2 0.6 1.1e-59 192.0 0.6 1.0 1 '..b'0 1 0 0 1 1 1 1 -\n+HBA2_GALCR - sp|P02024|HBB_GORGO - 2.7e-60 193.8 0.5 3e-60 193.7 0.5 1.0 1 0 0 1 1 1 1 -\n+HBA_FRAPO - sp|P02024|HBB_GORGO - 3e-60 193.7 0.4 3.3e-60 193.5 0.4 1.0 1 0 0 1 1 1 1 -\n+HBA_PHACO - sp|P02024|HBB_GORGO - 3e-60 193.7 0.4 3.4e-60 193.5 0.4 1.0 1 0 0 1 1 1 1 -\n+HBA2_BOSMU - sp|P02024|HBB_GORGO - 3.2e-60 193.6 0.3 3.5e-60 193.4 0.3 1.0 1 0 0 1 1 1 1 -\n+HBA_ERIEU - sp|P02024|HBB_GORGO - 1e-59 191.9 0.1 1.1e-59 191.8 0.1 1.0 1 0 0 1 1 1 1 -\n+HBA_PROLO - sp|P02024|HBB_GORGO - 1.4e-59 191.5 0.0 1.5e-59 191.4 0.0 1.0 1 0 0 1 1 1 1 -\n+HBA_ANSSE - sp|P02024|HBB_GORGO - 1.6e-59 191.3 0.4 1.8e-59 191.1 0.4 1.0 1 0 0 1 1 1 1 -\n+HBA_PAGLA - sp|P02024|HBB_GORGO - 1.7e-59 191.2 0.5 1.9e-59 191.1 0.5 1.0 1 0 0 1 1 1 1 -\n+HBA_TRIOC - sp|P02024|HBB_GORGO - 1.1e-58 188.6 0.5 1.2e-58 188.4 0.5 1.0 1 0 0 1 1 1 1 -\n+HBAD_CHLME - sp|P02024|HBB_GORGO - 2.9e-58 187.2 0.6 3.2e-58 187.1 0.6 1.0 1 0 0 1 1 1 1 -\n+HBAZ_HORSE - sp|P02024|HBB_GORGO - 3.4e-58 187.0 0.1 3.8e-58 186.9 0.1 1.0 1 0 0 1 1 1 1 -\n+HBA_COLLI - sp|P02024|HBB_GORGO - 6.7e-58 186.1 0.2 7.4e-58 185.9 0.2 1.0 1 0 0 1 1 1 1 -\n+HBAD_PASMO - sp|P02024|HBB_GORGO - 8.9e-58 185.7 0.1 9.9e-58 185.5 0.1 1.0 1 0 0 1 1 1 1 -\n+MYG_LYCPI - sp|P02024|HBB_GORGO - 1.1e-56 182.1 1.9 1.3e-56 181.9 1.9 1.0 1 0 0 1 1 1 1 -\n+MYG_SAISC - sp|P02024|HBB_GORGO - 1.1e-56 182.1 1.1 1.3e-56 181.9 1.1 1.0 1 0 0 1 1 1 1 -\n+MYG_ESCGI - sp|P02024|HBB_GORGO - 2.5e-56 181.0 1.7 2.8e-56 180.8 1.7 1.0 1 0 0 1 1 1 1 -\n+MYG_PROGU - sp|P02024|HBB_GORGO - 3.2e-56 180.6 0.2 3.6e-56 180.4 0.2 1.0 1 0 0 1 1 1 1 -\n+MYG_HORSE - sp|P02024|HBB_GORGO - 9.5e-56 179.1 1.0 1.1e-55 178.9 1.0 1.0 1 0 0 1 1 1 1 -\n+MYG_MOUSE - sp|P02024|HBB_GORGO - 1.8e-55 178.2 0.3 2e-55 178.0 0.3 1.0 1 0 0 1 1 1 1 -\n+HBA4_SALIR - sp|P02024|HBB_GORGO - 3.4e-55 177.3 0.1 3.8e-55 177.1 0.1 1.0 1 0 0 1 1 1 1 -\n+HBB2_TRICR - sp|P02024|HBB_GORGO - 1.8e-53 171.7 0.0 2e-53 171.6 0.0 1.0 1 0 0 1 1 1 1 -\n+MYG_MUSAN - sp|P02024|HBB_GORGO - 1e-44 143.3 0.3 1.1e-44 143.2 0.3 1.0 1 0 0 1 1 1 1 -\n+#\n+# Program: jackhmmer\n+# Version: 3.1b2 (February 2015)\n+# Pipeline mode: SEARCH\n+# Query file: /tmp/tmphb1nFG/files/000/dataset_1.dat\n+# Target file: /tmp/tmphb1nFG/files/000/dataset_2.dat\n+# Option settings: jackhmmer -N 5 --tblout /tmp/tmphb1nFG/files/000/dataset_4.dat --domtblout /tmp/tmphb1nFG/files/000/dataset_5.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --fast --hand --symfrac 0.5 --wpb --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmphb1nFG/files/000/dataset_1.dat /tmp/tmphb1nFG/files/000/dataset_2.dat \n+# Current dir: /tmp/tmphb1nFG/job_working_directory/000/3\n+# Date: Sat Jun 25 19:33:04 2016\n+# [ok]\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/nhmmer.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nhmmer.out Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| @@ -0,0 +1,113 @@ +# nhmmer :: search a DNA model or alignment against a DNA database +# HMMER 3.1b2 (February 2015); http://hmmer.org/ +# Copyright (C) 2015 Howard Hughes Medical Institute. +# Freely distributed under the GNU General Public License (GPLv3). +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# query file: /tmp/tmpprnvgs/files/000/dataset_1.dat +# target sequence database: /tmp/tmpprnvgs/files/000/dataset_2.dat +# hits tabular output: /tmp/tmpprnvgs/files/000/dataset_4.dat +# hits output in Dfam format: None +# max ASCII text line length: unlimited +# SSV filter P threshold: <= 0.02 +# Vit filter P threshold: <= 0.001 +# Fwd filter P threshold: <= 1e-05 +# input query is asserted as: DNA +# random number seed set to: 4 +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +Query: MADE1 [M=80] +Accession: DF0000629.2 +Description: MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +Scores for complete hits: + E-value score bias Sequence start end Description + ------- ------ ----- -------- ----- ----- ----------- + 1.2e-10 38.6 7.4 humanchr1/239220001-239550000 302390 302466 + 7.8e-08 29.6 8.3 humanchr1/239220001-239550000 174456 174498 + 1.2e-07 28.9 6.0 humanchr1/239220001-239550000 302466 302390 + 7.2e-06 23.3 7.0 humanchr1/239220001-239550000 174493 174456 + ------ inclusion threshold ------ + 1.4 6.3 7.0 humanchr1/239220001-239550000 304073 304104 + + +Annotation for each hit (and alignments): +>> humanchr1/239220001-239550000 + score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc + ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- + ! 38.6 7.4 1.2e-10 4 80 .] 302390 302466 .. 302387 302466 .. 330000 0.87 + + Alignment: + score: 38.6 bits + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF + MADE1 4 ggttggtgcaaaagtaattgcggtttttgccattacttttaatggc....aaaaaccgcaattacttttgcaccaacctaa 80 + ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc a aaa g a t ctttt caccaa ctaa + humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttA-AAA--GTA-ATGCTTTTACACCAATCTAA 302466 + 899******************************************955533.443..334.4689***********99986 PP + +>> humanchr1/239220001-239550000 + score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc + ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- + ! 29.6 8.3 7.8e-08 1 43 [. 174456 174498 .. 174456 174518 .. 330000 0.92 + + Alignment: + score: 29.6 bits + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF + MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt 43 + ttaggtt gtgcaaaagtaattg ggtttttg cattactttt + humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTT 174498 + 589************************************9975 PP + +>> humanchr1/239220001-239550000 + score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc + ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- + ! 28.9 6.0 1.2e-07 1 77 [. 302466 302390 .. 302466 302387 .. 330000 0.74 + + Alignment: + score: 28.9 bits + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF + MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt................aatggcaaaaaccgcaattacttttgcaccaacc 77 + ttag ttggtg aaaag cattactttt aatggcaaaaacc caatt ttttgcacc acc + humanchr1/239220001-239550000 302466 TTAGATTGGTGTAAAAG----------------CATTACTTTTaaaagcaattaaaagcAATGGCAAAAACCACAATTGATTTTGCACCGACC 302390 + 68999999999999998................5666777776222222222222222268****************************9998 PP + +>> humanchr1/239220001-239550000 + score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc + ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- + ! 23.3 7.0 7.2e-06 43 80 .] 174493 174456 .. 174513 174456 .. 330000 0.91 + + Alignment: + score: 23.3 bits + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF + MADE1 43 taatggcaaaaaccgcaattacttttgcaccaacctaa 80 + taatg caaaaacc caattacttttgcac aacctaa + humanchr1/239220001-239550000 174493 TAATGACAAAAACCACAATTACTTTTGCACTAACCTAA 174456 + 689********************************985 PP + +>> humanchr1/239220001-239550000 + score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc + ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- + ? 6.3 7.0 1.4 41 72 .. 304073 304104 .. 304053 304109 .. 330000 0.85 + + Alignment: + score: 6.3 bits + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF + MADE1 41 tttaatggcaaaaaccgcaattacttttgcac 72 + tt a tgg aaaaa ca tta ttttgca + humanchr1/239220001-239550000 304073 TTAAGTGGGAAAAAATACACTTATTTTTGCAT 304104 + 455779************************86 PP + + + +Internal pipeline statistics summary: +------------------------------------- +Query model(s): 1 (80 nodes) +Target sequences: 1 (660000 residues searched) +Residues passing SSV filter: 61794 (0.0936); expected (0.02) +Residues passing bias filter: 46199 (0.07); expected (0.02) +Residues passing Vit filter: 2752 (0.00417); expected (0.001) +Residues passing Fwd filter: 2526 (0.00383); expected (1e-05) +Total number of hits: 5 (0.000405) +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 +# Mc/sec: 1760.00 +// +[ok] |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/phmmer.domtblout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phmmer.domtblout Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,102 @@\n+# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord\n+# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target\n+#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------\n+sp|P02185|MYG_PHYCD - 154 MYG_ESCGI - 153 1.9e-97 310.4 5.6 1 1 2.1e-97 2.1e-97 310.3 5.6 1 153 2 154 2 154 1.00 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 MYG_ESCGI - 153 3.2e-11 30.7 0.1 1 1 3.5e-11 3.5e-11 30.6 0.1 6 146 8 146 3 147 0.91 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - 154 MYG_HORSE - 153 7.1e-93 295.7 5.0 1 1 7.9e-93 7.9e-93 295.6 5.0 2 153 3 154 2 154 0.99 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 MYG_HORSE - 153 7.5e-12 32.7 0.1 1 1 9e-12 9e-12 32.5 0.1 7 146 9 146 4 147 0.92 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - 154 MYG_PROGU - 153 7.4e-88 279.4 3.7 1 1 8.3e-88 8.3e-88 279.2 3.7 2 153 3 154 2 154 0.99 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 MYG_PROGU - 153 1.5e-12 35.0 0.1 1 1 1.6e-12 1.6e-12 34.9 0.1 6 146 8 146 3 147 0.92 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - 154 MYG_SAISC - 153 5e-87 276.6 4.6 1 1 5.5e-87 5.5e-87 276.5 4.6 2 153 3 154 2 154 0.99 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 MYG_SAISC - 153 1e-12 35.5 0.1 1 1 1.1e-12 1.1e-12 35.3 0.1 6 146 8 146 3 147 0.93 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - 154 MYG_LYCPI - 153 7e-86 272.9 4.1 1 1 7.8e-86 7.8e-86 272.8 4.1 2 153 3 154 2 154 0.99 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 MYG_LYCPI - 153 5.6e-15 42.8 0.0 1 1 6.1e-15 6.1e-15 42.7 0.0 6 146 8 146 3 147 0.94 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - 154 MYG_MOUSE - 153 6e-85 270.1 2.6 1 1 6.7e-85 6.7e-85 269.9 2.6 2 153 3 154 2 154 0.99 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 MYG_MOUSE - 153 3.2e-12 34.0 0.0 1 1 3.5e-12 3.5e-12 33.9 0.0 6 146 8 146 3 147 0.93 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - 154 MYG_MUSAN - 148 1e-35 110.0 0.1 1 1 1.1e-35 1.1e-35 109.9 0.1 2 148 7 154 6 154 0.98 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 MYG_MUSAN - 148 8.3e-09 22.9 0.0 1 1 9.1e-09 9.1e-09 22.7 0.0 6 131 12 136 7 147 0.87 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 HBA_AILME '..b' 30.0 0.1 1 1 4.5e-11 4.5e-11 29.7 0.1 7 145 7 147 2 148 0.89 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 HBB_TRIIN - 146 8.2e-84 265.9 0.4 1 1 9.1e-84 9.1e-84 265.8 0.4 1 146 2 147 2 147 1.00 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - 154 HBB_TRIIN - 146 1.2e-13 38.3 0.6 1 1 1.3e-13 1.3e-13 38.2 0.6 6 145 6 147 1 148 0.89 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 HBB_COLLI - 146 6e-72 227.2 0.1 1 1 6.7e-72 6.7e-72 227.1 0.1 1 146 2 147 2 147 0.99 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - 154 HBB_COLLI - 146 2.2e-16 47.0 0.1 1 1 2.5e-16 2.5e-16 46.8 0.1 6 145 6 147 2 148 0.94 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 HBB_LARRI - 146 6e-70 220.8 0.1 1 1 6.7e-70 6.7e-70 220.6 0.1 1 146 2 147 2 147 0.99 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - 154 HBB_LARRI - 146 1.3e-15 44.6 0.1 1 1 1.5e-15 1.5e-15 44.3 0.1 6 145 6 147 2 148 0.94 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 HBB1_VAREX - 146 4.4e-67 211.9 0.3 1 1 5e-67 5e-67 211.8 0.3 1 146 2 147 2 147 1.00 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - 154 HBB1_VAREX - 146 2e-13 37.8 0.4 1 1 2.4e-13 2.4e-13 37.6 0.4 7 145 7 147 3 148 0.90 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 HBB2_XENTR - 146 9.7e-53 165.2 0.1 1 1 1.1e-52 1.1e-52 165.0 0.1 1 145 2 146 2 147 0.99 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - 154 HBB2_XENTR - 146 8.5e-14 39.0 0.2 1 1 1.1e-13 1.1e-13 38.7 0.2 10 130 10 132 4 142 0.86 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 HBBL_RANCA - 146 6.8e-57 178.6 0.1 1 1 7.5e-57 7.5e-57 178.4 0.1 1 146 2 147 2 147 0.99 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - 154 HBBL_RANCA - 146 2.1e-11 31.0 0.4 1 1 2.5e-11 2.5e-11 30.8 0.4 10 134 10 136 3 147 0.87 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - 147 HBB2_TRICR - 145 2.7e-46 144.3 0.0 1 1 1.5e-46 3e-46 144.1 0.0 1 145 2 146 2 146 0.98 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+#\n+# Program: phmmer\n+# Version: 3.1b2 (February 2015)\n+# Pipeline mode: SEARCH\n+# Query file: /tmp/tmpqKBUss/files/000/dataset_1.dat\n+# Target file: /tmp/tmpqKBUss/files/000/dataset_2.dat\n+# Option settings: phmmer --tblout /tmp/tmpqKBUss/files/000/dataset_4.dat --domtblout /tmp/tmpqKBUss/files/000/dataset_5.dat --pfamtblout /tmp/tmpqKBUss/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmpqKBUss/files/000/dataset_1.dat /tmp/tmpqKBUss/files/000/dataset_2.dat \n+# Current dir: /tmp/tmpqKBUss/job_working_directory/000/3\n+# Date: Sat Jun 25 19:48:26 2016\n+# [ok]\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/phmmer.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phmmer.out Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,2210 @@\n+# phmmer :: search a protein sequence against a protein database\n+# HMMER 3.1b1 (May 2013); http://hmmer.org/\n+# Copyright (C) 2013 Howard Hughes Medical Institute.\n+# Freely distributed under the GNU General Public License (GPLv3).\n+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n+# query sequence file: test-data/globins45.fa\n+# target sequence database: test-data/uniprot_matches.fasta\n+# per-seq hits tabular output: test-data/phmmer.tblout\n+# per-dom hits tabular output: test-data/phmmer.domtblout\n+# pfam-style tabular hit output: test-data/phmmer.pfamtblout\n+# max ASCII text line length: unlimited\n+# Vit filter P threshold: <= 0.001\n+# Fwd filter P threshold: <= 1e-05\n+# random number seed set to: 4\n+# number of worker threads: 2\n+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n+\n+Query: MYG_ESCGI [L=153]\n+Scores for complete sequences (score includes all domains):\n+ --- full sequence --- --- best 1 domain --- -#dom-\n+ E-value score bias E-value score bias exp N Sequence Description\n+ ------- ------ ----- ------- ------ ----- ---- -- -------- -----------\n+ 1.9e-97 310.4 5.6 2.1e-97 310.3 5.6 1.0 1 sp|P02185|MYG_PHYCD Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+ 3.2e-11 30.7 0.1 3.5e-11 30.6 0.1 1.0 1 sp|P02024|HBB_GORGO Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+\n+\n+Domain annotation for each sequence (and alignments):\n+>> sp|P02185|MYG_PHYCD Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+ # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc\n+ --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----\n+ 1 ! 310.3 5.6 2.1e-97 2.1e-97 1 153 [] 2 154 .] 2 154 .] 1.00\n+\n+ Alignments for each domain:\n+ == domain 1 score: 310.3 bits; conditional E-value: 2.1e-97\n+ MYG_ESCGI 1 vlsdaewqlvlniwakveadvaghgqdilirlfkghpetlekfdkfkhlkteaemkasedlkkhgntvltalggilkkkghheaelkplaqshatkhkipikylefisdaiihvlhsrhpgdfgadaqaamnkalelfrkdiaakykelgfqg 153\n+ vls+ ewqlvl++wakveadvaghgqdilirlfk+hpetlekfd+fkhlkteaemkasedlkkhg tvltalg+ilkkkghheaelkplaqshatkhkipikylefis+aiihvlhsrhpgdfgadaq amnkalelfrkdiaakykelg+qg\n+ sp|P02185|MYG_PHYCD 2 VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG 154\n+ 79******************************************************************************************************************************************************8 PP\n+\n+>> sp|P02024|HBB_GORGO Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+ # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc\n+ --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----\n+ 1 ! 30.6 0.1 3.5e-11 3.5e-11 6 146 .. 8 146 .. 3 147 .] 0.91\n+\n+ Alignments for each domain:\n+ == domain 1 score: 30.6 bits; conditional E-value: 3.5e-11\n+ MYG_ESCGI 6 ewqlvlniwakveadvaghgqdilirlfkghpetlekfdkfkhlkteaemkasedlkkhgntvltalggilkkkghheaelkplaqshatkhkipikylefisdaiihvlhsrhpgdfgadaqaamnkalelfrkdiaaky 146\n+ e v +w kv d g + l rl+ +p t f+ f l t + + +k hg vl a++ l + + + l++ h k + + ++++ + ++ vl + +f qaa k + +a ky\n+ sp|P02024|HBB_GORGO 8 EKSAVTALWGKVNVDEVG--GEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY 146\n+ 6677889******99876..57899**********************9999*****************9999999****************99999999***********8888889**********99887777777776'..b'.. 0.87\n+\n+ Alignments for each domain:\n+ == domain 1 score: 30.8 bits; conditional E-value: 2.5e-11\n+ HBBL_RANCA 10 vinsvwqkvdveqdgh..ealtrlfivypwtqryfstfgdlsspaaiagnpkvhahgkkilgaidnaihnlddvkgtlhdlseehanelhvdpenfrrlgevlivvlgaklgkafspqvqhvwekfi 134\n+ ++ vw kv+ + gh + l rlf +p t + f f l + a + ++ + hg +l a+ + ++ l l++ ha + + + ++ ++e +i vl ++ f q k +\n+ sp|P02185|MYG_PHYCD 10 LVLHVWAKVEADVAGHgqDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKAL 136\n+ 56679***977766653389*********************************************999*******************988887888899*******999988888888887776665 PP\n+\n+\n+\n+Internal pipeline statistics summary:\n+-------------------------------------\n+Query model(s): 1 (146 nodes)\n+Target sequences: 2 (301 residues searched)\n+Passed MSV filter: 2 (1); expected 0.0 (0.02)\n+Passed bias filter: 2 (1); expected 0.0 (0.02)\n+Passed Vit filter: 2 (1); expected 0.0 (0.001)\n+Passed Fwd filter: 2 (1); expected 0.0 (1e-05)\n+Initial search space (Z): 2 [actual number of targets]\n+Domain search space (domZ): 2 [number of targets reported over threshold]\n+# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03\n+# Mc/sec: 1.46\n+//\n+Query: HBB2_TRICR [L=145]\n+Scores for complete sequences (score includes all domains):\n+ --- full sequence --- --- best 1 domain --- -#dom-\n+ E-value score bias E-value score bias exp N Sequence Description\n+ ------- ------ ----- ------- ------ ----- ---- -- -------- -----------\n+ 2.7e-46 144.3 0.0 3e-46 144.1 0.0 1.0 1 sp|P02024|HBB_GORGO Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+\n+\n+Domain annotation for each sequence (and alignments):\n+>> sp|P02024|HBB_GORGO Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+ # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc\n+ --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----\n+ 1 ! 144.1 0.0 1.5e-46 3e-46 1 145 [] 2 146 .. 2 146 .. 0.98\n+\n+ Alignments for each domain:\n+ == domain 1 score: 144.1 bits; conditional E-value: 1.5e-46\n+ HBB2_TRICR 1 vhltaedrkeiaailgkvnvdslggqclarlivvnpwsrryfhdfgdlsscdaicrnpkvlahgakvmrsiveatkhldnlreyyadlsvthslkfyvdpenfklfsgivivclaltlqtdfschkqlafeklmkgvshalghgy 145\n+ vhlt e++ + a+ gkvnvd +gg++l rl+vv pw++r+f+ fgdls+ da+ npkv ahg kv+ ++ + hldnl+ +a ls h k++vdpenfkl+ ++++ la + +f+ q a++k++ gv++al+h y\n+ sp|P02024|HBB_GORGO 2 VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY 146\n+ 8*********************************************************************************************************9998888999***************************87 PP\n+\n+\n+\n+Internal pipeline statistics summary:\n+-------------------------------------\n+Query model(s): 1 (145 nodes)\n+Target sequences: 2 (301 residues searched)\n+Passed MSV filter: 2 (1); expected 0.0 (0.02)\n+Passed bias filter: 2 (1); expected 0.0 (0.02)\n+Passed Vit filter: 2 (1); expected 0.0 (0.001)\n+Passed Fwd filter: 1 (0.5); expected 0.0 (1e-05)\n+Initial search space (Z): 2 [actual number of targets]\n+Domain search space (domZ): 1 [number of targets reported over threshold]\n+# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.04\n+# Mc/sec: 1.09\n+//\n+[ok]\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/phmmer.pfamtblout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phmmer.pfamtblout Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,683 @@\n+# Sequence scores\n+# ---------------\n+#\n+# name bits E-value n exp bias description\n+# ------------------- ------ --------- --- ----- ----- ---------------------\n+sp|P02185|MYG_PHYCD 310.4 1.9e-97 1 1.0 5.6 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO 30.7 3.2e-11 1 1.0 0.1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+\n+# Domain scores\n+# -------------\n+#\n+# name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description\n+# ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ ---------------------\n+sp|P02185|MYG_PHYCD 310.3 2.1e-97 1 5.6 2 154 2 154 1 153 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO 30.6 3.5e-11 1 0.1 3 147 8 146 6 146 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+# Sequence scores\n+# ---------------\n+#\n+# name bits E-value n exp bias description\n+# ------------------- ------ --------- --- ----- ----- ---------------------\n+sp|P02185|MYG_PHYCD 295.7 7.1e-93 1 1.0 5.0 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO 32.7 7.5e-12 1 1.0 0.1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+\n+# Domain scores\n+# -------------\n+#\n+# name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description\n+# ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ ---------------------\n+sp|P02185|MYG_PHYCD 295.6 7.9e-93 1 5.0 2 154 3 154 2 153 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO 32.5 9e-12 1 0.1 4 147 9 146 7 146 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+# Sequence scores\n+# ---------------\n+#\n+# name bits E-value n exp bias description\n+# ------------------- ------ --------- --- ----- ----- ---------------------\n+sp|P02185|MYG_PHYCD 279.4 7.4e-88 1 1.0 3.7 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO 35.0 1.5e-12 1 1.0 0.1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+\n+# Domain scores\n+# -------------\n+#\n+# name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description\n+# ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ ---------------------\n+sp|P02185|MYG_PHYCD 279.2 8.3e-88 1 3.7 2 154 3 154 2 153 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO 34.9 1.6e-12 1 0.1 3 147 8 146 6 146 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+# Sequence scores\n+# ---------------\n+#\n+# name bits E-value n exp bias description\n+# ------------------- ------ --------- --- ----- ----- ---------------------\n+sp|P02185|MYG_PHYCD 276.6 5e-87 1 1.0 4.6 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO 35.5 1e-12 1 1.0 0.1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+\n+# Domain scores\n+# -------------\n+#\n+# name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description\n+# ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ ---------------------\n+sp|P02185|MYG_PHYCD 276.5 5.5e-87 1 4.6 2 154 3 154 2 153 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO 35.3 1.1e-12 1 0.1 3 147 8 146 6 146 Hemoglobin subunit beta OS=Go'..b'ias env-st env-en ali-st ali-en hmm-st hmm-en description\n+# ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ ---------------------\n+sp|P02024|HBB_GORGO 211.8 5e-67 1 0.3 2 147 2 147 1 146 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD 37.6 2.4e-13 1 0.4 3 148 7 147 7 145 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+# Sequence scores\n+# ---------------\n+#\n+# name bits E-value n exp bias description\n+# ------------------- ------ --------- --- ----- ----- ---------------------\n+sp|P02024|HBB_GORGO 165.2 9.7e-53 1 1.0 0.1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD 39.0 8.5e-14 1 1.0 0.2 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+\n+# Domain scores\n+# -------------\n+#\n+# name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description\n+# ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ ---------------------\n+sp|P02024|HBB_GORGO 165.0 1.1e-52 1 0.1 2 147 2 146 1 145 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD 38.7 1.1e-13 1 0.2 4 142 10 132 10 130 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+# Sequence scores\n+# ---------------\n+#\n+# name bits E-value n exp bias description\n+# ------------------- ------ --------- --- ----- ----- ---------------------\n+sp|P02024|HBB_GORGO 178.6 6.8e-57 1 1.0 0.1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD 31.0 2.1e-11 1 1.0 0.4 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+\n+# Domain scores\n+# -------------\n+#\n+# name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description\n+# ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ ---------------------\n+sp|P02024|HBB_GORGO 178.4 7.5e-57 1 0.1 2 147 2 147 1 146 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD 30.8 2.5e-11 1 0.4 3 147 10 136 10 134 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+# Sequence scores\n+# ---------------\n+#\n+# name bits E-value n exp bias description\n+# ------------------- ------ --------- --- ----- ----- ---------------------\n+sp|P02024|HBB_GORGO 144.3 2.7e-46 1 1.0 0.0 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+\n+# Domain scores\n+# -------------\n+#\n+# name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description\n+# ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ ---------------------\n+sp|P02024|HBB_GORGO 144.1 3e-46 1 0.0 2 146 2 146 1 145 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+#\n+# Program: phmmer\n+# Version: 3.1b2 (February 2015)\n+# Pipeline mode: SEARCH\n+# Query file: /tmp/tmpqKBUss/files/000/dataset_1.dat\n+# Target file: /tmp/tmpqKBUss/files/000/dataset_2.dat\n+# Option settings: phmmer --tblout /tmp/tmpqKBUss/files/000/dataset_4.dat --domtblout /tmp/tmpqKBUss/files/000/dataset_5.dat --pfamtblout /tmp/tmpqKBUss/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmpqKBUss/files/000/dataset_1.dat /tmp/tmpqKBUss/files/000/dataset_2.dat \n+# Current dir: /tmp/tmpqKBUss/job_working_directory/000/3\n+# Date: Sat Jun 25 19:48:26 2016\n+# [ok]\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/phmmer.tblout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phmmer.tblout Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| b'@@ -0,0 +1,102 @@\n+# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----\n+# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target\n+#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------\n+sp|P02185|MYG_PHYCD - MYG_ESCGI - 1.9e-97 310.4 5.6 2.1e-97 310.3 5.6 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - MYG_ESCGI - 3.2e-11 30.7 0.1 3.5e-11 30.6 0.1 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - MYG_HORSE - 7.1e-93 295.7 5.0 7.9e-93 295.6 5.0 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - MYG_HORSE - 7.5e-12 32.7 0.1 9e-12 32.5 0.1 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - MYG_PROGU - 7.4e-88 279.4 3.7 8.3e-88 279.2 3.7 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - MYG_PROGU - 1.5e-12 35.0 0.1 1.6e-12 34.9 0.1 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - MYG_SAISC - 5e-87 276.6 4.6 5.5e-87 276.5 4.6 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - MYG_SAISC - 1e-12 35.5 0.1 1.1e-12 35.3 0.1 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - MYG_LYCPI - 7e-86 272.9 4.1 7.8e-86 272.8 4.1 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - MYG_LYCPI - 5.6e-15 42.8 0.0 6.1e-15 42.7 0.0 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - MYG_MOUSE - 6e-85 270.1 2.6 6.7e-85 269.9 2.6 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - MYG_MOUSE - 3.2e-12 34.0 0.0 3.5e-12 33.9 0.0 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - MYG_MUSAN - 1e-35 110.0 0.1 1.1e-35 109.9 0.1 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - MYG_MUSAN - 8.3e-09 22.9 0.0 9.1e-09 22.7 0.0 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02024|HBB_GORGO - HBA_AILME - 1.4e-34 106.1 0.2 1.7e-34 105.9 0.2 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - HBA_AILME - 5.4e-11 29.8 0.5 6.4e-11 29.6 0.5 1.1 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - HBA_PROLO - 1.9e-33 102.5 0.2 2.2e-33 102.3 0.2 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - HBA_PROLO - '..b'a gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - HBB_RABIT - 5.9e-10 26.2 0.4 6.4e-10 26.1 0.4 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - HBB_TUPGL - 8.5e-84 265.6 0.2 9.5e-84 265.4 0.2 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - HBB_TUPGL - 3.8e-11 30.0 0.1 4.5e-11 29.7 0.1 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - HBB_TRIIN - 8.2e-84 265.9 0.4 9.1e-84 265.8 0.4 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - HBB_TRIIN - 1.2e-13 38.3 0.6 1.3e-13 38.2 0.6 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - HBB_COLLI - 6e-72 227.2 0.1 6.7e-72 227.1 0.1 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - HBB_COLLI - 2.2e-16 47.0 0.1 2.5e-16 46.8 0.1 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - HBB_LARRI - 6e-70 220.8 0.1 6.7e-70 220.6 0.1 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - HBB_LARRI - 1.3e-15 44.6 0.1 1.5e-15 44.3 0.1 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - HBB1_VAREX - 4.4e-67 211.9 0.3 5e-67 211.8 0.3 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - HBB1_VAREX - 2e-13 37.8 0.4 2.4e-13 37.6 0.4 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - HBB2_XENTR - 9.7e-53 165.2 0.1 1.1e-52 165.0 0.1 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - HBB2_XENTR - 8.5e-14 39.0 0.2 1.1e-13 38.7 0.2 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - HBBL_RANCA - 6.8e-57 178.6 0.1 7.5e-57 178.4 0.1 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+sp|P02185|MYG_PHYCD - HBBL_RANCA - 2.1e-11 31.0 0.4 2.5e-11 30.8 0.4 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2\n+sp|P02024|HBB_GORGO - HBB2_TRICR - 2.7e-46 144.3 0.0 3e-46 144.1 0.0 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2\n+#\n+# Program: phmmer\n+# Version: 3.1b2 (February 2015)\n+# Pipeline mode: SEARCH\n+# Query file: /tmp/tmpqKBUss/files/000/dataset_1.dat\n+# Target file: /tmp/tmpqKBUss/files/000/dataset_2.dat\n+# Option settings: phmmer --tblout /tmp/tmpqKBUss/files/000/dataset_4.dat --domtblout /tmp/tmpqKBUss/files/000/dataset_5.dat --pfamtblout /tmp/tmpqKBUss/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmpqKBUss/files/000/dataset_1.dat /tmp/tmpqKBUss/files/000/dataset_2.dat \n+# Current dir: /tmp/tmpqKBUss/job_working_directory/000/3\n+# Date: Sat Jun 25 19:48:26 2016\n+# [ok]\n' |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/uniprot_globins_match.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/uniprot_globins_match.out Sat Jun 25 15:07:32 2016 -0400 |
| [ |
| @@ -0,0 +1,67 @@ +# hmmsearch :: search profile(s) against a sequence database +# HMMER 3.1b2 (February 2015); http://hmmer.org/ +# Copyright (C) 2015 Howard Hughes Medical Institute. +# Freely distributed under the GNU General Public License (GPLv3). +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# query HMM file: /tmp/tmpJW6ntL/files/000/dataset_1.dat +# target sequence database: /tmp/tmpJW6ntL/files/000/dataset_2.dat +# per-seq hits tabular output: /tmp/tmpJW6ntL/files/000/dataset_4.dat +# per-dom hits tabular output: /tmp/tmpJW6ntL/files/000/dataset_5.dat +# pfam-style tabular hit output: /tmp/tmpJW6ntL/files/000/dataset_6.dat +# max ASCII text line length: unlimited +# Vit filter P threshold: <= 0.001 +# Fwd filter P threshold: <= 1e-05 +# random number seed set to: 4 +# number of worker threads: 1 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +Query: globins4 [M=149] +Scores for complete sequences (score includes all domains): + --- full sequence --- --- best 1 domain --- -#dom- + E-value score bias E-value score bias exp N Sequence Description + ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- + 1.8e-70 222.7 3.2 2e-70 222.6 3.2 1.0 1 sp|P02185|MYG_PHYCD Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 + 9.2e-69 217.2 0.1 1e-68 217.0 0.1 1.0 1 sp|P02024|HBB_GORGO Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 + + +Domain annotation for each sequence (and alignments): +>> sp|P02185|MYG_PHYCD Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 + # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc + --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- + 1 ! 222.6 3.2 2e-70 2e-70 2 149 .] 2 148 .. 1 148 [. 0.99 + + Alignments for each domain: + == domain 1 score: 222.6 bits; conditional E-value: 2e-70 + globins4 2 vLseaektkvkavWakveadveesGadiLvrlfkstPatqefFekFkdLstedelkksadvkkHgkkvldAlsdalakldekleaklkdLselHakklkvdpkyfkllsevlvdvlaarlpkeftadvqaaleKllalvakllaskYk 149 + vLse+e++ v++vWakveadv+++G+diL+rlfks+P+t+e+F++Fk+L+te+e+k+s+d+kkHg++vl+Al+++l+k ++++ea+lk+L+++Ha+k+k+++ky++++se++++vl++r+p++f+ad+q+a++K+l+l++k++a+kYk + sp|P02185|MYG_PHYCD 2 VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKK-KGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYK 148 + 8*****************************************************************************.99******************************************************************7 PP + +>> sp|P02024|HBB_GORGO Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 + # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc + --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- + 1 ! 217.0 0.1 1e-68 1e-68 1 149 [] 2 147 .] 2 147 .] 0.99 + + Alignments for each domain: + == domain 1 score: 217.0 bits; conditional E-value: 1e-68 + globins4 1 vvLseaektkvkavWakveadveesGadiLvrlfkstPatqefFekFkdLstedelkksadvkkHgkkvldAlsdalakldekleaklkdLselHakklkvdpkyfkllsevlvdvlaarlpkeftadvqaaleKllalvakllaskYk 149 + v+L+++ek++v+a+W+kv +v+e+G+++L rl++++P+tq+fFe+F+dLst+d+++++++vk+Hgkkvl+A+sd+la+ld +l++++++LselH++kl+vdp++fkll++vlv+vla++++keft++vqaa++K++a va++la+kY+ + sp|P02024|HBB_GORGO 2 VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLD-NLKGTFATLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH 147 + 69****************..*************************************************************.******************************************************************7 PP + + + +Internal pipeline statistics summary: +------------------------------------- +Query model(s): 1 (149 nodes) +Target sequences: 2 (301 residues searched) +Passed MSV filter: 2 (1); expected 0.0 (0.02) +Passed bias filter: 2 (1); expected 0.0 (0.02) +Passed Vit filter: 2 (1); expected 0.0 (0.001) +Passed Fwd filter: 2 (1); expected 0.0 (1e-05) +Initial search space (Z): 2 [actual number of targets] +Domain search space (domZ): 2 [number of targets reported over threshold] +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: inf +// +[ok] |
| b |
| diff -r 000000000000 -r a6098dd0cb46 test-data/uniprot_matches.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/uniprot_matches.fasta Sat Jun 25 15:07:32 2016 -0400 |
| b |
| @@ -0,0 +1,8 @@ +>sp|P02185|MYG_PHYCD Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 +MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASE +DLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH +PGDFGADAQGAMNKALELFRKDIAAKYKELGYQG +>sp|P02024|HBB_GORGO Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 +MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK +VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFKLLGNVLVCVLAHHFG +KEFTPPVQAAYQKVVAGVANALAHKYH |
| b |
| diff -r 000000000000 -r a6098dd0cb46 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Jun 25 15:07:32 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="hmmer" version="3.1b2"> + <repository changeset_revision="2a1881410dc9" name="package_hmmer_3_1b2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |