| Previous changeset 4:1cd4d0cf8fd9 (2018-06-11) Next changeset 6:a6f41287ef2b (2021-01-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d" |
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modified:
hmmemit.xml macros.xml test-data/MADE1.hmm test-data/MADE1.nhmmscan_out test-data/MADE1.nhmmscan_out.dfamtblout test-data/MADE1.nhmmscan_out.tblout test-data/MADE1.out test-data/MADE1.out.domtblout test-data/MADE1.out.pfamtblout test-data/MADE1.out.tblout 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.hmm test-data/globins4.hmm2 test-data/jackhmmer.domtblout test-data/jackhmmer.out test-data/jackhmmer.tblout test-data/nhmmer.out test-data/nhmmer.out.dfamtblout test-data/nhmmer.out.tblout test-data/uniprot_globins_match.out |
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added:
test-data/nhmmer.out.aliscoresout |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 hmmemit.xml --- a/hmmemit.xml Mon Jun 11 15:51:54 2018 -0400 +++ b/hmmemit.xml Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| @@ -75,13 +75,12 @@ </when> </conditional> - <expand macro="seed"/> </inputs> <outputs> <data name="output" format="fasta" label="Sequences generated from $hmmfile.name"> <change_format> - <when input="oformat_select" value="aln" format="stockholm"/> + <when input="oformat.oformat_select" value="aln" format="stockholm"/> <!-- the rest are fasta --> </change_format> </data> @@ -92,14 +91,23 @@ <param name="oformat_select" value="aln"/> <param name="N_aln" value="10"/> <expand macro="seed_test" /> - <output name="output" file="globins4-emit.sto" compare="sim_size"/> + <output name="output" file="globins4-emit.sto" ftype="stockholm" compare="sim_size"> + <assert_contents> + <has_line_matching expression="# STOCKHOLM.*"/> + <has_line_matching expression="//"/> + </assert_contents> + </output> </test> <test> <param name="hmmfile" value="globins4.hmm"/> <param name="oformat_select" value="fasta"/> <param name="N_aln" value="10"/> <expand macro="seed_test" /> - <output name="output" file="globins4-emit-1.sto" compare="sim_size"/> + <output name="output" file="globins4-emit-1.sto" ftype="fasta" compare="sim_size"> + <assert_contents> + <has_line_matching expression=">.*"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 macros.xml --- a/macros.xml Mon Jun 11 15:51:54 2018 -0400 +++ b/macros.xml Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| @@ -6,7 +6,7 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">3.2</token> + <token name="@TOOL_VERSION@">3.3</token> <xml name="stdio"> <stdio> <!-- Anything other than zero is an error --> @@ -114,83 +114,96 @@ <param argument="--EfN" type="integer" min="1" value="200" label="Number of sequences for Forward exp tail tau fit" /> <param argument="--Eft" type="float" min="0" max="1" value="0.04" label="tail mass for Forward exponential tail tau fit" /> </xml> - <token name="@OFORMAT_WITH_OPTS_NOPFAM@"> -#if 'tblout' in str($oformat): - --tblout '$tblout' -#end if - -#if 'domtblout' in str($oformat): - --domtblout '$domtblout' + <token name="@OFORMAT_WITH_OPTS@"> +#if $oformat: + #for o in str($oformat).split(','): + --$o '$getVar($o, 'MISSING_OUTPUT'+$o)' + #end for #end if - -$acc $noali $notextw - </token> - <xml name="oformat_with_opts_nopfam"> - <!-- Options directing output --> - <param name="oformat" multiple="true" display="checkboxes" label="Output Formats" type="select"> - <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option> - <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option> - </param> - <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" /> - <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" /> - <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" /> - </xml> - <token name="@OFORMAT_WITH_OPTS@"> -#if 'tblout' in str($oformat): - --tblout '$tblout' -#end if - -#if 'domtblout' in str($oformat): - --domtblout '$domtblout' -#end if - -#if 'pfamtblout' in str($oformat): - --pfamtblout '$pfamtblout' -#end if - $acc $noali $notextw </token> <xml name="oformat_with_opts"> <!-- Options directing output --> <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats"> <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option> - <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option> - <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option> + <yield/> </param> <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" /> <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" /> <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" /> </xml> + + <xml name="oformat_with_opts_dom"> + <expand macro="oformat_with_opts"> + <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option> + <yield/> + </expand> + </xml> + + <xml name="oformat_with_opts_dom_pfam"> + <expand macro="oformat_with_opts_dom"> + <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option> + </expand> + </xml> + + <xml name="oformat_with_opts_dfam_alisc"> + <!-- Options directing output --> + <expand macro="oformat_with_opts"> + <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option> + <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option> + </expand> + </xml> + + <xml name="output" token_tool=""> + <data name="output" format="txt" label="@TOOL@ on ${on_string}"/> + <data name="tblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence hits from HMM matches"> + <filter>oformat and 'tblout' in oformat</filter> + </data> + <yield/> + </xml> + <xml name="output_dom" token_tool=""> + <expand macro="output" tool="@TOOL@"> + <data name="domtblout" format="txt" label="@TOOL@ on ${on_string}: per-domain hits from HMM matches"> + <filter>oformat and 'domtblout' in oformat</filter> + </data> + </expand> + <yield/> + </xml> + <xml name="output_dom_pfam" token_tool=""> + <expand macro="output_dom" tool="@TOOL@"> + <data name="pfamtblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence/per-domain hits from HMM matches"> + <filter>oformat and 'pfamtblout' in oformat</filter> + </data> + </expand> + </xml> + <xml name="output_dfam_alisc" token_tool="" token_ofvar="seqfile" token_invar="seqdb"> + <expand macro="output" tool="@TOOL@"> + <data name="dfamtblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence/per-domain hits from HMM matches"> + <filter>oformat and 'dfamtblout' in oformat</filter> + </data> + <data name="aliscoresout" format="txt" label="@TOOL@ on ${on_string}: scores for positional matches"> + <filter>oformat and 'aliscoresout' in oformat</filter> + </data> + </expand> + </xml> + + <xml name="assert_out" token_tool=""> + <assert_contents> + <has_line_matching expression="# @TOOL@.*"/> + <has_line_matching expression="\[ok\]"/> + </assert_contents> + </xml> + + <xml name="assert_tblout" token_tool=""> + <assert_contents> + <has_line_matching expression="# Program: @TOOL@"/> + <has_line_matching expression="# \[ok\]"/> + </assert_contents> + </xml> + <xml name="oformat_test"> <param name="notextw" value="true" /> </xml> - <!-- TODO: tblout will match 'pfamtblout,dfamtblout' --> - <token name="@OFORMAT_WITH_OPTS_N@"> -#if 'tblout' in str($oformat): - --tblout '$tblout' -#end if - -#if 'dfamtblout' in str($oformat): - --dfamtblout '$dfamtblout' -#end if - -#if 'aliscoresout' in str($oformat): - --aliscoresout '$aliscoresout' -#end if - -$acc $noali $notextw - </token> - <xml name="oformat_with_opts_n"> - <!-- Options directing output --> - <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats"> - <option value="tblout" selected="true">Table of hits (--tblout)</option> - <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option> - <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option> - </param> - <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" /> - <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" /> - <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" /> - </xml> <token name="@HSSI@"> #if $hssi.hssi_select == "singlemx": --popen $hssi.popen @@ -1077,7 +1090,7 @@ # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -The wrappers were written by Eric Rasche and is licensed under Apache2_. The +The wrappers were written by the IUC and are licensed under Apache2_. The documentation is copied from the HMMER3 documentation. .. _Apache2: http://www.apache.org/licenses/LICENSE-2.0 |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/MADE1.hmm --- a/test-data/MADE1.hmm Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/MADE1.hmm Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| b'@@ -1,268 +1,268 @@\n-HMMER3/f [3.2 | June 2018]\n+HMMER3/f [3.3 | Nov 2019]\n NAME MADE1\n ACC DF0000629.2\n DESC MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n LENG 80\n-MAXL 369\n+MAXL 190\n ALPH DNA\n RF yes\n MM no\n CONS yes\n CS no\n MAP yes\n-DATE Fri Jun 8 12:16:29 2018\n+DATE Thu May 14 18:28:16 2020\n NSEQ 1997\n-EFFN 3.911818\n+EFFN 4.772646\n CKSUM 3015610723\n GA 15.98\n TC 32.00\n NC 15.90\n-STATS LOCAL MSV -8.5408 0.71858\n-STATS LOCAL VITERBI -9.6095 0.71858\n-STATS LOCAL FORWARD -3.4185 0.71858\n+STATS LOCAL MSV -8.5015 0.71857\n+STATS LOCAL VITERBI -9.4437 0.71857\n+STATS LOCAL FORWARD -3.3601 0.71857\n HMM A C G T \n m->m m->i m->d i->m i->i d->m d->d\n- COMPO 1.24273 1.59618 1.63103 1.16152\n+ COMPO 1.26505 1.57847 1.62734 1.15507\n 1.38629 1.38629 1.38629 1.38629\n- 0.03960 3.94183 3.94183 1.46634 0.26236 0.00000 *\n- 1 2.69765 2.44396 2.81521 0.24089 1 t x - -\n+ 0.03610 4.03273 4.03273 1.46634 0.26236 0.00000 *\n+ 1 2.88347 2.59729 3.00766 0.19823 1 t x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03960 3.94183 3.94183 1.46634 0.26236 1.09861 0.40547\n- 2 2.72939 2.37873 2.85832 0.24244 2 t x - -\n+ 0.03610 4.03273 4.03273 1.46634 0.26236 1.09861 0.40547\n+ 2 2.84764 2.33775 2.99223 0.22904 2 t x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03725 4.00179 4.00179 1.46634 0.26236 1.09861 0.40547\n- 3 0.16099 3.16370 2.87328 2.99734 3 a x - -\n+ 0.03318 4.11545 4.11545 1.46634 0.26236 1.09861 0.40547\n+ 3 0.23331 2.81609 2.55800 2.64795 3 a x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03604 4.03416 4.03416 1.46634 0.26236 1.09861 0.40547\n- 4 1.98862 2.42132 0.42649 2.10770 4 g x - -\n+ 0.03194 4.15297 4.15297 1.46634 0.26236 1.09861 0.40547\n+ 4 2.10142 2.78158 0.31096 2.48849 4 g x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03539 4.05203 4.05203 1.46634 0.26236 1.09861 0.40547\n- 5 1.96369 2.69532 0.36534 2.32099 5 g x - -\n+ 0.03116 4.17730 4.17730 1.46634 0.26236 1.09861 0.40547\n+ 5 2.03766 2.72525 0.33174 2.44801 5 g x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03764 4.06427 3.92372 1.46634 0.26236 1.09861 0.40547\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 1.48830 0.25587 1.07889 0.41548\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 1.43264 0.27270 1.09736 0.40609\n- 8 2.18552 2.70201 0.28821 2.64645 14 g x - -\n+ 0.03089 4.19229 4.17979 1.46634 0.26236 1.09861 0.40547\n+ 6 2.50266 2.06695 2.58843 0.33348 6 t x - -\n+ 1.38538 1.38782 1.38660 1.38538\n+ 0.03244 4.19073 4.08723 1.46789 0.26190 1.09694 0.40630\n+ 7 2.60375 2.25725 2.67883 0.28406 12 t x - -\n+ 1.38907 1.38673 1.38907 1.38033\n+ 0.03193 4.10189 4.20735 1.39886 0.28353 1.08252 0.41361\n+ 8 2.19186 2.93555 0.26232 2.71924 14 g x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03628 4.09157 3.96779 1.46634 0.26236 1.09861 0.40547\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 1.42105 0.27636 1.08174 0.41401\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 1.42916 0.27379 1.09844 0.40555\n- 11 2.10260 2.954'..b'.82282 0.24188 1078 t x - -\n+ 1.38348 1.39069 1.38333 1.38769\n+ 0.03659 4.08849 3.95478 1.38473 0.28821 1.09815 0.40570\n+ 68 2.75338 2.37589 2.82611 0.24320 1081 t x - -\n+ 1.39439 1.40072 1.40186 1.34916\n+ 0.04141 3.82736 3.97406 1.27797 0.32657 1.05169 0.42978\n+ 69 2.30274 2.95739 0.24176 2.76754 1093 g x - -\n+ 1.38591 1.38591 1.38745 1.38591\n+ 0.03131 4.20335 4.14281 1.46244 0.26354 1.07083 0.41965\n+ 70 2.79994 0.28200 2.99446 2.00361 1097 c x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03412 4.08811 4.08811 1.46634 0.26236 0.97936 0.47089\n- 71 0.21870 2.83638 2.69251 2.65798 1098 a x - -\n- 1.37446 1.37942 1.39640 1.39509\n- 0.03670 3.93983 4.09935 1.43996 0.27041 1.09889 0.40532\n- 72 2.35233 0.46085 2.23804 1.78715 1103 c x - -\n- 1.38536 1.38781 1.38781 1.38421\n- 0.03493 4.03822 4.09272 1.42863 0.27396 1.09816 0.40569\n- 73 2.57111 0.32543 2.74124 1.98892 1105 c x - -\n+ 0.02990 4.21806 4.21806 1.46634 0.26236 1.08730 0.41117\n+ 71 0.32186 2.49114 2.38278 2.30165 1098 a x - -\n+ 1.38095 1.38549 1.38906 1.38970\n+ 0.03114 4.15948 4.19672 1.44935 0.26752 1.10226 0.40364\n+ 72 2.53966 0.34721 2.53815 1.99924 1103 c x - -\n+ 1.38409 1.38783 1.38783 1.38544\n+ 0.03178 4.15601 4.15995 1.42823 0.27409 1.09282 0.40837\n+ 73 2.68662 0.27379 2.88246 2.15931 1105 c x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03381 4.09688 4.09688 1.46634 0.26236 1.09814 0.40570\n- 74 0.27014 2.61416 2.53262 2.47636 1106 a x - -\n+ 0.03005 4.21307 4.21307 1.46634 0.26236 1.09252 0.40852\n+ 74 0.31501 2.49904 2.40066 2.32899 1106 a x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03461 4.09267 4.05587 1.46634 0.26236 1.09839 0.40558\n- 75 0.52873 2.16549 1.91736 1.90409 1107 a x - -\n+ 0.03236 4.20966 4.07504 1.46634 0.26236 1.09567 0.40694\n+ 75 0.36972 2.41288 2.17350 2.24680 1107 a x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03426 4.08396 4.08396 1.46634 0.26236 1.09364 0.40796\n- 76 2.33134 0.38082 2.65861 1.90055 1108 c x - -\n+ 0.03061 4.19489 4.19489 1.46634 0.26236 1.07976 0.41503\n+ 76 2.42454 0.36916 2.67422 1.88910 1108 c x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03466 4.07266 4.07266 1.46634 0.26236 1.09861 0.40547\n- 77 2.20588 0.45134 2.35553 1.84373 1109 c x - -\n+ 0.03111 4.17876 4.17876 1.46634 0.26236 1.09861 0.40547\n+ 77 2.40209 0.35459 2.62494 1.99827 1109 c x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03550 4.04912 4.04912 1.46634 0.26236 1.09861 0.40547\n- 78 2.69018 2.22054 2.82311 0.26898 1110 t x - -\n+ 0.03189 4.15446 4.15446 1.46634 0.26236 1.09861 0.40547\n+ 78 2.61838 2.21121 2.70403 0.28691 1110 t x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03711 4.00561 4.00561 1.46634 0.26236 1.09861 0.40547\n- 79 0.16248 3.15867 2.86159 2.98963 1111 a x - -\n+ 0.03345 4.10748 4.10748 1.46634 0.26236 1.09861 0.40547\n+ 79 0.16677 3.16394 2.79540 2.99064 1111 a x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.04048 3.92018 3.92018 1.46634 0.26236 1.09861 0.40547\n- 80 0.17484 3.04770 2.86638 2.88183 1112 a x - -\n+ 0.03607 4.03354 4.03354 1.46634 0.26236 1.09861 0.40547\n+ 80 0.12738 3.34162 3.14941 3.18577 1112 a x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.02045 3.90014 * 1.46634 0.26236 0.00000 *\n+ 0.01820 4.01567 * 1.46634 0.26236 0.00000 *\n //\n' |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/MADE1.nhmmscan_out --- a/test-data/MADE1.nhmmscan_out Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/MADE1.nhmmscan_out Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| b'@@ -1,12 +1,12 @@\n # nhmmscan :: search DNA sequence(s) against a DNA profile database\n-# HMMER 3.2 (June 2018); http://hmmer.org/\n-# Copyright (C) 2018 Howard Hughes Medical Institute.\n+# HMMER 3.3 (Nov 2019); http://hmmer.org/\n+# Copyright (C) 2019 Howard Hughes Medical Institute.\n # Freely distributed under the BSD open source license.\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n-# query sequence file: /tmp/tmpp4O0Ju/files/000/dataset_41.dat\n+# query sequence file: /tmp/tmpqydies2m/files/f/a/5/dataset_fa559c91-0436-48cb-a47d-20062d4af284.dat\n # target HMM database: localref.hmm\n-# per-seq hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_43.dat\n-# hits output in Dfam format: /tmp/tmpp4O0Ju/files/000/dataset_44.dat\n+# per-seq hits tabular output: /tmp/tmpqydies2m/files/4/7/2/dataset_4723128d-8711-4edb-8afe-a68476a6c127.dat\n+# hits output in Dfam format: /tmp/tmpqydies2m/files/1/a/e/dataset_1aeea50b-1263-4750-8237-4fc3f10c0999.dat\n # max ASCII text line length: unlimited\n # Vit filter P threshold: <= 0.001\n # Fwd filter P threshold: <= 1e-05\n@@ -18,79 +18,79 @@\n Scores for complete hit:\n E-value score bias Model start end Description\n ------- ------ ----- -------- ----- ----- -----------\n- 8.7e-11 39.2 7.4 MADE1 302390 302466 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n- 6.4e-08 30.0 8.3 MADE1 174456 174498 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n- 9.3e-08 29.5 6.1 MADE1 302466 302390 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n- 6.3e-06 23.7 7.0 MADE1 174493 174456 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+ 4e-11 41.3 7.5 MADE1 302390 302466 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+ 1.9e-08 32.8 8.3 MADE1 174456 174498 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+ 6.3e-08 31.0 6.7 MADE1 302466 302389 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+ 4.9e-06 25.0 7.0 MADE1 174493 174456 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n ------ inclusion threshold ------\n- 1.4 6.5 7.0 MADE1 304073 304104 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+ 2.2 6.9 7.2 MADE1 304073 304103 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n \n \n Annotation for each hit (and alignments):\n >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to mod len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ! 39.2 7.4 8.7e-11 4 80 .] 302390 302466 .. 302387 302466 .. 80 0.87\n+ ! 41.3 7.5 4e-11 4 80 .] 302390 302466 .. 302387 302466 .. 80 0.88\n \n Alignment:\n- score: 39.2 bits\n+ score: 41.3 bits\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 4 ggttggtgcaaaagtaattgcggtttttgccattacttttaatggc....aaaaaccgcaattacttttgcaccaacctaa 80 \n- ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc a aaa g a t ctttt caccaa ctaa\n- humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttA-AAA--GT-AATGCTTTTACACCAATCTAA 302466\n- 899******************************************955533.443..33.44689************9986 PP\n+ ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc aaaa g a t ctttt caccaa ctaa\n+ humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGC'..b' xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ MADE1 1 ttaggttggtgcaaaagtaattgcggttttt....gccattacttttaatggcaaaaaccgcaattacttttgcaccaacct 78 \n+ ttag ttggtg aaaag a t tttt gc atta +aatggcaaaaacc caatt ttttgcacc acc \n+ humanchr1/239220001-239550000 302466 TTAGATTGGTGTAAAAGCATT-A---CTTTTaaaaGCAATTAAAAGCAATGGCAAAAACCACAATTGATTTTGCACCGACCA 302389\n+ 6899************97543.2...23333455566666666666799*****************************9985 PP\n \n >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to mod len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ! 23.7 7.0 6.3e-06 43 80 .] 174493 174456 .. 174513 174456 .. 80 0.91\n+ ! 25.0 7.0 4.9e-06 43 80 .] 174493 174456 .. 174513 174456 .. 80 0.94\n \n Alignment:\n- score: 23.7 bits\n+ score: 25.0 bits\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 43 taatggcaaaaaccgcaattacttttgcaccaacctaa 80 \n taatg caaaaacc caattacttttgcac aacctaa\n humanchr1/239220001-239550000 174493 TAATGACAAAAACCACAATTACTTTTGCACTAACCTAA 174456\n- 689********************************986 PP\n+ 5899*******************************986 PP\n \n >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to mod len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ? 6.5 7.0 1.4 41 72 .. 304073 304104 .. 304053 304109 .. 80 0.85\n+ ? 6.9 7.2 2.2 41 71 .. 304073 304103 .. 304053 304109 .. 80 0.85\n \n Alignment:\n- score: 6.5 bits\n- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n- MADE1 41 tttaatggcaaaaaccgcaattacttttgcac 72 \n- tt a tgg aaaaa ca tta ttttgca \n- humanchr1/239220001-239550000 304073 TTAAGTGGGAAAAAATACACTTATTTTTGCAT 304104\n- 455779************************86 PP\n+ score: 6.9 bits\n+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ MADE1 41 tttaatggcaaaaaccgcaattacttttgca 71 \n+ tt a tgg aaaaa ca tta ttttgca\n+ humanchr1/239220001-239550000 304073 TTAAGTGGGAAAAAATACACTTATTTTTGCA 304103\n+ 456789************************8 PP\n \n \n \n@@ -98,12 +98,12 @@\n -------------------------------------\n Query sequence(s): 1 (660000 residues searched)\n Target model(s): 1 (80 nodes)\n-Residues passing SSV filter: 63737 (0.0966); expected (0.02)\n-Residues passing bias filter: 44695 (0.0677); expected (0.02)\n-Residues passing Vit filter: 2309 (0.0035); expected (0.001)\n-Residues passing Fwd filter: 2041 (0.00309); expected (1e-05)\n+Residues passing SSV filter: 60770 (0.0921); expected (0.02)\n+Residues passing bias filter: 35792 (0.0542); expected (0.02)\n+Residues passing Vit filter: 1612 (0.00244); expected (0.001)\n+Residues passing Fwd filter: 1194 (0.00181); expected (1e-05)\n Total number of hits: 5 (0.000405)\n # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02\n-# Mc/sec: 2407.09\n+# Mc/sec: 2289.06\n //\n [ok]\n' |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/MADE1.nhmmscan_out.dfamtblout --- a/test-data/MADE1.nhmmscan_out.dfamtblout Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/MADE1.nhmmscan_out.dfamtblout Tue Jun 16 05:27:39 2020 -0400 |
| b |
| @@ -3,8 +3,8 @@ # # target name acc query name bits e-value bias hmm-st hmm-en strand ali-st ali-en env-st env-en modlen description of target # ------------------- ------------------- ------------------- ------ --------- ----- ------- ------- ------ ------- ------- ------- ------- ------- --------------------- -MADE1 DF0000629.2 humanchr1/239220001-239550000 39.2 8.7e-11 7.4 4 80 + 302390 302466 302387 302466 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 30.0 6.4e-08 8.3 1 43 + 174456 174498 174456 174518 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 29.5 9.3e-08 6.1 1 77 - 302466 302390 302466 302387 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 23.7 6.3e-06 7.0 43 80 - 174493 174456 174513 174456 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 6.5 1.4 7.0 41 72 + 304073 304104 304053 304109 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 41.3 4e-11 7.5 4 80 + 302390 302466 302387 302466 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 32.8 1.9e-08 8.3 1 43 + 174456 174498 174456 174518 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 31.0 6.3e-08 6.7 1 78 - 302466 302389 302466 302387 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 25.0 4.9e-06 7.0 43 80 - 174493 174456 174513 174456 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 6.9 2.2 7.2 41 71 + 304073 304103 304053 304109 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/MADE1.nhmmscan_out.tblout --- a/test-data/MADE1.nhmmscan_out.tblout Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/MADE1.nhmmscan_out.tblout Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| @@ -1,17 +1,17 @@ # target name accession query name accession hmmfrom hmm to alifrom ali to envfrom env to modlen strand E-value score bias description of target #------------------- ---------- -------------------- ---------- ------- ------- ------- ------- ------- ------- ------- ------ --------- ------ ----- --------------------- -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 4 80 302390 302466 302387 302466 80 + 8.7e-11 39.2 7.4 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 1 43 174456 174498 174456 174518 80 + 6.4e-08 30.0 8.3 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 1 77 302466 302390 302466 302387 80 - 9.3e-08 29.5 6.1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 43 80 174493 174456 174513 174456 80 - 6.3e-06 23.7 7.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 41 72 304073 304104 304053 304109 80 + 1.4 6.5 7.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 4 80 302390 302466 302387 302466 80 + 4e-11 41.3 7.5 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 1 43 174456 174498 174456 174518 80 + 1.9e-08 32.8 8.3 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 1 78 302466 302389 302466 302387 80 - 6.3e-08 31.0 6.7 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 43 80 174493 174456 174513 174456 80 - 4.9e-06 25.0 7.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 41 71 304073 304103 304053 304109 80 + 2.2 6.9 7.2 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon # # Program: hmmscan -# Version: 3.2 (June 2018) +# Version: 3.3 (Nov 2019) # Pipeline mode: SCAN -# Query file: /tmp/tmpp4O0Ju/files/000/dataset_41.dat +# Query file: /tmp/tmpqydies2m/files/f/a/5/dataset_fa559c91-0436-48cb-a47d-20062d4af284.dat # Target file: localref.hmm -# Option settings: nhmmscan --tblout /tmp/tmpp4O0Ju/files/000/dataset_43.dat --dfamtblout /tmp/tmpp4O0Ju/files/000/dataset_44.dat --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --B1 110 --B2 240 --B3 1000 --cpu 1 localref.hmm /tmp/tmpp4O0Ju/files/000/dataset_41.dat -# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/33/working -# Date: Fri Jun 8 12:19:16 2018 +# Option settings: nhmmscan --tblout /tmp/tmpqydies2m/files/4/7/2/dataset_4723128d-8711-4edb-8afe-a68476a6c127.dat --dfamtblout /tmp/tmpqydies2m/files/1/a/e/dataset_1aeea50b-1263-4750-8237-4fc3f10c0999.dat --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --B1 110 --B2 240 --B3 1000 --cpu 1 localref.hmm /tmp/tmpqydies2m/files/f/a/5/dataset_fa559c91-0436-48cb-a47d-20062d4af284.dat +# Current dir: /tmp/tmpqydies2m/job_working_directory/000/20/working +# Date: Thu May 14 18:55:28 2020 # [ok] |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/MADE1.out --- a/test-data/MADE1.out Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/MADE1.out Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| b'@@ -1,13 +1,13 @@\n # hmmscan :: search sequence(s) against a profile database\n-# HMMER 3.2 (June 2018); http://hmmer.org/\n-# Copyright (C) 2018 Howard Hughes Medical Institute.\n+# HMMER 3.3 (Nov 2019); http://hmmer.org/\n+# Copyright (C) 2019 Howard Hughes Medical Institute.\n # Freely distributed under the BSD open source license.\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n-# query sequence file: /tmp/tmpp4O0Ju/files/000/dataset_20.dat\n+# query sequence file: /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat\n # target HMM database: localref.hmm\n-# per-seq hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_22.dat\n-# per-dom hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_23.dat\n-# pfam-style tabular hit output: /tmp/tmpp4O0Ju/files/000/dataset_24.dat\n+# per-seq hits tabular output: /tmp/tmpqydies2m/files/1/d/a/dataset_1da10e33-3e1c-48fc-abfb-7e3c263ec0df.dat\n+# per-dom hits tabular output: /tmp/tmpqydies2m/files/7/2/3/dataset_723f3cf1-e0de-4616-aec7-dd16680f3be3.dat\n+# pfam-style tabular hit output: /tmp/tmpqydies2m/files/7/3/4/dataset_734c7f25-0a22-431b-9a7a-58849fcd6009.dat\n # max ASCII text line length: unlimited\n # Vit filter P threshold: <= 0.001\n # Fwd filter P threshold: <= 1e-05\n@@ -20,54 +20,46 @@\n --- full sequence --- --- best 1 domain --- -#dom-\n E-value score bias E-value score bias exp N Model Description\n ------- ------ ----- ------- ------ ----- ---- -- -------- -----------\n- 5.7e-18 51.8 27.9 2e-12 34.1 0.7 9.6 5 MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+ 9.3e-18 51.2 26.3 1.3e-12 34.8 0.7 8.6 4 MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n \n \n Domain annotation for each model (and alignments):\n >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc\n --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----\n- 1 ? -4.5 0.0 1 1 30 54 .. 80044 80068 .. 80033 80072 .. 0.81\n- 2 ? -6.6 3.3 1 1 13 71 .. 154012 154072 .. 154011 154076 .. 0.75\n- 3 ! 27.4 0.7 2.4e-10 2.4e-10 1 43 [. 174456 174498 .. 174456 174577 .. 0.66\n- 4 ! 34.1 0.7 2e-12 2e-12 2 80 .] 302388 302466 .. 302387 302466 .. 0.86\n- 5 ? 2.8 0.7 0.011 0.011 27 75 .. 304060 304107 .. 304022 304109 .. 0.62\n+ 1 ! 27.4 0.6 2.4e-10 2.4e-10 1 43 [. 174456 174498 .. 174456 174520 .. 0.93\n+ 2 ? -8.4 5.8 1 1 12 79 .. 197274 197341 .. 197272 197342 .. 0.86\n+ 3 ! 34.8 0.7 1.3e-12 1.3e-12 2 80 .] 302388 302466 .. 302387 302466 .. 0.87\n+ 4 ? 1.4 0.4 0.033 0.033 27 74 .. 304060 304106 .. 304029 304108 .. 0.71\n \n Alignments for each domain:\n- == domain 1 score: -4.5 bits; conditional E-value: 1\n- xxxxxxxxxxxxxxxxxxxxxxxxx RF\n- MADE1 30 ttgccattacttttaatggcaaaaa 54 \n- t g catt ttt aatggcaaa a\n- humanchr1/239220001-239550000 80044 TAGTCATTCATTTCAATGGCAAATA 80068\n- 457899***************9865 PP\n-\n- == domain 2 score: -6.6 bits; conditional E-value: 1\n- xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n- MADE1 13 aaaagtaattgcggtttttgccatt......acttttaatggcaaaaaccgcaattacttttgca 71 \n- aaaagta tt + ttttgc att a tttaa gcaaa a + tta tttgca\n- humanchr1/239220001-239550000 154012 AAAAGTA'..b' xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt 43 \n ttaggtt gtgcaaaagtaattg+ggtttttg cattactttt\n humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTT 174498\n- 79**************************************996 PP\n+ 79**************************************997 PP\n+\n+ == domain 2 score: -8.4 bits; conditional E-value: 1\n+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ MADE1 12 caaaagtaattgcggtttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaaccta 79 \n+ caa gtaatt + tttt c att ttt t c aaa c c tta tt t ac a cta\n+ humanchr1/239220001-239550000 197274 CAATGGTAATTTTATTTTTAACTATTTTATTTTTTAACTAAACTCACTTTTATTTATTTACATATCTA 197341\n+ 567789*******************999999999999*****99999999999988877777776666 PP\n \n- == domain 4 score: 34.1 bits; conditional E-value: 2e-12\n- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n- MADE1 2 taggttggtgcaaaagtaattgcggtttttgccattacttttaatggca...aaaaccgcaattacttttgcaccaacctaa 80 \n- t ggt ggtgcaaaa aattg+ggtttttgccatt cttttaat gc aaaa g a t ctttt caccaa ctaa\n- humanchr1/239220001-239550000 302388 TTGGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCTtttAAAA--G-TAATGCTTTTACACCAATCTAA 302466\n- 56899******************************************962223333..3.45578**************997 PP\n+ == domain 3 score: 34.8 bits; conditional E-value: 1.3e-12\n+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ MADE1 2 taggttggtgcaaaagtaattgcggtttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaacctaa 80 \n+ t ggt ggtgcaaaa aattg+ggtttttgccatt cttttaat gc a a t ctttt caccaa ctaa\n+ humanchr1/239220001-239550000 302388 TTGGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCTTTTAAAAGTAATGCTTTTACACCAATCTAA 302466\n+ 6799*****************************************99953333333345578**************997 PP\n \n- == domain 5 score: 2.8 bits; conditional E-value: 0.011\n- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n- MADE1 27 tttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaa 75 \n- tttt g c ta tt a tgg aaaaa ++ca tta ttttgca aa\n- humanchr1/239220001-239550000 304060 TTTTAGACTATA-GTTAAGTGGGAAAAAATACACTTATTTTTGCATTAA 304107\n- 222223222222.3556779************************98765 PP\n+ == domain 4 score: 1.4 bits; conditional E-value: 0.033\n+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ MADE1 27 tttttgccattacttttaatggcaaaaaccgcaattacttttgcacca 74 \n+ tttt g c ta tt a tgg aaaaa + ca tta ttttgca a\n+ humanchr1/239220001-239550000 304060 TTTTAGACTATA-GTTAAGTGGGAAAAAATACACTTATTTTTGCATTA 304106\n+ 334444443333.356788*************************9766 PP\n \n \n \n@@ -81,7 +73,7 @@\n Passed Fwd filter: 1 (1); expected 0.0 (1e-05)\n Initial search space (Z): 1 [actual number of targets]\n Domain search space (domZ): 1 [number of targets reported over threshold]\n-# CPU time: 0.14u 0.01s 00:00:00.15 Elapsed: 00:00:00.14\n-# Mc/sec: 177.58\n+# CPU time: 0.21u 0.01s 00:00:00.22 Elapsed: 00:00:00.22\n+# Mc/sec: 117.29\n //\n [ok]\n' |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/MADE1.out.domtblout --- a/test-data/MADE1.out.domtblout Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/MADE1.out.domtblout Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| @@ -1,18 +1,17 @@ # --- 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 5.7e-18 51.8 27.9 1 5 1 1 -4.5 0.0 30 54 80044 80068 80033 80072 0.81 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 5.7e-18 51.8 27.9 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 5.7e-18 51.8 27.9 3 5 2.4e-10 2.4e-10 27.4 0.7 1 43 174456 174498 174456 174577 0.66 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 5.7e-18 51.8 27.9 4 5 2e-12 2e-12 34.1 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 5.7e-18 51.8 27.9 5 5 0.011 0.011 2.8 0.7 27 75 304060 304107 304022 304109 0.62 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 9.3e-18 51.2 26.3 1 4 2.4e-10 2.4e-10 27.4 0.6 1 43 174456 174498 174456 174520 0.93 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 9.3e-18 51.2 26.3 2 4 1 1 -8.4 5.8 12 79 197274 197341 197272 197342 0.86 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 9.3e-18 51.2 26.3 3 4 1.3e-12 1.3e-12 34.8 0.7 2 80 302388 302466 302387 302466 0.87 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 9.3e-18 51.2 26.3 4 4 0.033 0.033 1.4 0.4 27 74 304060 304106 304029 304108 0.71 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon # # Program: hmmscan -# Version: 3.2 (June 2018) +# Version: 3.3 (Nov 2019) # Pipeline mode: SCAN -# Query file: /tmp/tmpp4O0Ju/files/000/dataset_20.dat +# Query file: /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat # Target file: localref.hmm -# Option settings: hmmscan --tblout /tmp/tmpp4O0Ju/files/000/dataset_22.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_23.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_24.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 localref.hmm /tmp/tmpp4O0Ju/files/000/dataset_20.dat -# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/21/working -# Date: Fri Jun 8 12:17:53 2018 +# Option settings: hmmscan --tblout /tmp/tmpqydies2m/files/1/d/a/dataset_1da10e33-3e1c-48fc-abfb-7e3c263ec0df.dat --domtblout /tmp/tmpqydies2m/files/7/2/3/dataset_723f3cf1-e0de-4616-aec7-dd16680f3be3.dat --pfamtblout /tmp/tmpqydies2m/files/7/3/4/dataset_734c7f25-0a22-431b-9a7a-58849fcd6009.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 localref.hmm /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat +# Current dir: /tmp/tmpqydies2m/job_working_directory/000/8/working +# Date: Thu May 14 18:53:22 2020 # [ok] |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/MADE1.out.pfamtblout --- a/test-data/MADE1.out.pfamtblout Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/MADE1.out.pfamtblout Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| @@ -3,25 +3,24 @@ # # name bits E-value n exp bias description # ------------------- ------ --------- --- ----- ----- --------------------- -MADE1 51.8 5.7e-18 5 9.6 27.9 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 51.2 9.3e-18 4 8.6 26.3 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 34.1 2e-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 174498 1 43 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 2.8 0.011 5 0.7 304022 304109 304060 304107 27 75 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 -4.5 1 1 0.0 80033 80072 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 +MADE1 34.8 1.3e-12 3 0.7 302387 302466 302388 302466 2 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 27.4 2.4e-10 1 0.6 174456 174520 174456 174498 1 43 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 1.4 0.033 4 0.4 304029 304108 304060 304106 27 74 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 -8.4 1 2 5.8 197272 197342 197274 197341 12 79 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon # # Program: hmmscan -# Version: 3.2 (June 2018) +# Version: 3.3 (Nov 2019) # Pipeline mode: SEARCH -# Query file: /tmp/tmpp4O0Ju/files/000/dataset_20.dat +# Query file: /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat # Target file: localref.hmm -# Option settings: hmmscan --tblout /tmp/tmpp4O0Ju/files/000/dataset_22.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_23.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_24.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 localref.hmm /tmp/tmpp4O0Ju/files/000/dataset_20.dat -# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/21/working -# Date: Fri Jun 8 12:17:53 2018 +# Option settings: hmmscan --tblout /tmp/tmpqydies2m/files/1/d/a/dataset_1da10e33-3e1c-48fc-abfb-7e3c263ec0df.dat --domtblout /tmp/tmpqydies2m/files/7/2/3/dataset_723f3cf1-e0de-4616-aec7-dd16680f3be3.dat --pfamtblout /tmp/tmpqydies2m/files/7/3/4/dataset_734c7f25-0a22-431b-9a7a-58849fcd6009.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 localref.hmm /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat +# Current dir: /tmp/tmpqydies2m/job_working_directory/000/8/working +# Date: Thu May 14 18:53:22 2020 # [ok] |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/MADE1.out.tblout --- a/test-data/MADE1.out.tblout Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/MADE1.out.tblout Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| @@ -1,14 +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 - 5.7e-18 51.8 27.9 2e-12 34.1 0.7 9.6 5 0 0 5 5 5 2 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 9.3e-18 51.2 26.3 1.3e-12 34.8 0.7 8.6 4 0 0 4 4 4 2 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon # # Program: hmmscan -# Version: 3.2 (June 2018) +# Version: 3.3 (Nov 2019) # Pipeline mode: SCAN -# Query file: /tmp/tmpp4O0Ju/files/000/dataset_20.dat +# Query file: /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat # Target file: localref.hmm -# Option settings: hmmscan --tblout /tmp/tmpp4O0Ju/files/000/dataset_22.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_23.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_24.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 localref.hmm /tmp/tmpp4O0Ju/files/000/dataset_20.dat -# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/21/working -# Date: Fri Jun 8 12:17:53 2018 +# Option settings: hmmscan --tblout /tmp/tmpqydies2m/files/1/d/a/dataset_1da10e33-3e1c-48fc-abfb-7e3c263ec0df.dat --domtblout /tmp/tmpqydies2m/files/7/2/3/dataset_723f3cf1-e0de-4616-aec7-dd16680f3be3.dat --pfamtblout /tmp/tmpqydies2m/files/7/3/4/dataset_734c7f25-0a22-431b-9a7a-58849fcd6009.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 localref.hmm /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat +# Current dir: /tmp/tmpqydies2m/job_working_directory/000/8/working +# Date: Thu May 14 18:53:22 2020 # [ok] |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/globins-45-align.sto --- a/test-data/globins-45-align.sto Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/globins-45-align.sto Tue Jun 16 05:27:39 2020 -0400 |
| b |
| b'@@ -13,47 +13,47 @@\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+#=GR MYG_MUSAN PP 7......89***************************************9877.99*************************.99****************************************************************997******\n HBA_AILME .-VLSPADKTNVKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHF-DLS-----PGSAQVKAHGKKVADALTTAVGHLD-DLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPAEFTPAVHASLDKFFSAVSTVLTSKYR......\n-#=GR HBA_AILME PP ..69********************************************.9**.....9***********************9.******************************************************************7......\n+#=GR HBA_AILME PP ..69********************************************.***.....9************************.******************************************************************7......\n HBA_PROLO .-VLSPADKANIKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHF-DLS-----PGSAQVKAHGKKVADALTLAVGHLD-DLPGALSALSDLHAYKLRVDPVNFKLLSHCLLVTLACHHPAEFTPAVHASLDKFFTSVSTVLTSKYR......\n-#=GR HBA_PROLO PP ..69********************************************.9**.....9***********************9.******************************************************************7......\n+#=GR HBA_PROLO PP ..69********************************************.***.....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+#=GR HBA_MACFA PP ..69********************************************.***.....*************************.******************************************************************7......\n HBA_MACSI .-VLSPADKTNVKDAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALTLAVGHVD-DMPQALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR......\n-#=GR HBA_MACSI PP ..69********************************************.***.....************************9.******************************************************************7......\n+#=GR HBA_MACSI PP ..69********************************************.***.....*************************.******************************************************************7......\n HBA_PONPY .-VLSPADKTNVKTAWGKVGAHAGDYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKDHGKKVADALTNAVAHVD-DMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR......\n-#=GR HBA_PONPY PP ..69********************************************.***.....************************9.******************************************************************7......\n+#=GR HBA_PONPY PP ..69********************************************.***.....*************************.******************************************************************7......\n HBA2_GALCR .-VLSPTDKSNVKAAWEKVGAHAGDYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSTQVKG'..b'**********.******************************************************************7......\n HBB_RABIT .VHLSSEEKSAVTALWGKV--NVEEVGGEALGRLLVVYPWTQRFFESFGDLSSANAVMNNPKVKAHGKKVLAAFSEGLSHLD-NLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH......\n #=GR HBB_RABIT PP .69****************..*************************************************************.******************************************************************7......\n HBB_TUPGL .VHLSGEEKAAVTGLWGKV--DLEKVGGQSLGSLLIVYPWTQRFFDSFGDLSSPSAVMSNPKVKAHGKKVLTSFSDGLNHLD-NLKGTFAKLSELHCDKLHVDPENFRLLGNVLVRVLACNFGPEFTPQVQAAFQKVVAGVANALAHKYH......\n@@ -79,15 +79,15 @@\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+#=GR HBB_COLLI PP 5.789**************..*************************************************************.******************************************************************7......\n HBB_LARRI v-HWSAEEKQLITGLWGKV--NVADCGAEALARLLIVYPWTQRFFASFGNLSSPTAINGNPMVRAHGKKVLTSFGEAVKNLD-NIKNTFAQLSELHCDKLHVDPENFRLLGDILIIVLAAHFAKDFTPDSQAAWQKLVRVVAHALARKYH......\n-#=GR HBB_LARRI PP 5.779**************..*************************************************************.******************************************************************7......\n+#=GR HBB_LARRI PP 5.789**************..*************************************************************.******************************************************************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+#=GR HBB2_XENTR PP 6.6799*************..*************************************************************.**************************************************************9988.9.....\n HBBL_RANCA v-HWTAEEKAVINSVWQKV--DVEQDGHEALTRLFIVYPWTQRYFSTFGDLSSPAAIAGNPKVHAHGKKILGAIDNAIHNLD-DVKGTLHDLSEEHANELHVDPENFRRLGEVLIVVLGAKLGKAFSPQVQHVWEKFIAVLVDALSHSYH......\n-#=GR HBBL_RANCA PP 6.6799*************..************************************************************9.9*****************************************************************7......\n+#=GR HBBL_RANCA PP 6.6799*************..*************************************************************.******************************************************************7......\n HBB2_TRICR .VHLTAEDRKEIAAILGKV--NVDSLGGQCLARLIVVNPWSRRYFHDFGDLSSCDAICRNPKVLAHGAKVMRSIVEATKHLD-NLREYYADLSVTHSLKFYVDPENFKLFSGIVIVCLALTLQTDFSCHKQLAFEKLMKGVSHALGHGY-......\n #=GR HBB2_TRICR PP .69****************..*************************************************************.**************************************************************9988.......\n #=GC PP_cons .679*****************************************************************************99******************************************************************7......\n' |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/globins-masked.sto --- a/test-data/globins-masked.sto Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/globins-masked.sto Tue Jun 16 05:27:39 2020 -0400 |
| b |
| @@ -1,9 +1,9 @@ # 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 +#=GS HBB_HUMAN WT 0.97 +#=GS HBA_HUMAN WT 0.89 +#=GS MYG_PHYCA WT 1.11 +#=GS GLB5_PETMA WT 1.03 HBB_HUMAN --------VHLTPEEKSAVTALWGKV----NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHL---D--NLKGTFATLSELHCDKL--HVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------ HBA_HUMAN ---------VLSPADKTNVKAAWGKVGA--HAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALTNAVAHV---D--DMPNALSALSDLHAHKL--RVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------ |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/globins.domtblout --- a/test-data/globins.domtblout Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/globins.domtblout Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| @@ -1,15 +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 dataset_x - 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 dataset_x - 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 +# --- 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|P02024|HBB_GORGO - 147 dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2 - 149 1.3e-70 223.2 0.1 1 1 1.4e-70 1.4e-70 223.0 0.1 1 149 2 147 2 147 0.99 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 +sp|P02185|MYG_PHYCD - 154 dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2 - 149 5.8e-70 221.1 3.3 1 1 6.4e-70 6.4e-70 220.9 3.3 2 149 2 148 1 148 0.99 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 # # Program: hmmsearch -# Version: 3.2 (June 2018) +# Version: 3.3 (Nov 2019) # Pipeline mode: SEARCH -# Query file: /tmp/tmpp4O0Ju/files/000/dataset_25.dat -# Target file: /tmp/tmpp4O0Ju/files/000/dataset_26.dat -# Option settings: hmmsearch --tblout /tmp/tmpp4O0Ju/files/000/dataset_28.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_29.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_30.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_25.dat /tmp/tmpp4O0Ju/files/000/dataset_26.dat -# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/24/working -# Date: Fri Jun 8 12:18:13 2018 +# Query file: /tmp/tmpqydies2m/files/6/d/6/dataset_6d69e63c-e7d8-450d-b7f8-3e08a51472f0.dat +# Target file: /tmp/tmpqydies2m/files/8/2/8/dataset_8282288a-91ea-4a46-89c2-d1f3b4e67c52.dat +# Option settings: hmmsearch --tblout /tmp/tmpqydies2m/files/4/6/b/dataset_46bff7ad-a6de-481d-adb4-50ccab8aacb8.dat --domtblout /tmp/tmpqydies2m/files/b/2/5/dataset_b258e52b-de8c-4e23-86d8-c69ebf229c95.dat --pfamtblout /tmp/tmpqydies2m/files/f/b/8/dataset_fb8cde04-dee0-4b38-9125-bf4766986c0c.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpqydies2m/files/6/d/6/dataset_6d69e63c-e7d8-450d-b7f8-3e08a51472f0.dat /tmp/tmpqydies2m/files/8/2/8/dataset_8282288a-91ea-4a46-89c2-d1f3b4e67c52.dat +# Current dir: /tmp/tmpqydies2m/job_working_directory/000/11/working +# Date: Thu May 14 18:54:00 2020 # [ok] |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/globins.pfamtblout --- a/test-data/globins.pfamtblout Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/globins.pfamtblout Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| @@ -3,23 +3,23 @@ # # 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 +sp|P02024|HBB_GORGO 223.2 1.3e-70 1 1.0 0.1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 +sp|P02185|MYG_PHYCD 221.1 5.8e-70 1 1.0 3.3 Myoglobin OS=Physeter catodon GN=MB 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 +sp|P02024|HBB_GORGO 223.0 1.4e-70 1 0.1 2 147 2 147 1 149 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 +sp|P02185|MYG_PHYCD 220.9 6.4e-70 1 3.3 1 148 2 148 2 149 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 # # Program: hmmsearch -# Version: 3.2 (June 2018) +# Version: 3.3 (Nov 2019) # Pipeline mode: SEARCH -# Query file: /tmp/tmpp4O0Ju/files/000/dataset_25.dat -# Target file: /tmp/tmpp4O0Ju/files/000/dataset_26.dat -# Option settings: hmmsearch --tblout /tmp/tmpp4O0Ju/files/000/dataset_28.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_29.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_30.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_25.dat /tmp/tmpp4O0Ju/files/000/dataset_26.dat -# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/24/working -# Date: Fri Jun 8 12:18:13 2018 +# Query file: /tmp/tmpqydies2m/files/6/d/6/dataset_6d69e63c-e7d8-450d-b7f8-3e08a51472f0.dat +# Target file: /tmp/tmpqydies2m/files/8/2/8/dataset_8282288a-91ea-4a46-89c2-d1f3b4e67c52.dat +# Option settings: hmmsearch --tblout /tmp/tmpqydies2m/files/4/6/b/dataset_46bff7ad-a6de-481d-adb4-50ccab8aacb8.dat --domtblout /tmp/tmpqydies2m/files/b/2/5/dataset_b258e52b-de8c-4e23-86d8-c69ebf229c95.dat --pfamtblout /tmp/tmpqydies2m/files/f/b/8/dataset_fb8cde04-dee0-4b38-9125-bf4766986c0c.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpqydies2m/files/6/d/6/dataset_6d69e63c-e7d8-450d-b7f8-3e08a51472f0.dat /tmp/tmpqydies2m/files/8/2/8/dataset_8282288a-91ea-4a46-89c2-d1f3b4e67c52.dat +# Current dir: /tmp/tmpqydies2m/job_working_directory/000/11/working +# Date: Thu May 14 18:54:00 2020 # [ok] |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/globins.tblout --- a/test-data/globins.tblout Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/globins.tblout Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| @@ -1,15 +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 - dataset_x - 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 - dataset_x - 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 +# --- 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|P02024|HBB_GORGO - dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2 - 1.3e-70 223.2 0.1 1.4e-70 223.0 0.1 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 +sp|P02185|MYG_PHYCD - dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2 - 5.8e-70 221.1 3.3 6.4e-70 220.9 3.3 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 # # Program: hmmsearch -# Version: 3.2 (June 2018) +# Version: 3.3 (Nov 2019) # Pipeline mode: SEARCH -# Query file: /tmp/tmpp4O0Ju/files/000/dataset_25.dat -# Target file: /tmp/tmpp4O0Ju/files/000/dataset_26.dat -# Option settings: hmmsearch --tblout /tmp/tmpp4O0Ju/files/000/dataset_28.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_29.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_30.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_25.dat /tmp/tmpp4O0Ju/files/000/dataset_26.dat -# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/24/working -# Date: Fri Jun 8 12:18:13 2018 +# Query file: /tmp/tmpqydies2m/files/6/d/6/dataset_6d69e63c-e7d8-450d-b7f8-3e08a51472f0.dat +# Target file: /tmp/tmpqydies2m/files/8/2/8/dataset_8282288a-91ea-4a46-89c2-d1f3b4e67c52.dat +# Option settings: hmmsearch --tblout /tmp/tmpqydies2m/files/4/6/b/dataset_46bff7ad-a6de-481d-adb4-50ccab8aacb8.dat --domtblout /tmp/tmpqydies2m/files/b/2/5/dataset_b258e52b-de8c-4e23-86d8-c69ebf229c95.dat --pfamtblout /tmp/tmpqydies2m/files/f/b/8/dataset_fb8cde04-dee0-4b38-9125-bf4766986c0c.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpqydies2m/files/6/d/6/dataset_6d69e63c-e7d8-450d-b7f8-3e08a51472f0.dat /tmp/tmpqydies2m/files/8/2/8/dataset_8282288a-91ea-4a46-89c2-d1f3b4e67c52.dat +# Current dir: /tmp/tmpqydies2m/job_working_directory/000/11/working +# Date: Thu May 14 18:54:00 2020 # [ok] |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/globins4.hmm --- a/test-data/globins4.hmm Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/globins4.hmm Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| b'@@ -1,5 +1,5 @@\n-HMMER3/f [3.2 | June 2018]\n-NAME dataset_6\n+HMMER3/f [3.3 | Nov 2019]\n+NAME dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2\n LENG 149\n ALPH amino\n RF no\n@@ -7,463 +7,463 @@\n CONS yes\n CS no\n MAP yes\n-DATE Fri Jun 8 12:16:18 2018\n+DATE Thu May 14 18:27:55 2020\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+STATS LOCAL MSV -9.7384 0.70955\n+STATS LOCAL VITERBI -10.7806 0.70955\n+STATS LOCAL FORWARD -4.5807 0.70955\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+ COMPO 2.36800 4.52198 2.96929 2.70577 3.20715 3.01836 3.40293 2.90711 2.55482 2.34699 3.67768 3.19591 3.45289 3.16361 3.08198 2.67062 2.85417 2.56574 4.55599 3.63079\n+ 2.68638 4.42245 2.77499 2.73143 3.46374 2.40505 3.72514 3.29307 2.67761 2.69375 4.24709 2.90366 2.73721 3.18166 2.89820 2.37880 2.77499 2.98440 4.58497 3.61523\n+ 0.55970 1.87270 1.29132 1.73023 0.19509 0.00000 *\n+ 1 1.75819 4.17850 3.77264 3.37715 3.71018 3.31297 4.28273 2.37054 3.30099 2.52201 3.62331 3.56321 3.94404 3.62536 3.57311 2.73559 2.84831 1.62714 5.32308 4.09587 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+ 0.03182 3.85936 4.58171 0.61958 0.77255 0.34183 1.23951\n+ 2 2.62833 4.47006 3.32205 2.82847 3.63376 3.49826 2.70724 3.02941 2.75408 2.74418 3.64789 3.24903 2.69825 3.12221 3.11180 2.79427 2.89380 1.86602 5.05970 3.76787 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+ 4 2.34111 4.28748 3.51587 3.21760 4.36970 3.06332 4.28987 3.74396 3.23937 3.46805 4.31385 3.39181 3.80269 3.55639 3.55063 1.10193 1.96408 3.'..b'.32906 4.22624 160 l - - -\n+ 144 3.41562 4.71152 5.04825 4.51772 3.21713 4.71088 5.05924 1.61570 4.34688 0.89959 3.01777 4.76079 4.89439 4.48250 4.45829 4.09361 3.64777 2.14627 5.32798 4.22526 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+ 145 1.64545 4.54507 3.30239 2.79573 4.08635 3.33530 3.86939 3.43545 2.62727 3.10791 3.96105 3.19477 3.86964 3.06898 2.22810 2.66738 2.25088 3.08980 5.38530 4.12191 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+ 146 1.97930 4.60841 3.08761 2.66875 4.09801 3.30524 2.59926 3.55507 2.68392 3.18586 4.02113 3.10803 3.84781 3.04317 3.09131 1.74059 2.88109 3.18571 5.40870 4.09330 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+ 147 2.07919 4.89791 3.15343 2.71272 4.41597 3.46550 3.80102 3.74225 1.27587 3.35721 4.22375 3.15594 3.96302 2.96045 2.63970 2.84441 3.07513 3.39525 5.54416 4.28193 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+ 0.17579 4.17053 1.92576 0.61958 0.77255 0.48576 0.95510\n+ 149 2.93078 5.12630 3.29219 2.66308 4.49202 3.60568 2.46960 3.89623 1.58600 3.36230 4.20249 3.10939 3.97321 2.72893 1.82467 2.92177 3.11172 3.56247 5.42994 4.19803 165 k - - -\n+ 2.68634 4.42241 2.77535 2.73098 3.46370 2.40469 3.72510 3.29370 2.67757 2.69331 4.24706 2.90363 2.73755 3.18098 2.89817 2.37903 2.77535 2.98534 4.58493 3.61420\n+ 0.21295 1.65128 * 1.49930 0.25268 0.00000 *\n //\n' |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/globins4.hmm2 --- a/test-data/globins4.hmm2 Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/globins4.hmm2 Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| b'@@ -1,463 +1,463 @@\n-HMMER2.0 [converted from 3.2]\n-NAME dataset_x\n+HMMER2.0 [converted from 3.3]\n+NAME dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2\n LENG 149\n ALPH Amino\n RF no\n CS no\n MAP yes\n NSEQ 4\n-DATE Fri Jun 8 12:14:52 2018\n+DATE Thu May 14 18:27:55 2020\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+ -464 * -1863\n+ 1 1129 15 -1219 -969 -698 -933 -731 663 -690 -263 167 -548 -1318 -571 -947 -75 100 1545 -1226 -870 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+ - -46 -5568 -6610 -894 -1115 -493 -1788 -807 *\n+ 2 -126 -405 -569 -177 -588 -1200 1542 -288 99 -584 132 -94 479 155 -281 -160 34 1200 -846 -397 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+ 4 288 -142 -849 -739 -1650 -573 -742 -1318 -601 -1628 -829 -300 -1114 -471 -914 2281 1375 -768 -1798 -1440 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+ 5 656 -1000 234 1120 -1593 -966 -18 -1310 287 -1451 -624 312 1325 404 -236 -33 -80 -962 -1587 -1054 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+ 6 1216 -894 221 1056 -1629 550 -98 -1356 158 -1507 -679 275 -1191 308 -368 -9 -73 -976 -1643 -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 -131'..b' -756 -254 193 -1049 -1172 102 387 1098 -915 -119 1037 -1230 496 48 -56 747 -464 -1128 -670 158\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+ 143 505 -486 667 -64 -738 -1256 -96 -54 95 180 133 -40 -1332 215 -361 -167 33 692 -1001 -577 159\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+ 144 -1262 -754 -3059 -2614 13 -2950 -1852 1752 -2199 2077 1041 -2275 -2689 -1807 -2224 -2035 -1054 796 -1234 -1057 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+ 145 1292 -514 -541 -130 -1241 -965 -135 -873 282 -1109 -320 -16 -1211 232 994 23 962 -565 -1316 -908 161\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+ 146 810 -605 -231 53 -1258 -922 1697 -1046 200 -1221 -407 109 -1179 269 -252 1360 53 -704 -1350 -866 162\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+ 147 666 -1023 -326 -10 -1716 -1153 -36 -1316 2232 -1468 -699 40 -1345 389 400 -232 -227 -1006 -1545 -1138 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+ - -254 -6017 -2778 -894 -1115 -701 -1378 * *\n+ 149 -562 -1352 -526 61 -1826 -1355 1884 -1538 1784 -1476 -668 107 -1360 723 1576 -344 -280 -1247 -1381 -1017 165\n - * * * * * * * * * * * * * * * * * * * *\n - * * * * * * * * 0\n //\n' |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/jackhmmer.domtblout --- a/test-data/jackhmmer.domtblout Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/jackhmmer.domtblout Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| b'@@ -46,58 +46,58 @@\n HBA4_SALIR - 142 sp|P02185|MYG_PHYCD - 154 5.3e-56 180.0 0.1 1 1 5.9e-56 5.9e-56 179.9 0.1 3 148 2 142 1 142 0.99 -\n MYG_MUSAN - 148 sp|P02185|MYG_PHYCD - 154 2.5e-54 174.6 0.4 1 1 2.8e-54 2.8e-54 174.5 0.4 7 154 2 148 1 148 0.99 -\n HBB2_TRICR - 145 sp|P02185|MYG_PHYCD - 154 2e-52 168.4 0.0 1 1 2.2e-52 2.2e-52 168.3 0.0 3 147 3 145 1 145 0.99 -\n-HBB_MANSP - 146 sp|P02024|HBB_GORGO - 147 3.6e-74 238.9 0.1 1 1 4e-74 4e-74 238.8 0.1 2 147 1 146 1 146 1.00 -\n-HBB_URSMA - 146 sp|P02024|HBB_GORGO - 147 1.7e-73 236.7 0.3 1 1 1.9e-73 1.9e-73 236.6 0.3 2 147 1 146 1 146 1.00 -\n-HBB_RABIT - 146 sp|P02024|HBB_GORGO - 147 2.2e-72 233.1 0.8 1 1 2.4e-72 2.4e-72 233.0 0.8 2 147 1 146 1 146 1.00 -\n-HBB_SUNMU - 146 sp|P02024|HBB_GORGO - 147 5.4e-72 231.8 0.1 1 1 6e-72 6e-72 231.7 0.1 2 147 1 146 1 146 1.00 -\n-HBB_CALAR - 146 sp|P02024|HBB_GORGO - 147 7e-72 231.5 0.2 1 1 7.7e-72 7.7e-72 231.3 0.2 2 147 1 146 1 146 1.00 -\n-HBB_COLLI - 146 sp|P02024|HBB_GORGO - 147 9.6e-72 231.0 0.0 1 1 1.1e-71 1.1e-71 230.9 0.0 2 147 1 146 1 146 1.00 -\n-HBB_TACAC - 146 sp|P02024|HBB_GORGO - 147 2.5e-71 229.7 0.4 1 1 2.8e-71 2.8e-71 229.6 0.4 2 147 1 146 1 146 1.00 -\n-HBE_PONPY - 146 sp|P02024|HBB_GORGO - 147 4.8e-71 228.8 0.4 1 1 5.3e-71 5.3e-71 228.6 0.4 2 147 1 146 1 146 1.00 -\n-HBB_EQUHE - 146 sp|P02024|HBB_GORGO - 147 5.1e-71 228.7 0.2 1 1 5.7e-71 5.7e-71 228.5 0.2 2 147 1 146 1 146 0.99 -\n-HBB_SPECI - 146 sp|P02024|HBB_GORGO - 147 1.3e-70 227.3 1.0 1 1 1.5e-70 1.5e-70 227.2 1.0 2 147 1 146 1 146 1.00 -\n-HBB_SPETO - 146 sp|P02024|HBB_GORGO - 147 2e-70 226.8 0.6 1 1 2.2e-70 2.2e-70 226.6 0.6 2 147 1 146 1 146 1.00 -\n-HBB_TRIIN - 146 sp|P02024|HBB_GORGO - 147 3.7e-70 225.9 0.1 1 1 4.1e-70 4.1e-70 225.8 0.1 2 147 1 146 1 146 1.00 -\n-HBB_ORNAN - 146 sp|P02024|HBB_GORGO - 147 4.1e-70 225.7 0.0 1 1 4.6e-70 4.6e-70 225.6 0.0 2 147 1 146 1 146 1.00 -\n-HBB_LARRI - 146 sp|P02024|HBB_GORGO - 147 5.7e-70 225.3 0.0 1 1 6.4e-70 6.4e-70 225.1 0.0 2 147 1 146 1 146 1.00 -\n-HBB_TUPGL - 146 sp|P02024|HBB_GORGO - 147 1.8e-68 220.5 0.0 1 1 1.9e-68 1.9e-68 220.3 0.0 2 147 1 146 1 146 1.00 -\n-HBB1_VAREX - 146 sp|P02024|HBB_GORGO - 147 1.5e-67 217.4 0.1 1 1 1.7e-67 1.7e-67 217.3 0.1 2 147 1 146 1 146 1.00 -\n-HBBL_RANCA - 146 sp|P02024|HBB_GORGO - 147 7.8e-64 205.4 0.3 1 1 8.7e-64 8.7e-64 205.2 0.3 2 147 1 146 1 146 1.00 -\n-HBA_MESAU - 141 sp|P02024|HBB_GORGO - 147 4.5e-63 202.9 0.3 1 1 5e-63 5e-63 202.8 0.3 4 146 2 140 1 141 0.99 -\n-HBB2_XENTR - 146 sp|P02024|HBB_GORGO - 147 2e-62 200.8 0.8 1 1 2.3e-'..b' 140 1 141 0.98 -\n+HBAD_CHLME - 141 sp|P02024|HBB_GORGO - 147 6e-59 189.5 0.5 1 1 6.6e-59 6.6e-59 189.4 0.5 4 146 2 140 1 141 0.98 -\n+HBAZ_HORSE - 141 sp|P02024|HBB_GORGO - 147 2.2e-58 187.7 0.1 1 1 2.5e-58 2.5e-58 187.5 0.1 4 146 2 140 1 141 0.98 -\n+HBAD_PASMO - 141 sp|P02024|HBB_GORGO - 147 2.4e-58 187.6 0.1 1 1 2.7e-58 2.7e-58 187.4 0.1 4 146 2 140 1 141 0.98 -\n+HBA_COLLI - 141 sp|P02024|HBB_GORGO - 147 2.5e-58 187.5 0.2 1 1 2.8e-58 2.8e-58 187.4 0.2 4 146 2 140 1 141 0.98 -\n+HBB2_TRICR - 145 sp|P02024|HBB_GORGO - 147 1.9e-56 181.4 0.0 1 1 2.2e-56 2.2e-56 181.2 0.0 2 146 1 145 1 145 1.00 -\n+HBA4_SALIR - 142 sp|P02024|HBB_GORGO - 147 5.3e-56 180.0 0.1 1 1 5.8e-56 5.8e-56 179.8 0.1 4 146 2 141 1 142 0.98 -\n+MYG_LYCPI - 153 sp|P02024|HBB_GORGO - 147 9.5e-56 179.1 1.8 1 1 1.1e-55 1.1e-55 179.0 1.8 4 146 2 146 1 147 0.97 -\n+MYG_SAISC - 153 sp|P02024|HBB_GORGO - 147 1.3e-55 178.7 1.0 1 1 1.4e-55 1.4e-55 178.6 1.0 4 146 2 146 1 147 0.98 -\n+MYG_ESCGI - 153 sp|P02024|HBB_GORGO - 147 3.1e-55 177.5 2.2 1 1 3.4e-55 3.4e-55 177.3 2.2 4 146 2 146 1 147 0.97 -\n+MYG_PROGU - 153 sp|P02024|HBB_GORGO - 147 5.1e-55 176.8 0.2 1 1 5.7e-55 5.7e-55 176.6 0.2 4 146 2 146 1 147 0.97 -\n+MYG_HORSE - 153 sp|P02024|HBB_GORGO - 147 9.3e-55 175.9 1.0 1 1 1e-54 1e-54 175.8 1.0 4 146 2 146 1 147 0.97 -\n+MYG_MOUSE - 153 sp|P02024|HBB_GORGO - 147 1.4e-54 175.3 0.3 1 1 1.6e-54 1.6e-54 175.2 0.3 4 146 2 146 1 147 0.97 -\n+MYG_MUSAN - 148 sp|P02024|HBB_GORGO - 147 1.6e-44 142.7 0.3 1 1 1.8e-44 1.8e-44 142.6 0.3 8 146 2 141 1 142 0.96 -\n #\n # Program: jackhmmer\n-# Version: 3.2 (June 2018)\n+# Version: 3.3 (Nov 2019)\n # Pipeline mode: SEARCH\n-# Query file: /tmp/tmpw5_nj0/files/000/dataset_1.dat\n-# Target file: /tmp/tmpw5_nj0/files/000/dataset_2.dat\n-# Option settings: jackhmmer -N 5 --tblout /tmp/tmpw5_nj0/files/000/dataset_4.dat --domtblout /tmp/tmpw5_nj0/files/000/dataset_5.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --wpb --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmpw5_nj0/files/000/dataset_1.dat /tmp/tmpw5_nj0/files/000/dataset_2.dat \n-# Current dir: /tmp/tmpw5_nj0/job_working_directory/000/3/working\n-# Date: Mon Jun 11 17:59:06 2018\n+# Query file: /tmp/tmpfvu1k4r6/files/e/a/d/dataset_ead1ef79-dd40-459b-b072-01fc401e229a.dat\n+# Target file: /tmp/tmpfvu1k4r6/files/c/9/e/dataset_c9eb6990-14c2-41da-9304-1bdf155f29e9.dat\n+# Option settings: jackhmmer -N 5 --tblout /tmp/tmpfvu1k4r6/files/c/c/a/dataset_cca87e56-6fd4-49f3-b29f-dca9b665fb4e.dat --domtblout /tmp/tmpfvu1k4r6/files/a/9/3/dataset_a93530ef-2a8d-4611-9764-b317aa42a6b4.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --wpb --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmpfvu1k4r6/files/e/a/d/dataset_ead1ef79-dd40-459b-b072-01fc401e229a.dat /tmp/tmpfvu1k4r6/files/c/9/e/dataset_c9eb6990-14c2-41da-9304-1bdf155f29e9.dat \n+# Current dir: /tmp/tmpfvu1k4r6/job_working_directory/000/3/working\n+# Date: Thu May 14 18:30:01 2020\n # [ok]\n' |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/jackhmmer.out --- a/test-data/jackhmmer.out Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/jackhmmer.out Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| b'@@ -1,12 +1,10 @@\n # jackhmmer :: iteratively search a protein sequence against a protein database\n-# HMMER 3.2 (June 2018); http://hmmer.org/\n-# Copyright (C) 2018 Howard Hughes Medical Institute.\n+# HMMER 3.3 (Nov 2019); http://hmmer.org/\n+# Copyright (C) 2019 Howard Hughes Medical Institute.\n # Freely distributed under the BSD open source license.\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n-# query sequence file: /tmp/tmpw5_nj0/files/000/dataset_1.dat\n-# target sequence database: /tmp/tmpw5_nj0/files/000/dataset_2.dat\n-# per-seq hits tabular output: /tmp/tmpw5_nj0/files/000/dataset_4.dat\n-# per-dom hits tabular output: /tmp/tmpw5_nj0/files/000/dataset_5.dat\n+# query sequence file: /tmp/tmpfvu1k4r6/files/5/c/1/dataset_5c1435bb-ab6c-4203-863c-578c4a331ea1.dat\n+# target sequence database: /tmp/tmpfvu1k4r6/files/0/c/2/dataset_0c23de62-c430-473e-92ee-a18da9f58231.dat\n # max ASCII text line length: unlimited\n # Vit filter P threshold: <= 0.001\n # Fwd filter P threshold: <= 1e-05\n@@ -608,8 +606,8 @@\n Passed Fwd filter: 44 (0.977778); expected 0.0 (1e-05)\n Initial search space (Z): 45 [actual number of targets]\n Domain search space (domZ): 44 [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: 31.40\n+# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04\n+# Mc/sec: 20.54\n \n @@ New targets included: 44\n @@ New alignment includes: 45 subseqs (was 1), including original query\n@@ -1270,8 +1268,8 @@\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: 0.19u 0.00s 00:00:00.19 Elapsed: 00:00:00.20\n-# Mc/sec: 5.00\n+# CPU time: 0.22u 0.00s 00:00:00.22 Elapsed: 00:00:00.22\n+# Mc/sec: 4.45\n \n @@ New targets included: 1\n @@ New alignment includes: 46 subseqs (was 45), including original query\n@@ -1932,8 +1930,8 @@\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: 0.19u 0.00s 00:00:00.19 Elapsed: 00:00:00.18\n-# Mc/sec: 5.41\n+# CPU time: 0.20u 0.00s 00:00:00.20 Elapsed: 00:00:00.20\n+# Mc/sec: 5.00\n \n @@ New targets included: 0\n @@ New alignment includes: 46 subseqs (was 46), including original query\n@@ -2549,8 +2547,8 @@\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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03\n-# Mc/sec: 31.81\n+# CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.04\n+# Mc/sec: 20.84\n \n @@ New targets included: 45\n @@ New alignment includes: 46 subseqs (was 1), including original query\n@@ -2566,638 +2564,638 @@\n --- full sequence --- --- best 1 domain --- -#dom-\n E-value score bias E-value score bias exp N Sequence Description\n ------- ------ ----- ------- ------ ----- ---- -- -------- -----------\n- 3.6e-74 238.9 0.1 4e-74 238.8 0.1 1.0 1 HBB_MANSP \n- 1.7e-73 236.7 0.3 1.9e-73 236.6 0.3 1.0 1 HBB_URSMA \n- 2.2e-72 233.1 0.8 2.4e-72 233.0 0.8 1.0 1 HBB_RABIT \n- 5.4e-72 231.8 0.1 6e-72 231.7 0.1 1.0 1 HBB_SUNMU \n- 7e-72 231.5 0.2 7.7e-72 231.3 0.2 1.0 1 HBB_CALAR \n- 9.6e-72 231.0 0.0 1.1e-71 230.9 0.0 1.0 1 HBB_COLLI \n- 2.5e-71 229.7 0.4 2.8e-71 229.6 0.4 1.0 1 HBB_TACAC \n- 4.8e-71 228.8 0.4 5.3e-71 228.6 0.4 1.0 1 HBE_PONPY \n- '..b' vhl+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 1 VHLTAEDRKEIAAILGKVNVDSLGGQCLARLIVVNPWSRRYFHDFGDLSSCDAICRNPKVLAHGAKVMRSIVEATKHLDNLREYYADLSVTHSLKFYVDPENFKLFSGIVIVCLALTLQTDFSCHKQLAFEKLMKGVSHALGHGY 145\n- 8**********************************************************************************************************************************************99 PP\n+ == domain 1 score: 175.2 bits; conditional E-value: 1.6e-54\n+ xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ sp|P02024|HBB_GORGO-i1 4 lsaeekalvkavwgkveadevG..aeaLerllvvyPetkryFdkFgdlssedavkgsakvkahgkkvltalgeavkklddlkgalakLselHatklkvdpenfkllsevlvvvLaakfpkeftpevqaaldkllaavanalaakY 146\n+ ls+ e++lv +vwgkvead +G +e+L+ l++++Pet ++FdkF++l+se+++kgs+++k+hg +vltalg+++kk++++++++++L+++Hatk+k+++++++++se+++ vL+++++++f++++q a++k+l++++n++aakY\n+ MYG_MOUSE 2 LSDGEWQLVLNVWGKVEADLAGhgQEVLIGLFKTHPETLDKFDKFKNLKSEEDMKGSEDLKKHGCTVLTALGTILKKKGQHAAEIQPLAQSHATKHKIPVKYLEFISEIIIEVLKKRHSGDFGADAQGAMSKALELFRNDIAAKY 146\n+ 7899*************9966544************************************************************************************************************************* 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 ! 144.3 0.3 5.1e-45 5.1e-45 8 146 .. 2 141 .. 1 142 [. 0.96\n+ 1 ! 142.6 0.3 1.8e-44 1.8e-44 8 146 .. 2 141 .. 1 142 [. 0.96\n \n Alignments for each domain:\n- == domain 1 score: 144.3 bits; conditional E-value: 5.1e-45\n+ == domain 1 score: 142.6 bits; conditional E-value: 1.8e-44\n xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n- sp|P02024|HBB_GORGO-i1 8 ekalvkavwgkvead..evGaeaLerllvvyPetkryFdkFkdlssedavkgsakvkahGkkvltalgeavkklddlkgalakLselHatklkvdpenfkllsevlvvvLaakfpkeftpevqaaldkllaavanalaakY 146\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+ sp|P02024|HBB_GORGO-i1 8 ekalvkavwgkvead..evGaeaLerllvvyPetkryFdkFgdlssedavkgsakvkahgkkvltalgeavkklddlkgalakLselHatklkvdpenfkllsevlvvvLaakfpkeftpevqaaldkllaavanalaakY 146\n+ ++++v++vw+ ve+d ++G+++L rl+++yPe++++F+kF+++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****************************************************************************************9999 PP\n+ 7899********9886699**********************9998.667****************************************************************************************9999 PP\n \n \n \n@@ -3211,8 +3209,8 @@\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: 0.17u 0.00s 00:00:00.17 Elapsed: 00:00:00.17\n-# Mc/sec: 5.33\n+# CPU time: 0.22u 0.00s 00:00:00.22 Elapsed: 00:00:00.24\n+# Mc/sec: 3.96\n \n @@ New targets included: 0\n @@ New alignment includes: 46 subseqs (was 46), including original query\n' |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/jackhmmer.tblout --- a/test-data/jackhmmer.tblout Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/jackhmmer.tblout Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| b'@@ -46,58 +46,58 @@\n HBA4_SALIR - sp|P02185|MYG_PHYCD - 5.3e-56 180.0 0.1 5.9e-56 179.9 0.1 1.0 1 0 0 1 1 1 1 -\n MYG_MUSAN - sp|P02185|MYG_PHYCD - 2.5e-54 174.6 0.4 2.8e-54 174.5 0.4 1.0 1 0 0 1 1 1 1 -\n HBB2_TRICR - sp|P02185|MYG_PHYCD - 2e-52 168.4 0.0 2.2e-52 168.3 0.0 1.0 1 0 0 1 1 1 1 -\n-HBB_MANSP - sp|P02024|HBB_GORGO - 3.6e-74 238.9 0.1 4e-74 238.8 0.1 1.0 1 0 0 1 1 1 1 -\n-HBB_URSMA - sp|P02024|HBB_GORGO - 1.7e-73 236.7 0.3 1.9e-73 236.6 0.3 1.0 1 0 0 1 1 1 1 -\n-HBB_RABIT - sp|P02024|HBB_GORGO - 2.2e-72 233.1 0.8 2.4e-72 233.0 0.8 1.0 1 0 0 1 1 1 1 -\n-HBB_SUNMU - sp|P02024|HBB_GORGO - 5.4e-72 231.8 0.1 6e-72 231.7 0.1 1.0 1 0 0 1 1 1 1 -\n-HBB_CALAR - sp|P02024|HBB_GORGO - 7e-72 231.5 0.2 7.7e-72 231.3 0.2 1.0 1 0 0 1 1 1 1 -\n-HBB_COLLI - sp|P02024|HBB_GORGO - 9.6e-72 231.0 0.0 1.1e-71 230.9 0.0 1.0 1 0 0 1 1 1 1 -\n-HBB_TACAC - sp|P02024|HBB_GORGO - 2.5e-71 229.7 0.4 2.8e-71 229.6 0.4 1.0 1 0 0 1 1 1 1 -\n-HBE_PONPY - sp|P02024|HBB_GORGO - 4.8e-71 228.8 0.4 5.3e-71 228.6 0.4 1.0 1 0 0 1 1 1 1 -\n-HBB_EQUHE - sp|P02024|HBB_GORGO - 5.1e-71 228.7 0.2 5.7e-71 228.5 0.2 1.0 1 0 0 1 1 1 1 -\n-HBB_SPECI - sp|P02024|HBB_GORGO - 1.3e-70 227.3 1.0 1.5e-70 227.2 1.0 1.0 1 0 0 1 1 1 1 -\n-HBB_SPETO - sp|P02024|HBB_GORGO - 2e-70 226.8 0.6 2.2e-70 226.6 0.6 1.0 1 0 0 1 1 1 1 -\n-HBB_TRIIN - sp|P02024|HBB_GORGO - 3.7e-70 225.9 0.1 4.1e-70 225.8 0.1 1.0 1 0 0 1 1 1 1 -\n-HBB_ORNAN - sp|P02024|HBB_GORGO - 4.1e-70 225.7 0.0 4.6e-70 225.6 0.0 1.0 1 0 0 1 1 1 1 -\n-HBB_LARRI - sp|P02024|HBB_GORGO - 5.7e-70 225.3 0.0 6.4e-70 225.1 0.0 1.0 1 0 0 1 1 1 1 -\n-HBB_TUPGL - sp|P02024|HBB_GORGO - 1.8e-68 220.5 0.0 1.9e-68 220.3 0.0 1.0 1 0 0 1 1 1 1 -\n-HBB1_VAREX - sp|P02024|HBB_GORGO - 1.5e-67 217.4 0.1 1.7e-67 217.3 0.1 1.0 1 0 0 1 1 1 1 -\n-HBBL_RANCA - sp|P02024|HBB_GORGO - 7.8e-64 205.4 0.3 8.7e-64 205.2 0.3 1.0 1 0 0 1 1 1 1 -\n-HBA_MESAU - sp|P02024|HBB_GORGO - 4.5e-63 202.9 0.3 5e-63 202.8 0.3 1.0 1 0 0 1 1 1 1 -\n-HBB2_XENTR - sp|P02024|HBB_GORGO - 2e-62 200.8 0.8 2.3e-62 200.6 0.8 1.0 1 0 0 1 1 1 1 -\n-HBA_PONPY - sp|P02024|HBB_GORGO - 4.6e-62 199.6 0.7 5e-62 199.5 0.7 1.0 1 0 0 1 1 1 1 -\n-HBA_MACFA - sp|P02024|HBB_GORGO - 8.7e-62 198.7 0.3 9.6e-62 198.6 0.3 1.0 1 0 0 1 1 1 1 -\n-HBA_MACSI - sp|P02024|HBB_GORGO - 1.3e-61 198.2 0.3 1.4e-61 198.1 0.3 1.0 1 0 0 1 1 1 1 -\n-HBA_AILME - sp|P02024|HBB_GORGO - 2.1e-61 197.5 0.1 2.4e-61 197.3 0.1 1.0 1 0 0 1 1 1 1 -\n-HBA2_GALCR - sp|P02024|HBB_GORGO - 6.6e-61 195.9 0.6 7.3e-61 195.7 0.6 1.0 1 0 0 1 1 1 1 -\n-HBA_FRAPO'..b' 0.0 5.6e-60 192.9 0.0 1.0 1 0 0 1 1 1 1 -\n+HBA_ANSSE - sp|P02024|HBB_GORGO - 7.4e-60 192.5 0.4 8.1e-60 192.3 0.4 1.0 1 0 0 1 1 1 1 -\n+HBA_PAGLA - sp|P02024|HBB_GORGO - 7.4e-60 192.5 0.5 8.1e-60 192.3 0.5 1.0 1 0 0 1 1 1 1 -\n+HBA_TRIOC - sp|P02024|HBB_GORGO - 4.5e-59 189.9 0.5 5e-59 189.8 0.5 1.0 1 0 0 1 1 1 1 -\n+HBAD_CHLME - sp|P02024|HBB_GORGO - 6e-59 189.5 0.5 6.6e-59 189.4 0.5 1.0 1 0 0 1 1 1 1 -\n+HBAZ_HORSE - sp|P02024|HBB_GORGO - 2.2e-58 187.7 0.1 2.5e-58 187.5 0.1 1.0 1 0 0 1 1 1 1 -\n+HBAD_PASMO - sp|P02024|HBB_GORGO - 2.4e-58 187.6 0.1 2.7e-58 187.4 0.1 1.0 1 0 0 1 1 1 1 -\n+HBA_COLLI - sp|P02024|HBB_GORGO - 2.5e-58 187.5 0.2 2.8e-58 187.4 0.2 1.0 1 0 0 1 1 1 1 -\n+HBB2_TRICR - sp|P02024|HBB_GORGO - 1.9e-56 181.4 0.0 2.2e-56 181.2 0.0 1.0 1 0 0 1 1 1 1 -\n+HBA4_SALIR - sp|P02024|HBB_GORGO - 5.3e-56 180.0 0.1 5.8e-56 179.8 0.1 1.0 1 0 0 1 1 1 1 -\n+MYG_LYCPI - sp|P02024|HBB_GORGO - 9.5e-56 179.1 1.8 1.1e-55 179.0 1.8 1.0 1 0 0 1 1 1 1 -\n+MYG_SAISC - sp|P02024|HBB_GORGO - 1.3e-55 178.7 1.0 1.4e-55 178.6 1.0 1.0 1 0 0 1 1 1 1 -\n+MYG_ESCGI - sp|P02024|HBB_GORGO - 3.1e-55 177.5 2.2 3.4e-55 177.3 2.2 1.0 1 0 0 1 1 1 1 -\n+MYG_PROGU - sp|P02024|HBB_GORGO - 5.1e-55 176.8 0.2 5.7e-55 176.6 0.2 1.0 1 0 0 1 1 1 1 -\n+MYG_HORSE - sp|P02024|HBB_GORGO - 9.3e-55 175.9 1.0 1e-54 175.8 1.0 1.0 1 0 0 1 1 1 1 -\n+MYG_MOUSE - sp|P02024|HBB_GORGO - 1.4e-54 175.3 0.3 1.6e-54 175.2 0.3 1.0 1 0 0 1 1 1 1 -\n+MYG_MUSAN - sp|P02024|HBB_GORGO - 1.6e-44 142.7 0.3 1.8e-44 142.6 0.3 1.0 1 0 0 1 1 1 1 -\n #\n # Program: jackhmmer\n-# Version: 3.2 (June 2018)\n+# Version: 3.3 (Nov 2019)\n # Pipeline mode: SEARCH\n-# Query file: /tmp/tmpw5_nj0/files/000/dataset_1.dat\n-# Target file: /tmp/tmpw5_nj0/files/000/dataset_2.dat\n-# Option settings: jackhmmer -N 5 --tblout /tmp/tmpw5_nj0/files/000/dataset_4.dat --domtblout /tmp/tmpw5_nj0/files/000/dataset_5.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --wpb --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmpw5_nj0/files/000/dataset_1.dat /tmp/tmpw5_nj0/files/000/dataset_2.dat \n-# Current dir: /tmp/tmpw5_nj0/job_working_directory/000/3/working\n-# Date: Mon Jun 11 17:59:06 2018\n+# Query file: /tmp/tmpfvu1k4r6/files/e/a/d/dataset_ead1ef79-dd40-459b-b072-01fc401e229a.dat\n+# Target file: /tmp/tmpfvu1k4r6/files/c/9/e/dataset_c9eb6990-14c2-41da-9304-1bdf155f29e9.dat\n+# Option settings: jackhmmer -N 5 --tblout /tmp/tmpfvu1k4r6/files/c/c/a/dataset_cca87e56-6fd4-49f3-b29f-dca9b665fb4e.dat --domtblout /tmp/tmpfvu1k4r6/files/a/9/3/dataset_a93530ef-2a8d-4611-9764-b317aa42a6b4.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --wpb --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmpfvu1k4r6/files/e/a/d/dataset_ead1ef79-dd40-459b-b072-01fc401e229a.dat /tmp/tmpfvu1k4r6/files/c/9/e/dataset_c9eb6990-14c2-41da-9304-1bdf155f29e9.dat \n+# Current dir: /tmp/tmpfvu1k4r6/job_working_directory/000/3/working\n+# Date: Thu May 14 18:30:01 2020\n # [ok]\n' |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/nhmmer.out --- a/test-data/nhmmer.out Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/nhmmer.out Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| b'@@ -1,12 +1,13 @@\n # nhmmer :: search a DNA model, alignment, or sequence against a DNA database\n-# HMMER 3.2 (June 2018); http://hmmer.org/\n-# Copyright (C) 2018 Howard Hughes Medical Institute.\n+# HMMER 3.3 (Nov 2019); http://hmmer.org/\n+# Copyright (C) 2019 Howard Hughes Medical Institute.\n # Freely distributed under the BSD open source license.\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n-# query file: /tmp/tmpp4O0Ju/files/000/dataset_36.dat\n-# target sequence database: /tmp/tmpp4O0Ju/files/000/dataset_37.dat\n-# hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_39.dat\n-# hits output in Dfam format: None\n+# query file: /tmp/tmpqydies2m/files/c/4/e/dataset_c4e67f40-cb86-438e-8bc0-6020ada9fc86.dat\n+# target sequence database: /tmp/tmpqydies2m/files/a/1/b/dataset_a1b4364c-0e9a-4709-b4ef-ab7e5661d9e9.dat\n+# hits tabular output: /tmp/tmpqydies2m/files/b/d/d/dataset_bdd87d82-1ce1-4051-8d5f-f7251bf7fd18.dat\n+# hits output in Dfam format: /tmp/tmpqydies2m/files/d/8/e/dataset_d8ee0d50-d171-4e8a-9c7d-1cbd4394296f.dat\n+# alignment scores output: /tmp/tmpqydies2m/files/5/1/3/dataset_5139892f-c507-40c4-b43d-f73023c634f4.dat\n # max ASCII text line length: unlimited\n # SSV filter P threshold: <= 0.02\n # Vit filter P threshold: <= 0.001\n@@ -22,79 +23,79 @@\n Scores for complete hits:\n E-value score bias Sequence start end Description\n ------- ------ ----- -------- ----- ----- -----------\n- 8.7e-11 39.2 7.4 humanchr1/239220001-239550000 302390 302466 \n- 6.4e-08 30.0 8.3 humanchr1/239220001-239550000 174456 174498 \n- 9.3e-08 29.5 6.1 humanchr1/239220001-239550000 302466 302390 \n- 6.3e-06 23.7 7.0 humanchr1/239220001-239550000 174493 174456 \n+ 4e-11 41.3 7.5 humanchr1/239220001-239550000 302390 302466 \n+ 1.9e-08 32.8 8.3 humanchr1/239220001-239550000 174456 174498 \n+ 6.3e-08 31.0 6.7 humanchr1/239220001-239550000 302466 302389 \n+ 4.9e-06 25.0 7.0 humanchr1/239220001-239550000 174493 174456 \n ------ inclusion threshold ------\n- 1.4 6.5 7.0 humanchr1/239220001-239550000 304073 304104 \n+ 2.2 6.9 7.2 humanchr1/239220001-239550000 304073 304103 \n \n \n Annotation for each hit (and alignments):\n >> humanchr1/239220001-239550000 \n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ! 39.2 7.4 8.7e-11 4 80 .] 302390 302466 .. 302387 302466 .. 330000 0.87\n+ ! 41.3 7.5 4e-11 4 80 .] 302390 302466 .. 302387 302466 .. 330000 0.88\n \n Alignment:\n- score: 39.2 bits\n+ score: 41.3 bits\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 4 ggttggtgcaaaagtaattgcggtttttgccattacttttaatggc....aaaaaccgcaattacttttgcaccaacctaa 80 \n- ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc a aaa g a t ctttt caccaa ctaa\n- humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttA-AAA--GT-AATGCTTTTACACCAATCTAA 302466\n- 899******************************************955533.443..33.44689************9986 PP\n+ ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc aaaa g a t ctttt caccaa ctaa\n+ humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttAAAA---GT-AATGCTTTTACACCAATCTAA 302466\n+ 89*******************************************966644554...34.4578**************997 PP\n \n >> humanchr1/239220001-23955'..b' xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ MADE1 1 ttaggttggtgcaaaagtaattgcggttttt....gccattacttttaatggcaaaaaccgcaattacttttgcaccaacct 78 \n+ ttag ttggtg aaaag a t tttt gc atta +aatggcaaaaacc caatt ttttgcacc acc \n+ humanchr1/239220001-239550000 302466 TTAGATTGGTGTAAAAGCATT-A---CTTTTaaaaGCAATTAAAAGCAATGGCAAAAACCACAATTGATTTTGCACCGACCA 302389\n+ 6899************97543.2...23333455566666666666799*****************************9985 PP\n \n >> humanchr1/239220001-239550000 \n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ! 23.7 7.0 6.3e-06 43 80 .] 174493 174456 .. 174513 174456 .. 330000 0.91\n+ ! 25.0 7.0 4.9e-06 43 80 .] 174493 174456 .. 174513 174456 .. 330000 0.94\n \n Alignment:\n- score: 23.7 bits\n+ score: 25.0 bits\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 43 taatggcaaaaaccgcaattacttttgcaccaacctaa 80 \n taatg caaaaacc caattacttttgcac aacctaa\n humanchr1/239220001-239550000 174493 TAATGACAAAAACCACAATTACTTTTGCACTAACCTAA 174456\n- 689********************************986 PP\n+ 5899*******************************986 PP\n \n >> humanchr1/239220001-239550000 \n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ? 6.5 7.0 1.4 41 72 .. 304073 304104 .. 304053 304109 .. 330000 0.85\n+ ? 6.9 7.2 2.2 41 71 .. 304073 304103 .. 304053 304109 .. 330000 0.85\n \n Alignment:\n- score: 6.5 bits\n- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n- MADE1 41 tttaatggcaaaaaccgcaattacttttgcac 72 \n- tt a tgg aaaaa ca tta ttttgca \n- humanchr1/239220001-239550000 304073 TTAAGTGGGAAAAAATACACTTATTTTTGCAT 304104\n- 455779************************86 PP\n+ score: 6.9 bits\n+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ MADE1 41 tttaatggcaaaaaccgcaattacttttgca 71 \n+ tt a tgg aaaaa ca tta ttttgca\n+ humanchr1/239220001-239550000 304073 TTAAGTGGGAAAAAATACACTTATTTTTGCA 304103\n+ 456789************************8 PP\n \n \n \n@@ -102,12 +103,12 @@\n -------------------------------------\n Query model(s): 1 (80 nodes)\n Target sequences: 1 (660000 residues searched)\n-Residues passing SSV filter: 63737 (0.0966); expected (0.02)\n-Residues passing bias filter: 44695 (0.0677); expected (0.02)\n-Residues passing Vit filter: 2309 (0.0035); expected (0.001)\n-Residues passing Fwd filter: 2041 (0.00309); expected (1e-05)\n+Residues passing SSV filter: 60770 (0.0921); expected (0.02)\n+Residues passing bias filter: 35792 (0.0542); expected (0.02)\n+Residues passing Vit filter: 1612 (0.00244); expected (0.001)\n+Residues passing Fwd filter: 1194 (0.00181); expected (1e-05)\n Total number of hits: 5 (0.000405)\n-# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02\n-# Mc/sec: 1854.66\n+# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.05\n+# Mc/sec: 1031.54\n //\n [ok]\n' |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/nhmmer.out.aliscoresout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nhmmer.out.aliscoresout Tue Jun 16 05:27:39 2020 -0400 |
| b |
| @@ -0,0 +1,5 @@ +MADE1 humanchr1/239220001-239550000 302390 302466 : 1.505 1.476 1.474 -1.303 1.575 1.513 1.539 1.563 1.587 1.551 1.559 1.631 1.323 -1.950 -1.070 1.284 1.511 1.493 1.439 1.532 0.215 1.006 1.428 1.270 1.536 1.556 1.535 1.251 1.434 1.337 1.298 1.388 1.496 1.422 -0.923 1.338 1.437 1.555 1.502 0.815 1.411 1.353 1.353 -1.471 1.456 1.441 > > > -9.001 1.391 1.512 1.535 1.467 > > -6.804 1.052 -0.886 -7.639 1.407 -1.765 1.411 -1.266 1.469 1.387 1.594 1.606 1.596 -1.382 1.548 1.493 1.454 1.559 1.502 1.420 -0.770 1.444 1.540 1.711 1.764 +MADE1 humanchr1/239220001-239550000 174456 174498 : 1.714 1.617 1.616 1.505 1.476 1.474 1.543 -1.208 1.513 1.539 1.563 1.587 1.551 1.559 1.631 1.323 1.534 1.499 1.284 1.511 1.493 1.439 1.532 0.215 1.006 1.428 1.270 1.536 1.556 1.535 1.251 1.434 -0.637 1.298 1.388 1.496 1.422 1.152 1.338 1.437 1.555 1.502 0.815 +MADE1 humanchr1/239220001-239550000 302466 302389 : 1.714 1.617 1.616 1.505 -0.985 1.474 1.543 1.575 1.513 1.539 1.563 -1.318 1.551 1.559 1.631 1.323 1.534 -1.070 1.284 -1.401 1.493 -6.677 -1.165 > > -7.988 -0.943 1.536 1.556 1.535 1.251 > > > -7.961 1.434 1.337 -1.137 1.388 1.496 1.422 1.152 -1.577 -1.499 -1.909 -1.825 0.193 1.411 1.353 1.353 1.449 1.456 1.441 1.391 1.512 1.535 1.467 1.110 1.369 0.819 -0.062 1.496 1.358 1.407 1.540 1.411 -1.266 -1.753 1.387 1.594 1.606 1.596 1.591 1.548 1.493 1.454 1.559 -1.507 1.420 1.423 1.444 -1.824 +MADE1 humanchr1/239220001-239550000 174493 174456 : 0.815 1.411 1.353 1.353 1.449 -0.996 1.441 1.391 1.512 1.535 1.467 1.110 1.369 0.819 -0.062 1.496 1.358 1.407 1.540 1.411 1.448 1.469 1.387 1.594 1.606 1.596 1.591 1.548 1.493 1.454 -1.161 1.502 1.420 1.423 1.444 1.540 1.711 1.764 +MADE1 humanchr1/239220001-239550000 304073 304103 : 1.555 1.502 -1.100 1.411 -1.130 1.353 1.449 1.456 -1.897 1.391 1.512 1.535 1.467 1.110 -1.439 0.155 -0.062 1.496 1.358 -1.596 1.540 1.411 1.448 -0.907 1.387 1.594 1.606 1.596 1.591 1.548 1.493 |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/nhmmer.out.dfamtblout --- a/test-data/nhmmer.out.dfamtblout Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/nhmmer.out.dfamtblout Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| @@ -1,17 +1,10 @@ -# target name accession query name accession hmmfrom hmm to alifrom ali to envfrom env to sq len strand E-value score bias description of target -# ------------------- ---------- -------------------- ---------- ------- ------- ------- ------- ------- ------- ------- ------ --------- ------ ----- --------------------- -humanchr1/239220001-239550000 - MADE1 DF0000629.2 4 80 302390 302466 302387 302466 330000 + 8.7e-11 39.2 7.4 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 43 174456 174498 174456 174518 330000 + 6.4e-08 30.0 8.3 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 77 302466 302390 302466 302387 330000 - 9.3e-08 29.5 6.1 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 43 80 174493 174456 174513 174456 330000 - 6.3e-06 23.7 7.0 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 41 72 304073 304104 304053 304109 330000 + 1.4 6.5 7.0 - +# hit scores +# ---------- # -# Program: nhmmer -# Version: 3.2 (June 2018) -# Pipeline mode: SEARCH -# Query file: /tmp/tmpp4O0Ju/files/000/dataset_36.dat -# Target file: /tmp/tmpp4O0Ju/files/000/dataset_37.dat -# Option settings: nhmmer --tblout /tmp/tmpp4O0Ju/files/000/dataset_39.dat --dfamtblout None --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --dna --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_36.dat /tmp/tmpp4O0Ju/files/000/dataset_37.dat -# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/30/working -# Date: Fri Jun 8 12:18:56 2018 -# [ok] +# target name acc query name bits e-value bias hmm-st hmm-en strand ali-st ali-en env-st env-en sq-len description of target +# ------------------- ------------------- ------------------- ------ --------- ----- ------- ------- ------ ------- ------- ------- ------- ------- --------------------- +humanchr1/239220001-239550000 DF0000629.2 MADE1 41.3 4e-11 7.5 4 80 + 302390 302466 302387 302466 330000 - +humanchr1/239220001-239550000 DF0000629.2 MADE1 32.8 1.9e-08 8.3 1 43 + 174456 174498 174456 174518 330000 - +humanchr1/239220001-239550000 DF0000629.2 MADE1 31.0 6.3e-08 6.7 1 78 - 302466 302389 302466 302387 330000 - +humanchr1/239220001-239550000 DF0000629.2 MADE1 25.0 4.9e-06 7.0 43 80 - 174493 174456 174513 174456 330000 - +humanchr1/239220001-239550000 DF0000629.2 MADE1 6.9 2.2 7.2 41 71 + 304073 304103 304053 304109 330000 - |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/nhmmer.out.tblout --- a/test-data/nhmmer.out.tblout Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/nhmmer.out.tblout Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| @@ -1,17 +1,17 @@ # target name accession query name accession hmmfrom hmm to alifrom ali to envfrom env to sq len strand E-value score bias description of target # ------------------- ---------- -------------------- ---------- ------- ------- ------- ------- ------- ------- ------- ------ --------- ------ ----- --------------------- -humanchr1/239220001-239550000 - MADE1 DF0000629.2 4 80 302390 302466 302387 302466 330000 + 8.7e-11 39.2 7.4 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 43 174456 174498 174456 174518 330000 + 6.4e-08 30.0 8.3 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 77 302466 302390 302466 302387 330000 - 9.3e-08 29.5 6.1 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 43 80 174493 174456 174513 174456 330000 - 6.3e-06 23.7 7.0 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 41 72 304073 304104 304053 304109 330000 + 1.4 6.5 7.0 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 4 80 302390 302466 302387 302466 330000 + 4e-11 41.3 7.5 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 43 174456 174498 174456 174518 330000 + 1.9e-08 32.8 8.3 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 78 302466 302389 302466 302387 330000 - 6.3e-08 31.0 6.7 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 43 80 174493 174456 174513 174456 330000 - 4.9e-06 25.0 7.0 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 41 71 304073 304103 304053 304109 330000 + 2.2 6.9 7.2 - # # Program: nhmmer -# Version: 3.2 (June 2018) +# Version: 3.3 (Nov 2019) # Pipeline mode: SEARCH -# Query file: /tmp/tmpp4O0Ju/files/000/dataset_36.dat -# Target file: /tmp/tmpp4O0Ju/files/000/dataset_37.dat -# Option settings: nhmmer --tblout /tmp/tmpp4O0Ju/files/000/dataset_39.dat --dfamtblout None --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --dna --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_36.dat /tmp/tmpp4O0Ju/files/000/dataset_37.dat -# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/30/working -# Date: Fri Jun 8 12:18:56 2018 +# Query file: /tmp/tmpqydies2m/files/c/4/e/dataset_c4e67f40-cb86-438e-8bc0-6020ada9fc86.dat +# Target file: /tmp/tmpqydies2m/files/a/1/b/dataset_a1b4364c-0e9a-4709-b4ef-ab7e5661d9e9.dat +# Option settings: nhmmer --tblout /tmp/tmpqydies2m/files/b/d/d/dataset_bdd87d82-1ce1-4051-8d5f-f7251bf7fd18.dat --dfamtblout /tmp/tmpqydies2m/files/d/8/e/dataset_d8ee0d50-d171-4e8a-9c7d-1cbd4394296f.dat --aliscoresout /tmp/tmpqydies2m/files/5/1/3/dataset_5139892f-c507-40c4-b43d-f73023c634f4.dat --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --dna --seed 4 --cpu 1 /tmp/tmpqydies2m/files/c/4/e/dataset_c4e67f40-cb86-438e-8bc0-6020ada9fc86.dat /tmp/tmpqydies2m/files/a/1/b/dataset_a1b4364c-0e9a-4709-b4ef-ab7e5661d9e9.dat +# Current dir: /tmp/tmpqydies2m/job_working_directory/000/17/working +# Date: Thu May 14 18:54:51 2020 # [ok] |
| b |
| diff -r 1cd4d0cf8fd9 -r 9415f29a3926 test-data/uniprot_globins_match.out --- a/test-data/uniprot_globins_match.out Mon Jun 11 15:51:54 2018 -0400 +++ b/test-data/uniprot_globins_match.out Tue Jun 16 05:27:39 2020 -0400 |
| [ |
| @@ -1,13 +1,10 @@ # hmmsearch :: search profile(s) against a sequence database -# HMMER 3.2 (June 2018); http://hmmer.org/ -# Copyright (C) 2018 Howard Hughes Medical Institute. +# HMMER 3.3 (Nov 2019); http://hmmer.org/ +# Copyright (C) 2019 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -# query HMM file: /tmp/tmpp4O0Ju/files/000/dataset_25.dat -# target sequence database: /tmp/tmpp4O0Ju/files/000/dataset_26.dat -# per-seq hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_28.dat -# per-dom hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_29.dat -# pfam-style tabular hit output: /tmp/tmpp4O0Ju/files/000/dataset_30.dat +# query HMM file: /tmp/tmpqydies2m/files/1/e/c/dataset_1eca2f81-02d4-4cd0-9081-3ea0f7eb36d7.dat +# target sequence database: /tmp/tmpqydies2m/files/a/4/d/dataset_a4d3f992-2c56-4231-9590-fe0ab1f6413b.dat # max ASCII text line length: unlimited # Vit filter P threshold: <= 0.001 # Fwd filter P threshold: <= 1e-05 @@ -15,39 +12,39 @@ # number of worker threads: 1 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Query: dataset_x [M=149] +Query: dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2 [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 + 1.3e-70 223.2 0.1 1.4e-70 223.0 0.1 1.0 1 sp|P02024|HBB_GORGO Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 + 5.8e-70 221.1 3.3 6.4e-70 220.9 3.3 1.0 1 sp|P02185|MYG_PHYCD Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 Domain annotation for each sequence (and alignments): +>> 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 ! 223.0 0.1 1.4e-70 1.4e-70 1 149 [] 2 147 .] 2 147 .] 0.99 + + Alignments for each domain: + == domain 1 score: 223.0 bits; conditional E-value: 1.4e-70 + dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2 1 vvLseaektkvkavWakveadveevGadiLvrlfvsyPetqefFekFkdLstedelkgsadvkkHgkkvldAlsdalakldekleaelkaLselHakklkvdpkyfkllsevlvvvlaarlpkeftadvqaaleKllalvakalaskYk 149 + v+L+++ek++v+a+W+kv +v+evG+++L rl+v+yP+tq+fFe+F+dLst+d+++g+++vk+Hgkkvl+A+sd+la+ld +l++++++LselH++kl+vdp++fkll++vlv+vla++++keft++vqaa++K++a+va+ala+kY+ + sp|P02024|HBB_GORGO 2 VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLD-NLKGTFATLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH 147 + 69****************..*************************************************************.******************************************************************7 PP + >> 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 + 1 ! 220.9 3.3 6.4e-70 6.4e-70 2 149 .] 2 148 .. 1 148 [. 0.99 Alignments for each domain: - == domain 1 score: 222.6 bits; conditional E-value: 2e-70 - dataset_x 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 - dataset_x 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 + == domain 1 score: 220.9 bits; conditional E-value: 6.4e-70 + dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2 2 vLseaektkvkavWakveadveevGadiLvrlfvsyPetqefFekFkdLstedelkgsadvkkHgkkvldAlsdalakldekleaelkaLselHakklkvdpkyfkllsevlvvvlaarlpkeftadvqaaleKllalvakalaskYk 149 + vLse+e++ v++vWakveadv+++G+diL+rlf+s+Pet+e+F++Fk+L+te+e+k+s+d+kkHg++vl+Al+++l+k ++++eaelk+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 @@ -62,6 +59,6 @@ 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: 20.02 +# Mc/sec: 18.86 // [ok] |