changeset 0:0dd6880ff950 draft

"planemo upload commit 2ce78baac81e5fc7df43ca3ec81a3c51fdb98003"
author guerler
date Tue, 23 Mar 2021 21:38:01 +0000
parents
children 589e4d51bda4
files hhsearch.xml test-data/6VYB_A.fasta test-data/6VYB_A.hhr test-data/dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata test-data/dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex test-data/dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata test-data/dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex test-data/ffindex_indices.loc tool-data/ffindex_indices.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 11 files changed, 1620 insertions(+), 0 deletions(-) [+]
line wrap: on
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hhsearch.xml	Tue Mar 23 21:38:01 2021 +0000
@@ -0,0 +1,138 @@
+<tool id="hhsearch" name="HHsearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>detecting remote homologues of proteins</description>
+    <macros>
+        <token name="@TOOL_VERSION@">3.2.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <xml name="ffindex_single_inputs">
+            <param name="ffdata" type="data" format="ffdata" label="PDB Database" help="Database Data file." />
+            <param name="ffindex" type="data" format="ffindex" label="PDB Database Index" help="Database Index file." />
+        </xml>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">hhsuite</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $db_source.db_source_selector == 'indexed':
+            ln -s '${db_source.ffindex.fields.path}.ffdata' hhdb_hhm.ffdata &&
+            ln -s '${db_source.ffindex.fields.path}.ffindex' hhdb_hhm.ffindex &&
+        #else
+            ln -s '$db_source.ffdata' hhdb_hhm.ffdata &&
+            ln -s '$db_source.ffindex' hhdb_hhm.ffindex &&
+        #end if
+
+        #if $db_source_cs219.db_source_selector == 'indexed':
+            ln -s '${db_source_cs219.ffindex.fields.path}.ffdata' hhdb_cs219.ffdata &&
+            ln -s '${db_source_cs219.ffindex.fields.path}.ffindex' hhdb_cs219.ffindex &&
+        #else
+            ln -s '$db_source_cs219.ffdata' hhdb_cs219.ffdata &&
+            ln -s '$db_source_cs219.ffindex' hhdb_cs219.ffindex &&
+        #end if
+
+        $method
+        -cpu \${GALAXY_SLOTS:-1}
+        -e '$e'
+        -i '$i'
+        -d hhdb
+        -o '$output'
+    ]]>    </command>
+    <inputs>
+        <param argument="--i" type="data" format="fasta,hmm3" label="Query Sequence" help="Single sequence or multiple sequence alignment (MSA)
+                in FASTA format, or HMM in hhm3 format." />
+        <param name="method" type="select" display="radio" label="Search Method" help="Select a search method. See help below for more information.">
+            <option value="hhsearch" selected="true">HHsearch</option>
+            <option value="hhblits">HHblits</option>
+        </param>
+        <conditional name="db_source">
+            <param name="db_source_selector" type="select" label="Custom or built-in HHM index" help="Built-ins have been indexed using ffindex">
+                <option value="indexed" selected="true">Use a built-in index</option>
+                <option value="history">Use a HHM index from history</option>
+            </param>
+            <when value="indexed">
+                <param name="ffindex" type="select" label="Select ffindex" help="">
+                    <options from_data_table="ffindex_indices">
+                        <filter type="sort_by" column="0" />
+                        <filter type="static_value" column="3" value="hhm" />
+                        <validator type="no_options" message="No indices are available" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <expand macro="ffindex_single_inputs" />
+            </when>
+        </conditional>
+
+        <conditional name="db_source_cs219">
+            <param name="db_source_selector" type="select" label="Custom or built-in cs219 index" help="Built-ins have been indexed using ffindex">
+                <option value="indexed" selected="true">Use a built-in index</option>
+                <option value="history">Use a cs219 index from history</option>
+            </param>
+            <when value="indexed">
+                <param name="ffindex" type="select" label="Select ffindex" help="">
+                    <options from_data_table="ffindex_indices">
+                        <filter type="sort_by" column="0" />
+                        <filter type="static_value" column="3" value="cs219" />
+                        <validator type="no_options" message="No indices are available" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <expand macro="ffindex_single_inputs" />
+            </when>
+        </conditional>
+        <param name="e" type="float" value="0.001" min="0" max="1" label="E-value cutoff for inclusion in result alignment. (-e)" />
+    </inputs>
+    <outputs>
+        <data format="hhr" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="method" value="hhblits" />
+            <param name="i" value="6VYB_A.fasta" />
+            <conditional name="db_source">
+                <param name="db_source_selector" value="history" />
+                <param name="ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex" />
+                <param name="ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata" />
+            </conditional>
+            <conditional name="db_source_cs219">
+                <param name="db_source_selector" value="history" />
+                <param name="ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex" />
+                <param name="ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata" />
+            </conditional>
+            <output name="output" file="6VYB_A.hhr" lines_diff="4" ftype="hhr" />
+        </test>
+        <test>
+            <param name="method" value="hhblits" />
+            <param name="i" value="6VYB_A.fasta" />
+            <conditional name="db_source">
+                <param name="db_source_selector" value="indexed" />
+                <param name="ffindex" value="hmm_dbcan" />
+            </conditional>
+            <conditional name="db_source_cs219">
+                <param name="db_source_selector" value="indexed" />
+                <param name="ffindex" value="cs219_dbcan" />
+            </conditional>
+            <output name="output" file="6VYB_A.hhr" lines_diff="4" ftype="hhr" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+HHsearch aligns a profile HMM against a database of target profile HMMs. The search first aligns the
+query HMM with each of the target HMMs using the Viterbi dynamic programming algorithm, which finds the
+alignment with the maximum score. The E-value for the target HMM is calculated from the Viterbi score. 
+Target HMMs that reach sufficient significance to be reported are realigned using the Maximum Accuracy algorithm (MAC).
+This algorithm maximizes the expected number of correctly aligned pairs of residues minus a penalty between 0 and 1.
+Values near 0 produce greedy, long, nearly global alignments, values above 0.3 result in shorter, local alignments.
+
+HHblits is an accelerated version of HHsearch that is fast enough to perform iterative searches through millions of profile HMMs,
+e.g. through the Uniclust profile HMM databases, generated by clustering the UniProt database into clusters of globally alignable sequences. 
+Analogously to PSI-BLAST and HMMER3, such iterative searches can be used to build MSAs by starting from a single query sequence.
+Sequences from matches to profile HMMs below some E-value threshold (e.g. 10−3) are added to the query MSA for the next search iteration.
+
+Download databases from: http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bti125</citation>
+    </citations>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/6VYB_A.fasta	Tue Mar 23 21:38:01 2021 +0000
@@ -0,0 +1,20 @@
+>6VYB_A
+AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHPVLPFNDG
+VYFASTEKSNIIRGWIFGTTLDSKSLLIVNNATNVVIKVCEFQFCNDPFLG
+VCTFEYVSFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVD
+LPIGINITRFQTLLAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSET
+KCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASV
+YAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFV
+IRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDNYNYLYRLFR
+KSNLKPFERDISTFPLQSYGFQPTNVGYQPYRVVVLSFELLHAPATVCGPK
+KSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDP
+QTLEILDITPCSFGGVSVITPGTNTSNEVAVLYQDVNCTEVNVFQTRAGCL
+IGAEHVNNSYECDIPIGAGICASYQTQSIIAYTMSLGAENSVAYSNNSIAI
+PTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNR
+ALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKSKRSF
+IEDLLFNKVTFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQ
+IPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALG
+KLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLI
+TGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYH
+LMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNG
+THWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/6VYB_A.hhr	Tue Mar 23 21:38:01 2021 +0000
@@ -0,0 +1,156 @@
+Query         6VYB_A
+Match_columns 966
+No_of_seqs    1 out of 1
+Neff          1
+Searched_HMMs 100
+Date          Sun Jul 26 21:21:46 2020
+Command       hhblits -i test-data/query.fasta -o query.hhr -d test-data/dbCAN-fam-V8/dbCAN-fam-V8 
+
+ No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
+  1 ABN54336.1|CE12|183-378|9.5e-5  17.2     1.1  0.0014   32.1   0.0   13  586-598     1-13  (210)
+  2 ANU56961.1|PL12_2.hmm|1.8e-61|   3.4     9.9   0.013   24.9   0.0   32  900-931    38-69  (131)
+  3 CAX58257.1|CE11|4-276|4.9e-122   2.1      18   0.023   25.0   0.0   38  857-894     6-54  (277)
+  4 APK54672.1|GT103                 2.1      18   0.023   24.9   0.0  168  629-825     1-184 (232)
+  5 AAD04130.1|GT13|24-440|6.3e-18   1.7      23    0.03   25.6   0.0   47  302-349   156-203 (390)
+  6 ACR10769.1|PL1|79-276|1.4e-54    1.3      33   0.041   21.6   0.0   53   59-111    59-115 (196)
+  7 AAR43340.1|GT19|17-374|6.8e-14   1.3      33   0.041   23.4   0.0   14  254-267   116-129 (357)
+  8 BAD47100.1|GH125|74-473|3.2e-1   1.3      32   0.041   24.6   0.0   41   98-138   291-338 (402)
+  9 ACY95489.1|CBM14|33-88|9.4e-16   1.1      38   0.047   18.2   0.0   36  238-277    39-74  (81)
+ 10 AAK92730.1|PL1_1.hmm|3.6e-111|   0.9      49   0.063   21.4   0.0   50  277-326    18-67  (199)
+
+No 1
+>ABN54336.1|CE12|183-378|9.5e-54
+Probab=17.23  E-value=1.1  Score=32.05  Aligned_cols=13  Identities=38%  Similarity=0.705  Sum_probs=11.0  Template_Neff=5.400
+
+Q 6VYB_A          586 TMYICGDSTECSN  598 (966)
+Q Consensus       586 tmyicgdstecsn  598 (966)
+                      |+|||||||-|..
+T Consensus         1 tI~l~GDSTva~~   13 (210)
+T ABN54336.1|CE1    1 TIFLAGDSTVANY   13 (210)
+Confidence            6899999998853
+
+
+No 2
+>ANU56961.1|PL12_2.hmm|1.8e-61|404-534
+Probab=3.41  E-value=9.9  Score=24.92  Aligned_cols=32  Identities=25%  Similarity=0.544  Sum_probs=26.7  Template_Neff=2.600
+
+Q 6VYB_A          900 ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEP  931 (966)
+Q Consensus       900 ichdgkahfpregvfvsngthwfvtqrnfyep  931 (966)
+                      .-++|+-.||..|.||-.|..--..+|+.|..
+T Consensus        38 Lw~~GRnf~PDaG~yvY~Gd~~~~~~R~wfR~   69 (131)
+T ANU56961.1|PL1   38 LWVKGRNFFPDAGSYVYAGDSEINKLRNWFRQ   69 (131)
+Confidence            56899999999999999998866777777753
+
+
+No 3
+>CAX58257.1|CE11|4-276|4.9e-122
+Probab=2.10  E-value=18  Score=25.00  Aligned_cols=38  Identities=32%  Similarity=0.532  Sum_probs=26.5  Template_Neff=4.700
+
+Q 6VYB_A          857 KRVDFCGKGYHL------MSFPQSAPHGVVFLHVT-----YVPAQEKNF  894 (966)
+Q Consensus       857 krvdfcgkgyhl------msfpqsaphgvvflhvt-----yvpaqeknf  894 (966)
+                      +.|.+.|.|.|-      --.|..+.+|++|..+-     .+||.-.+.
+T Consensus         6 ~~v~~~GiGLHsG~~v~l~l~PA~~~tGIvF~R~dl~~~~~IpA~~~~V   54 (277)
+T CAX58257.1|CE1    6 RSVSLTGVGLHSGKKVTLTLRPAPANTGIVFRRTDLDGPPEIPADADNV   54 (277)
+Confidence            456778888773      44688888999998875     555554443
+
+
+No 4
+>APK54672.1|GT103
+Probab=2.06  E-value=18  Score=24.88  Aligned_cols=168  Identities=24%  Similarity=0.353  Sum_probs=95.1  Template_Neff=2.800
+
+Q 6VYB_A          629 FAQVKQIYKTPPIKDFGGFNFSQILPDPSKSKRSFIEDLLFNKVTFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFG  708 (966)
+Q Consensus       629 faqvkqiyktppikdfggfnfsqilpdpskskrsfiedllfnkvtfngltvlpplltdemiaqytsallagtitsgwtfg  708 (966)
+                      |.|-|.|+.-+.+.+-..--+.--||..-..++.|-.+.-.+---|.||--                      ..||.  
+T Consensus         1 ~~~~~~~~s~~~~~~~d~~~i~LsLPET~~RR~~f~~~~~~G~q~FdGlR~----------------------~~GWI--   56 (232)
+T APK54672.1|GT1    1 FSQYKSIFSQCEISPQDVDFICLSLPETIERRRDFEQDNPYGIQLFDGLRH----------------------RPGWI--   56 (232)
+Confidence            456667776666666555445555777666666666555544444555432                      34663  
+
+
+Q 6VYB_A          709 AGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTAS------AL-------GKLQDVVNQNA  775 (966)
+Q Consensus       709 agaalqipfamqmayrfngigvtqnvlyenqklianqfnsaigkiqdslsstas------al-------gklqdvvnqna  775 (966)
+                       |+++..-+..+-|-   --+..+-.+-|..-+....|.+.+..+++-|...-+      .|       -|+..|-....
+T Consensus        57 -GCglSyk~l~r~al---~~~~~~lti~EDDV~fp~df~~~~~~v~~yL~~~~~~WDvFsGliAdlH~dtkIl~ve~~~g  132 (232)
+T APK54672.1|GT1   57 -GCGLSYKFLARKAL---ENGIPQLTICEDDVLFPPDFESKYSQVKDYLDTRRNDWDVFSGLIADLHPDTKILKVERFDG  132 (232)
+Confidence             33333333222222   234455567788888888888888888887753221      11       23444444444
+
+
+Q 6VYB_A          776 QALNTLVKQLSSNFGAISSVLNDILSRLDPPEAE---VQIDRLITGRLQSLQT  825 (966)
+Q Consensus       776 qalntlvkqlssnfgaissvlndilsrldppeae---vqidrlitgrlqslqt  825 (966)
+                      ...-++=|-.|--|..-+.-.-++|+..||....   ..|||.+.. .+.|..
+T Consensus       133 ~~yv~iDkMtSmV~NIYs~~al~~L~~Wd~~~~d~~TNTIDRylE~-~~~LrV  184 (232)
+T APK54672.1|GT1  133 IEYVTIDKMTSMVFNIYSESALEKLAQWDEKNHDAETNTIDRYLEN-QEGLRV  184 (232)
+Confidence            4555555555555555555555788888876544   468998753 334433
+
+
+No 5
+>AAD04130.1|GT13|24-440|6.3e-183
+Probab=1.69  E-value=23  Score=25.58  Aligned_cols=47  Identities=28%  Similarity=0.384  Sum_probs=24.8  Template_Neff=3.500
+
+Q 6VYB_A          302 ADSFVIRGDEVRQIAPGQTGKIADYNYKLP-DDFTGCVIAWNSNNLDNY  349 (966)
+Q Consensus       302 adsfvirgdevrqiapgqtgkiadynyklp-ddftgcviawnsnnldny  349 (966)
+                      +++++|-.|. -.|||.--.-...--+-|. |+---||-|||.|.....
+T Consensus       156 ~~~VII~EdD-m~iapDFf~yf~~~~~lL~~D~sl~cvSaWNDNG~~~~  203 (390)
+T AAD04130.1|GT1  156 FSRVIIVEDD-LEIAPDFFSYFSATYPLLDRDPSLWCVSAWNDNGKEQF  203 (390)
+Confidence            3344444433 3566653322222222233 444579999999987654
+
+
+No 6
+>ACR10769.1|PL1|79-276|1.4e-54
+Probab=1.28  E-value=33  Score=21.64  Aligned_cols=53  Identities=25%  Similarity=0.395  Sum_probs=33.8  Template_Neff=5.700
+
+Q 6VYB_A           59 KSN-IIRGWIFGTTLD--SKSLLIVNNATNVVIKVCEFQFCNDPFLGVCTF-EYVSF  111 (966)
+Q Consensus        59 ksn-iirgwifgttld--sksllivnnatnvvikvcefqfcndpflgvctf-eyvsf  111 (966)
+                      .+| |||-.-|-...+  ...-+-++++.+|.|--|+|.-..|-.+.+..- .||.+
+T Consensus        59 ~~NVIIRnl~~~~~~~~~~~Dai~i~~s~nVWIDHcsfs~~~Dg~ldv~~~s~~VTi  115 (196)
+T ACR10769.1|PL1   59 ASNVIIRNLRIRDGNDGFDGDAISIDGSSNVWIDHCSFSWGGDGLIDIKKGSDNVTI  115 (196)
+Confidence            344 566666655553  223333578899999999999998887755432 34443
+
+
+No 7
+>AAR43340.1|GT19|17-374|6.8e-144
+Probab=1.27  E-value=33  Score=23.45  Aligned_cols=14  Identities=36%  Similarity=0.700  Sum_probs=11.3  Template_Neff=5.700
+
+Q 6VYB_A          254 SVYAWNRKRISNCV  267 (966)
+Q Consensus       254 svyawnrkrisncv  267 (966)
+                      +|+||..+|+..-.
+T Consensus       116 qvWAWr~~R~k~i~  129 (357)
+T AAR43340.1|GT1  116 QVWAWRPGRIKKIK  129 (357)
+Confidence            79999999987643
+
+
+No 8
+>BAD47100.1|GH125|74-473|3.2e-189
+Probab=1.27  E-value=32  Score=24.58  Aligned_cols=41  Identities=32%  Similarity=0.588  Sum_probs=32.3  Template_Neff=3.500
+
+Q 6VYB_A           98 DPFLGVCTFEYVSFKNLREFVFKNIDGYF-------KIYSKHTPINLV  138 (966)
+Q Consensus        98 dpflgvctfeyvsfknlrefvfknidgyf-------kiyskhtpinlv  138 (966)
+                      -|+||-|.-+---+.|-|+|+...-.-||       -|=|.|++.+-+
+T Consensus       291 lPylG~~~~~DpiYqnTR~~iLS~~NPYy~~G~~~~GIGsPHtg~~~i  338 (402)
+T BAD47100.1|GH1  291 LPYLGYCSKDDPIYQNTRRFILSKENPYFYEGKAAEGIGSPHTGPRYI  338 (402)
+Confidence            48899999888889999999988766665       266778876655
+
+
+No 9
+>ACY95489.1|CBM14|33-88|9.4e-16
+Probab=1.13  E-value=38  Score=18.15  Aligned_cols=36  Identities=31%  Similarity=0.470  Sum_probs=23.4  Template_Neff=6.300
+
+Q 6VYB_A          238 TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSA  277 (966)
+Q Consensus       238 tnlcpfgevfnatrfasvyawnrkrisncvadysvlynsa  277 (966)
+                      ...||.|.+|+...-.=++.++-+   .|--| |+-|||.
+T Consensus        39 ~~~Cp~g~~FD~~~~~C~~~~~v~---~C~~~-~~~~~~~   74 (81)
+T ACY95489.1|CBM   39 EFSCPPGLVFDPETQTCDWPENVD---DCSNC-SIRYNSG   74 (81)
+Confidence            458999999998876666644431   24433 5666664
+
+
+No 10
+>AAK92730.1|PL1_1.hmm|3.6e-111|138-336
+Probab=0.87  E-value=49  Score=21.39  Aligned_cols=50  Identities=28%  Similarity=0.484  Sum_probs=43.2  Template_Neff=2.500
+
+Q 6VYB_A          277 ASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADY  326 (966)
+Q Consensus       277 asfstfkcygvsptklndlcftnvyadsfvirgdevrqiapgqtgkiady  326 (966)
+                      .|+.|..--|++-.--+.-|+|--|+....|.|=.+..+.|+..|-|.|-
+T Consensus        18 ~S~KTIDGRGa~V~I~~g~citiq~v~nVIIHgi~IH~c~p~~~g~ir~s   67 (199)
+T AAK92730.1|PL1   18 NSFKTIDGRGANVHIANGACITIQYVSNVIIHGIHIHDCKPGGNGMVRDS   67 (199)
+Confidence            46777777888888888899999999999999999999999998888764
+
+
Binary file test-data/dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex	Tue Mar 23 21:38:01 2021 +0000
@@ -0,0 +1,641 @@
+AA1	130000	614
+AA10	98449	182
+AA11	89861	198
+AA12	161477	401
+AA13	205723	233
+AA14	84523	269
+AA15	202053	196
+AA16	2537	168
+AA1_1	72683	316
+AA1_2	163839	340
+AA1_3	13117	316
+AA2	50468	260
+AA3	175231	645
+AA3_1	132900	776
+AA3_2	109017	591
+AA3_3	152711	592
+AA3_4	117354	551
+AA4	29900	535
+AA5	101197	751
+AA5_1	127310	826
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Binary file test-data/dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex	Tue Mar 23 21:38:01 2021 +0000
@@ -0,0 +1,641 @@
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+GH29	13529185	46319
+GH3	20193005	34349
+GH30	9507467	58508
+GH30_1	9565975	51730
+GH30_2	9312489	48736
+GH30_3	9155615	55009
+GH30_4	7655338	59255
+GH30_5	8392788	55167
+GH30_6	8503031	45541
+GH30_7	8858377	49174
+GH30_8	10474566	44407
+GH30_9	8816018	42359
+GH31	9765578	60003
+GH32	18012894	41764
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+GH34	8047999	48229
+GH35	16168069	41458
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+GH4	22443823	23500
+GH42	11265935	49358
+GH43	19771686	37755
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+GH48	4771540	70910
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+GH5	18711093	41253
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+GH51	7522665	67913
+GH52	9461847	45620
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+GH54	14931063	35059
+GH55	2819498	89900
+GH56	13622907	41285
+GH57	10608286	52610
+GH58	8714489	40981
+GH59	4568953	72481
+GH5_1	15403452	38974
+GH5_10	15652666	35107
+GH5_11	15149637	35103
+GH5_12	6438270	65532
+GH5_13	18616345	32766
+GH5_14	18426387	28614
+GH5_15	16318898	31003
+GH5_16	13409806	35930
+GH5_17	16916274	27347
+GH5_18	17950326	32154
+GH5_19	18649111	31135
+GH5_2	19996434	31249
+GH5_20	12807194	36963
+GH5_21	16287054	31844
+GH5_22	17423400	32225
+GH5_23	18151533	28090
+GH5_24	14966122	31167
+GH5_25	19400652	31690
+GH5_26	18243809	29263
+GH5_27	13711517	33756
+GH5_28	13445736	35104
+GH5_29	13062663	34007
+GH5_30	9009202	43187
+GH5_31	17720441	27000
+GH5_32	13096670	33926
+GH5_33	18400446	25941
+GH5_34	20344074	25302
+GH5_35	23236734	14283
+GH5_36	17390619	32781
+GH5_37	15224359	34718
+GH5_38	15259077	33389
+GH5_39	15914673	36096
+GH5_4	16877426	38848
+GH5_40	17689738	30703
+GH5_41	19589691	27894
+GH5_42	19617585	28210
+GH5_43	11227453	38482
+GH5_44	16053855	33061
+GH5_45	16427329	28663
+GH5_46	19494873	31339
+GH5_47	18121689	29844
+GH5_48	14818222	34998
+GH5_49	16770788	33581
+GH5_5	17555058	36593
+GH5_50	17591651	31764
+GH5_51	12558566	37121
+GH5_52	17528048	27010
+GH5_53	10568579	39707
+GH5_54	17922402	27924
+GH5_55	19210828	27179
+GH5_56	22811327	14778
+GH5_7	16663093	39258
+GH5_8	19118075	32130
+GH5_9	15876013	38660
+GH6	17352841	37778
+GH62	18368278	32168
+GH63	2143308	91052
+GH64	11457840	45344
+GH65	10784632	50493
+GH66	5949001	65799
+GH67	3438081	80943
+GH68	10031323	48127
+GH7	10173001	49178
+GH70	1774525	90546
+GH71	11180658	46795
+GH72	15838831	37182
+GH73	23695590	18908
+GH74	14416625	39695
+GH75	20679482	26619
+GH76	12158210	49615
+GH77	7774745	68111
+GH78	7385633	70624
+GH79	8548572	59099
+GH8	14051431	44520
+GH80	24323836	6256
+GH81	3601511	86553
+GH82	20965729	23393
+GH83	6246159	64774
+GH84	16389363	37966
+GH85	15442426	39125
+GH86	5186277	73331
+GH87	983697	106982
+GH88	13818094	42902
+GH89	3519024	82487
+GH9	9825581	58416
+GH90	6136708	51820
+GH91	10281286	42513
+GH92	7456257	66408
+GH93	15365093	38359
+GH94	509710	145659
+GH95	2495876	99876
+GH96	4842450	57462
+GH97	4486992	81961
+GH98	14016766	34665
+GH99	13977770	38996
+GT1	8096228	72211
+GT10	12108747	49463
+GT101	20740151	26304
+GT102	11635708	39839
+GT103	20491630	24915
+GT104	10705003	37352
+GT105	24294179	8996
+GT106	14565846	39499
+GT107	1383440	116092
+GT11	18784599	39298
+GT12	23422325	14930
+GT13	10429278	45288
+GT14	19895596	35011
+GT15	18209308	34501
+GT16	12638922	38702
+GT17	17654970	34768
+GT18	2595752	77072
+GT19	12060304	48443
+GT20	7888569	64430
+GT21	20429652	30274
+GT22	9883997	55033
+GT23	13938788	38982
+GT24	19837137	28373
+GT25	22291745	26347
+GT26	22601102	23956
+GT27	16248738	38316
+GT28	22845740	23714
+GT29	19930607	34333
+GT2_Cellulose_synt	2321677	73509
+GT2_Chitin_synth_1	22791030	20297
+GT2_Chitin_synth_2	6907165	52810
+GT2_Glyco_tranf_2_2	18530945	26913
+GT2_Glyco_tranf_2_3	20596093	29194
+GT2_Glyco_tranf_2_4	24065412	13403
+GT2_Glyco_tranf_2_5	21205841	25429
+GT2_Glyco_trans_2_3	21732640	28243
+GT2_Glycos_transf_2	22667797	24592
+GT3	4350457	75068
+GT30	22512883	24951
+GT31	22179250	26598
+GT32	24190168	11970
+GT33	9617705	50028
+GT34	19964940	31494
+GT35	3888040	90060
+GT37	8340009	52779
+GT38	7952999	44365
+GT39	20459926	31704
+GT4	23581318	20771
+GT40	21143249	22975
+GT41	5616252	81261
+GT42	17085403	31735
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+GT55	10742355	42277
+GT56	11801304	42374
+GT57	7714593	60152
+GT58	11592957	42751
+GT59	9411401	50446
+GT6	17888984	33418
+GT60	14376949	39676
+GT61	20227354	30700
+GT62	19179683	31145
+GT63	13212617	30834
+GT64	19709954	30262
+GT65	13174985	37632
+GT66	2395186	100690
+GT67	13370984	38822
+GT68	10660896	44107
+GT69	20369376	28362
+GT7	19740216	31470
+GT70	11140895	39763
+GT71	19296491	36435
+GT72	12287028	30664
+GT73	20135190	28110
+GT74	17858011	30973
+GT75	12438249	39405
+GT76	9100038	55577
+GT77	20649668	29814
+GT78	23454678	12377
+GT79	1197474	87535
+GT8	18080237	41452
+GT80	10835125	40570
+GT81	17822289	35722
+GT82	16493545	31218
+GT83	7010085	77484
+GT84	21096867	25062
+GT85	9052389	47649
+GT87	20397738	31914
+GT88	6618219	55593
+GT89	5333360	67388
+GT9	21491858	30134
+GT90	19083690	34385
+GT91	8284884	55125
+GT92	14286868	40690
+GT93	15622243	30423
+GT94	17785718	36571
+GT95	16738160	32628
+GT96	16019060	34795
+GT97	13788113	29981
+GT98	3978100	76854
+GT99	10875695	42942
+PL1	21853525	26137
+PL10	17491681	36367
+PL10_1	17316730	36111
+PL10_2	18587082	29263
+PL10_3	18916942	29012
+PL11	5042312	73799
+PL11_1	5259608	73752
+PL11_2	5697513	61239
+PL12	23251017	18413
+PL12_1	23405911	16414
+PL12_2	23566714	14604
+PL12_3	23133222	17145
+PL13	11764724	36580
+PL14	21619103	24677
+PL14_1	21384043	19539
+PL14_2	21259515	20012
+PL14_3	21999479	23591
+PL14_4	20945064	20665
+PL14_5	21186624	19217
+PL15	23484889	15189
+PL15_1	23269430	14992
+PL15_2	22962553	14521
+PL16	18340591	27687
+PL17	23304827	16455
+PL17_1	23391194	14717
+PL17_2	22826105	19635
+PL18	22122520	18678
+PL1_1	21643780	22004
+PL1_10	22537834	16865
+PL1_11	22403877	19486
+PL1_12	22385426	18451
+PL1_13	22162176	17074
+PL1_2	22205848	23409
+PL1_3	21279527	20414
+PL1_4	22141198	20978
+PL1_5	21359240	24803
+PL1_6	21071580	25287
+PL1_7	22246456	19216
+PL1_8	21832147	21378
+PL1_9	22229257	17199
+PL2	6731453	56466
+PL20	20625287	24381
+PL21	24303175	7581
+PL21_1	24310756	6855
+PL22	22490903	21980
+PL22_1	22625058	19002
+PL22_2	20317851	26223
+PL23	4641434	74342
+PL24	7997364	50635
+PL25	8236332	48552
+PL26	1090679	106795
+PL27	4279868	70589
+PL28	17182161	30138
+PL29	11722396	42328
+PL2_1	6787919	50408
+PL2_2	6564213	54006
+PL3	21594049	25054
+PL30	2672824	68482
+PL31	22099939	22581
+PL32	4715776	55764
+PL33	21568156	25893
+PL33_1	22889954	19670
+PL33_2	22942768	19785
+PL34	21472104	19754
+PL35	21784855	24652
+PL36	21121929	21320
+PL36_1	21715403	17237
+PL36_2	21927223	19004
+PL37	4209038	70830
+PL3_1	22423363	20460
+PL3_2	21809507	22640
+PL3_3	21166224	20400
+PL3_4	21692795	22608
+PL3_5	21452167	19937
+PL4	5819903	70415
+PL4_1	7275853	55496
+PL4_2	4978765	63547
+PL4_3	4425525	61467
+PL4_4	6014800	60264
+PL4_5	6959975	50110
+PL5	14894547	36516
+PL5_1	14709843	33316
+PL6	11411272	46568
+PL6_1	10918637	48373
+PL6_2	11927186	40781
+PL6_3	11101377	39518
+PL7	20540178	30757
+PL7_1	20843621	24675
+PL7_2	20796915	22716
+PL7_3	21046459	25121
+PL7_4	20819631	23990
+PL7_5	18752346	32253
+PL8	19365185	35467
+PL8_1	18823897	29268
+PL8_2	19865510	30086
+PL8_3	19809441	27696
+PL8_4	20086567	21148
+PL9	11542828	50129
+PL9_1	10518973	49606
+PL9_2	11055542	45835
+PL9_3	12520166	38400
+PL9_4	23041368	17471
+SLH	24362798	6012
+cohesin	24400055	3247
+dockerin	23437255	17423
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ffindex_indices.loc	Tue Mar 23 21:38:01 2021 +0000
@@ -0,0 +1,4 @@
+##ffindex indices
+#unique_id	display name	path	type
+hmm_dbcan	HMM 2021-03-17-dbCAN	${__HERE__}/dbCAN-fam-V8/dbCAN-fam-V8_hhm	hhm
+cs219_dbcan	cs19 2021-03-17-dbCAN	${__HERE__}/dbCAN-fam-V8/dbCAN-fam-V8_cs219	cs219
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ffindex_indices.loc.sample	Tue Mar 23 21:38:01 2021 +0000
@@ -0,0 +1,7 @@
+# ffindex collection, you can add multiple indices here and seperate them via the type (last column)
+# The path should point to a directory and the file-prefix ('pdb_prefix').
+# The folder needs to contain two files pdb_prefix.ffindex and pdb_prefix.ffdata
+#
+#identifer	description from the PDB set	/mnt/pdb_indices/pdb/pdb_prefix	pdb
+#identifer	description from the HHR set	/mnt/hhr/hhr_prefix	hhr
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Mar 23 21:38:01 2021 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="ffindex_indices" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, path, type</columns>
+        <file path="tool-data/ffindex_indices.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Tue Mar 23 21:38:01 2021 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of ffindex indexes for testing -->
+    <table name="ffindex_indices" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, path, type</columns>
+        <file path="${__HERE__}/test-data/ffindex_indices.loc" />
+    </table>
+</tables>