v4.0.0

Author: cariann09

doc/Install.html

@@ -62,9 +62,9 @@ <h2>Installation</h2>
 
 <i><b><u>Step 1:</u></b></i> Decide where you want the main TCW directory to go, and untar the package in that location.
 <pre>
-	tar -xvf TCW_3.tar.gz
+	tar -xvf TCW_4.tar.gz
 </pre>
-The untar will create a <ttp>TCW_3</ttp> directory, with the following content:
+The untar will create a <ttp>TCW_4</ttp> directory, with the following content:
 	<pre>
 	Executables:		
 		 execLoadLib     execAssm        execAnno
@@ -299,7 +299,7 @@ <h4>Blast and Diamond</h4>
 If you are going to use the <ttp>runSingleTCW</ttp> assembler, you MUST specify the full path of where the Blast executables reside,
 even if your going to use the default executables, e.g
 <pre>
-	blast_path = /Users/cari/Workspace/TCW_3/Ext/mac/blast
+	blast_path = /Users/cari/Workspace/TCW_4/Ext/mac/blast
 </pre>
 To verify what diamond and blast paths are being used, run 
 <pre>

doc/Release.html

@@ -13,7 +13,7 @@
 
 There have been many improvements, but the following provides some recent critical points.
 <table>
-<tr><td><a href=#v341>v3.4.2</a><td>08-Mar-22<td><ttp>Assorted<td>Make color of buttons consistent.
+<tr><td><a href=#v343>v4.0.0</a><td>22-Mar-22<td><ttp>Assorted<td>Tidy up somethings in order to start v4.
 <tr><td><a href=#v339>v3.3.9</a><td>27-Dec-21<td><ttp><ttp>runAS</ttp></ttp><td>Improved interface for full subset UniProt; updated Demo.
 <tr><td><a href=#v335>v3.3.5</a><td>04-Nov-21<td><ttp>viewSingle</ttp><td>log2FC TPM analysis 
 <tr><td><a href=#v334>v3.3.4</a><td>18-Oct-21<td><ttp>runSingle</ttp><td><ttl>ORF finder</ttl> improvements
@@ -27,6 +27,33 @@
 <tr><td><a href=#early>Earlier</a><td>2020<td>&nbsp;<td>&nbsp;
 </table>
 
+<a name=v343>
+<h4>v4.0.0 22-Mar-2022</h4>
+
+<p>General
+<ul>
+<li>Documentation and Help updates - mostly for mTCW. 
+</ul>
+
+<p><ttp>runAS</ttp>
+<ul>
+<li>The <ttc>Check</ttc> function will write to the terminal the UniProts added to an existing goDB.
+For existing goDBs, they will be updated on first <ttc>Check</ttc>  and stored in the goDB.
+</ul>
+
+<p><ttp>viewMultiTCW</ttp>
+<ul>
+<li><ttc>Explain</ttc> on <ttc>Overview</ttc>: rewrote much of it for clarity.
+<li>A lot of little tidy up things. 
+(1) <ttc>Overview</ttc>: removed "(Avg %Sim)" on AA and NT pairs. Slight change to KaKs counts.
+(2) <ttc>Pair Filter</ttc>: If KaKs set to be at least &gt;=0.0, got 
+Kaks with no values or NA. If pairs&clusters removed, pairs added but no clusters, the
+pairs filter crashed. 
+(3) <ttc>Sequence Table</ttc>: check to see if it is !NTonly database, if so, do
+not give options of Export CDS/NT sequence. If !GO, do not give option of exports GOs.
+<li><ttc>Details</ttc>: Add <ttc>Copy...</ttc> option to copy the displayed Detail sequence.
+</ul>
+
 <a name=v342>
 <h4>v3.4.2 8-Mar-2022</h4>
 A few improvements and tiny little bug fixes.

doc/index.html

@@ -11,6 +11,7 @@
 
 <tr><td colspan=3> Getting started</td></tr>
 <tr>	<td>&nbsp;&nbsp;<td><a href="Summary.html">Summary</a>		<td>A summary of the input, processing and suite of programs.
+<tr>	<td>&nbsp;&nbsp;<td><a href="./tour">TCW Tour</a> </td> 	<td>Snapshots of different TCW screens</td></tr>
 
 <tr>	<td>&nbsp;&nbsp;<td><a href="Install.html">Installation</a><td>Installing TCW and other necessary and optional software.
 <tr>	<td colspan=3>&nbsp;&nbsp;
@@ -46,7 +47,6 @@
 <tr>	<td colspan=3>&nbsp;&nbsp;
 <tr><td colspan=3> Other docs</td></tr>
 <tr>	<td>&nbsp;&nbsp;<td><a href="External.html">External Software</a></td><td>Packages used by TCW</td></tr>
-<tr>	<td>&nbsp;&nbsp;<td><a href="./tour">TCW Tour</a> </td> 	<td>Snapshots of different TCW screens</td></tr>
 
 <tr>	<td>&nbsp;&nbsp;<td><a href="Mac-OSX.html">MacOS</a></td>	<td>Installing MySQL, etc on MacOS</td></tr>
 <tr>	<td>&nbsp;&nbsp;<td><a href="./Trouble.html">Trouble Shooting</a></td>

doc/mtcw/UserGuide.html

@@ -558,8 +558,8 @@ <h4>Details on running <ttp>KaKs_calculator</ttp></h4>
 called <ttx>runKaKs</ttx> which has the commands to run the <ttp>KaKs_calculator</ttp>
 on each file, e.g. 
 <pre>
-/Users/cari/Workspace/TCW_3/Ext/mac/KaKs_Calculator -i oTCW1.awt -o iTCW1.tsv -m YN &amp;
-/Users/cari/Workspace/TCW_3/Ext/mac/KaKs_Calculator -i oTCW2.awt -o iTCW2.tsv -m YN &amp;
+/Users/cari/Workspace/TCW_4/Ext/mac/KaKs_Calculator -i oTCW1.awt -o iTCW1.tsv -m YN &amp;
+/Users/cari/Workspace/TCW_4/Ext/mac/KaKs_Calculator -i oTCW2.awt -o iTCW2.tsv -m YN &amp;
 </pre>
 The only reason the method "YN" is used here is because it is fastest; this should probably
 be changed. The default method is "MA", which will be used if you remove the "-m YN" on all lines.

doc/ov/mDemo.html

@@ -1,24 +1,23 @@
 <html><title>mTCW_ex overview</title><body><center>
 <h2>mTCW overview for ex</h2>
-<table width=600 border=1><tr><td><pre>Project: ex  Cluster: 1.3k  Pairs: 846  Seqs: 707  Hits: 4.0k   PCC Stats KaKs Multi
+<table width=600 border=1><tr><td><pre>Project: ex  Cluster: 1.0k  Pairs: 846  Seqs: 707  Hits: 4.0k  GOs: 8.0k   PCC Stats KaKs Multi
 
-Created: 28-Feb-22 v3.4.2
+Created: 15-Mar-22 v4.0.0     Last Update: 20-Mar-22 v4.0.0
 
 DATASETS: 3
            Type  #Seq  #annotated  #annoDB  Created    Remark  
-      bar  NT     250         250        3  25-Feb-22  exBar   
-      fly  NT     207         207        3  13-Aug-21  exFly   
-      foo  NT     250         250        3  13-Aug-21  exFoo   
+      bar  NT     250         250        3  15-Mar-22  exBar   
+      fly  NT     207         207        3  15-Mar-22  exFly   
+      foo  NT     250         250        3  15-Mar-22  exFoo   
 
-CLUSTER SETS: 6
+CLUSTER SETS: 5
    Statistics
       Prefix  Method         conLen  sdLen     Score1  SD    Score2  SD    
       CL      Closure        579.80  58.50       0.48  0.08    0.78  0.15  
-      OM      orthoMCL.OM-4  606.37  85.26       0.45  0.10    0.75  0.16  
+      OM      orthoMCL.OM-4  606.32  85.26       0.45  0.10    0.75  0.16  
       B12     BBH bar,fly    540.22  62.63       0.50  0.07    0.72  0.18  
       B13     BBH bar,foo    558.75  34.11       0.53  0.07    0.79  0.15  
       B23     BBH fly,foo    559.57  70.82       0.47  0.08    0.80  0.21  
-      OM2     orthoMCL.OM-4  606.32  85.26       0.45  0.10    0.75  0.16  
 
    Sizes
       Prefix   =2   =3  4-5  6-10  11-15  16-20  21-25  >25  Total  #Seqs  
@@ -27,12 +26,11 @@ <h2>mTCW overview for ex</h2>
       B12     157    0    0     0      0      0      0    0    157  44.4%  
       B13     239    0    0     0      0      0      0    0    239  67.6%  
       B23     166    0    0     0      0      0      0    0    166  47.0%  
-      OM2      50  186    3     3      0      0      0    0    242  98.0%  
 
 PAIRS: 846
    Hits
-      AA   Diff 753     Same 60       Similarity 76.4% (77.0%)  Coverage 84.7% (86.6%)
-      NT   Diff 663     Same 4        Similarity 86.4% (87.0%)  Coverage 59.4% (63.7%)
+      AA   Diff 753     Same 60       Similarity 76.4%   Coverage 84.7% 
+      NT   Diff 663     Same 4        Similarity 86.4%   Coverage 59.4% 
 
    Aligned: 700   CDS: 1.0Mb   5UTR: 61.5kb   3UTR: 96.5kb
       Codons         311.0k     Amino Acids                Nucleotides         
@@ -49,10 +47,10 @@ <h2>mTCW overview for ex</h2>
 
    KaKs method: YN    Pairs: 700
       Ka/Ks           Quartiles             Average            P-value       
-      NA       16     Q1(Lower)   0.019     Ka       0.102     <1E-100  419  
-      KaKs~1    0     Q2(Median)  0.044     Ks       2.793     <1E-10    85  
-      KaKs<1  675     Q3(Upper)   0.113     P-value  0.036     <0.001    44  
-      KaKs>1    9                                              Other    152  
+      NA       16     Q1(Lower)   0.019     Ka       0.102     NA        48  
+      KaKs<1  675     Q2(Median)  0.044     Ks       2.793     <1E-100  419  
+      KaKs~1    0     Q3(Upper)   0.113     P-value  0.036     <1E-10    85  
+      KaKs>1    9                                              <1.0     148  
 
 SEQUENCES: 707
            Average  Lengths              %GC                     CpG O/E                
@@ -86,6 +84,5 @@ <h2>mTCW overview for ex</h2>
       B12     BBH           Sim 60; Cov 40(Both); AA; bar,fly  
       B13     BBH           Sim 60; Cov 40(Both); AA; bar,foo  
       B23     BBH           Sim 60; Cov 40(Both); AA; fly,foo  
-      OM2     User Defined  orthoMCL.OM-4                      
 
 </pre></table></body></html>

doc/ov/sDemo.html

@@ -5,10 +5,10 @@
 <h2>Overview for sTCW_demoTra </h2>
 <table width=700 border=1><tr><td>
 <pre>
-Project:  tra   #Seqs: 211   #Hits: 11,957   #GOs: 6,076    TPM  Seq-DE  GO-Enrich   Pairs
+Project:  tra   #Seqs: 211   #Hits: 12,296   #GOs: 6,144    TPM  Seq-DE  GO-Enrich   Pairs
 
-28-Feb-22 Build Database  sequences loaded from external source
-06-Mar-22 Last Annotation with sTCW v3.4.2
+15-Mar-22 Build Database  sequences loaded from external source
+15-Mar-22 Last Annotation with sTCW v4.0.0
 
 INPUT
    Counts:
@@ -23,40 +23,40 @@ <h2>Overview for sTCW_demoTra </h2>
 
 ANNOTATION
    Hit statistics:
-      Sequences with hits     210  (99.5%)     Bases covered by hit  180,288  (79.2%)  
-      Unique hits          11,957              Total bases           227,683           
-      Total sequence hits  17,549                                                      
+      Sequences with hits     210  (99.5%)     Bases covered by hit  180,339  (79.2%)  
+      Unique hits          12,296              Total bases           227,683           
+      Total sequence hits  17,763                                                      
 
    Annotation databases (annoDBs): 7   (see Legend below)
       ANNODB            ONLY  BITS  ANNO  UNIQUE  TOTAL   AVG  Rank  HAS (%Seqs)   AVG  COVER  COVER  
                                                          %SIM   =1   HIT          %SIM   >=50   >=90  
       SP-plants            0     0     0   1,344  2,959  53.8    |   193 (91.5%)  70.0  61.7%   3.1%  
-      SP-invertebrates     0     0     0     624  1,271  42.5    |   126 (59.7%)  47.5  30.2%   0.8%  
-      SP-fungi             0     0     0     895  1,516  43.1    |   121 (57.3%)  46.5  24.8%   0.8%  
+      SP-invertebrates     0     0     0     624  1,270  42.5    |   126 (59.7%)  47.5  30.2%   0.8%  
+      SP-fungi             0     0     0     896  1,517  43.0    |   122 (57.8%)  46.4  24.6%   0.8%  
       SP-bacteria          0     0     0     790  1,126  44.1    |    63 (29.9%)  45.8  25.4%     0%  
-      SP-full_BFIP         0     0     0     740  1,742  45.4    |   144 (68.2%)  47.5  25.0%   0.7%  
-      TR-plants            8   207   207   4,614  5,235  76.0    |   210 (99.5%)  82.3  68.6%  11.0%  
-      TR-invertebrates     0     3     3   2,950  3,700  50.0    |   181 (85.8%)  54.3  38.7%   2.2%  
+      SP-full_BFIP         0     0     0     744  1,696  45.7    |   125 (59.2%)  49.1  32.0%   0.8%  
+      TR-plants            7   207   207   4,626  5,241  76.0    |   210 (99.5%)  82.3  68.6%  11.0%  
+      TR-invertebrates     0     3     3   3,272  3,954  48.9    |   186 (88.2%)  53.8  37.6%   2.2%  
 
-   Top 15 species from total: 1,571
+   Top 15 species from total: 1,594
       SPECIES (25 char)         BITS   ANNO  TOTAL     SPECIES                 BITS   ANNO   TOTAL  
-      Musa acuminata              97      2    491     Dendrobium catenatum       2      2      70  
-      Musa balbisiana             52     71    313     Macleaya cordata           2      2      38  
-      Elaeis guineensis           12     45    351     Pinus tabuliformis         2      2       4  
-      Ensete ventricosum          11     14    207     Curcuma alismatifolia      2      2       2  
-      Zingiber officinale          7      7     27     Vitis vinifera             1      3      86  
-      Ananas comosus               3     17    452     Apostasia shenzhenica      1      3      60  
-      Meloidogyne enterolobii      3      2     10     Ricinus communis           1      2      41  
-      Anthurium amnicola           2      4     96     Other                     12     32  15,301  
+      Musa acuminata              97      2    490     Dendrobium catenatum       2      2      70  
+      Musa balbisiana             52     71    312     Macleaya cordata           2      2      38  
+      Elaeis guineensis           12     45    347     Curcuma alismatifolia      2      2       2  
+      Ensete ventricosum          11     14    206     Vitis vinifera             1      3      86  
+      Zingiber officinale          7      7     27     Apostasia shenzhenica      1      3      59  
+      Ananas comosus               3     17    456     Ricinus communis           1      2      41  
+      Meloidogyne enterolobii      3      2     10     Pinus tabuliformis         1      2       4  
+      Anthurium amnicola           2      4     96     Other                     13     32  15,519  
 
    Gene ontology statistics:
-      Unique GOs          6,076              Unique hits with GOs  10,332  (86.4%)  
+      Unique GOs          6,144              Unique hits with GOs  10,632  (86.5%)  
       Sequences with GOs    208  (98.6%)     Seq best hit has GOs     107  (50.7%)  
       Has goslim_plant       94                                                     
 
-      biological_process  4,387  (72.2%)     is_a                   9,762           
-      molecular_function    967  (15.9%)     part_of                1,044           
-      cellular_component    722  (11.9%)                                            
+      biological_process  4,442  (72.3%)     is_a                   9,866           
+      molecular_function    979  (15.9%)     part_of                1,057           
+      cellular_component    723  (11.8%)                                            
 
 EXPRESSION
    TPM: (% of 211)
@@ -71,11 +71,11 @@ <h2>Overview for sTCW_demoTra </h2>
       StOl  0 (0%)   2 (1%)  12 (6%)  65(31%)  101(48%)  
       RoOl  1(<1%)  16 (8%)  37(18%)  74(35%)  110(52%)  
 
-   Gene ontology enrichment:  (% of 6,076)
+   Gene ontology enrichment:  (% of 6,144)
              <1E-5   <1E-4  <0.001    <0.01     <0.05  
-      StRo  0 (0%)  0 (0%)  4(<1%)  59 (1%)  310 (5%)  
-      StOl  0 (0%)  0 (0%)  0 (0%)   1(<1%)   40 (1%)  
-      RoOl  0 (0%)  1(<1%)  2(<1%)  26(<1%)  182 (3%)  
+      StRo  0 (0%)  1(<1%)  6(<1%)  59 (1%)  306 (5%)  
+      StOl  0 (0%)  0 (0%)  0 (0%)   1(<1%)   43 (1%)  
+      RoOl  0 (0%)  1(<1%)  2(<1%)  26(<1%)  183 (3%)  
 
 SEQUENCES
    Sequence lengths:
@@ -91,7 +91,7 @@ <h2>Overview for sTCW_demoTra </h2>
       0(0%)  62(29%)   92(44%)    47(22%)      4(2%)      6(3%)      0(0%)  0(0%)  
 
    ORF stats:   Average length 862
-      Has Hit            210  (99.5%)    Both Ends     69  (32.7%)    Multi-frame    4   (1.9%)  
+      Has Hit            210  (99.5%)    Both Ends     69  (32.7%)    Multi-frame    6   (2.8%)  
       Is Longest ORF     192  (91.0%)    ORF>=300     190  (90.0%)    Stops in Hit   6   (2.8%)  
       Markov Best Score  210  (99.5%)    ORF=Hit      109  (51.7%)    >=9 Ns in ORF  1    (<1%)  
       All of the above   191  (90.5%)      with Ends   32  (15.2%)                               
@@ -116,18 +116,18 @@ <h2>Overview for sTCW_demoTra </h2>
 -------------------------------------------------------------------
 PROCESSING INFORMATION
    AnnoDB files:
-      Type  Taxo           FILE                                DB DATE    ADD DATE   EXECUTE                  
-      sp    plants         uniprot_sprot_plants.fasta          27-Jan-21  06-Mar-22  Load tra_SPpla.dmnd.tab  
-      sp    invertebrates  uniprot_sprot_invertebrates.fasta   27-Jan-21  06-Mar-22  Load tra_SPinv.dmnd.tab  
-      sp    fungi          uniprot_sprot_fungi.fasta           27-Jan-21  06-Mar-22  Load tra_SPfun.dmnd.tab  
-      sp    bacteria       uniprot_sprot_bacteria.fasta        27-Jan-21  06-Mar-22  Load tra_SPbac.dmnd.tab  
-      sp    full_BFIP      uniprot_sprot_xBFxIxPxxx.fasta      27-Jan-21  06-Mar-22  Load tra_SPful.dmnd.tab  
-      tr    plants         uniprot_trembl_plants.fasta         27-Jan-21  06-Mar-22  Load tra_TRpla.dmnd.tab  
-      tr    invertebrates  uniprot_trembl_invertebrates.fasta  27-Jan-21  06-Mar-22  Load tra_TRinv.dmnd.tab  
+      Type  Taxo           FILE                                DB DATE    ADD DATE   EXECUTE               
+      sp    plants         uniprot_sprot_plants.fasta          27-Jan-21  15-Mar-22  diamond  --masking 0  
+      sp    invertebrates  uniprot_sprot_invertebrates.fasta   27-Jan-21  15-Mar-22  diamond  --masking 0  
+      sp    fungi          uniprot_sprot_fungi.fasta           27-Jan-21  15-Mar-22  diamond  --masking 0  
+      sp    bacteria       uniprot_sprot_bacteria.fasta        27-Jan-21  15-Mar-22  diamond  --masking 0  
+      sp    full_BFIP      uniprot_sprot_xBFxIxPxxx.fasta      27-Jan-21  15-Mar-22  diamond  --masking 0  
+      tr    plants         uniprot_trembl_plants.fasta         27-Jan-21  15-Mar-22  diamond  --masking 0  
+      tr    invertebrates  uniprot_trembl_invertebrates.fasta  27-Jan-21  15-Mar-22  diamond  --masking 0  
 
    Prune: none
 
-   Gene ontology: go-basic.obo-Nov2021  GOdb: go_demo  [GOs added with sTCW v3.4.2]
+   Gene ontology: go-basic.obo-Nov2021  GOdb: go_demo  [GOs added with sTCW v4.0.0]
    GO slim: goslim_plant
 
    ORF finder:

doc/stcw/AnnoDBs.html

@@ -106,7 +106,7 @@ <h2>Demo annotation setup </h2>
 		<td class="top"> The TCW package provides subsets of UniProt for annotating the demo. 
 		In order to add GO annotations, a local GO mySQL 'demo' database needs to be created. 
 		<ol type="A">
-			<li>From the TCW_3 directory, execute:
+			<li>From the TCW_4 directory, execute:
 			<br><ttx>./runAS -d</ttx>		
 			<br>The "-d" will cause it to enter the demo parameters, as shown on the right. 
 			The highlighted entries already exist. Its only necessary to build the GO database. 
@@ -168,11 +168,10 @@ <h2>Java graphical interface -- <ttp>runAS</ttp> </h2>
 			that contains all the information downloaded; this can be used as input to <ttp>runSingleTCW</ttp> 
 			(see <a href="#runstcw">Import AnnoDBs</a>). <br>
 			&nbsp; 
-			<li><ttc>Check</ttc>: Selecting this button highlights everything that has been done. 
-			For example, the figure on the right shows that fungi and plant SwissProt have been downloaded and processed.
-			If <ttc>Build Tax</ttc> is run again, 3 more SwissProt and plant TrEMBL will be downloaded and processed.
-			The Full SwissProt and the GOdb have not been done. 
-			The <ttc>Check</ttc> automatically runs on startup. 
+			<li><ttc>Check</ttc>: The Check function automatically runs on startup and after any Build.
+			It highlights everything that has been done. 
+			For example, the figure on the right shows that fungi and plant SwissProt have been downloaded and processed. 
+			<i>To force a check, or to view the UniProts in an existing goDB,  select this button.</i>
 		</ol>
 		<td><a href="img/runAS.png"><img src="img/runAS.png" alt="runAS" style="border: 1px solid black; width: 350px"></a>
 	</tr>