| Previous changeset 0:b1ac138f0287 (2015-01-26) Next changeset 2:4db310b7e37c (2016-01-25) |
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Commit message:
Uploaded |
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modified:
Hammock/dist/Hammock.jar Hammock/settings/settings.prop hammock.xml |
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added:
Hammock/settings/misc/blosum62.freq_rownorm |
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removed:
Hammock/settings/settings-hhalign.txt |
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| diff -r b1ac138f0287 -r d90f4809ccc6 Hammock/dist/Hammock.jar |
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| Binary file Hammock/dist/Hammock.jar has changed |
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| diff -r b1ac138f0287 -r d90f4809ccc6 Hammock/settings/misc/blosum62.freq_rownorm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/settings/misc/blosum62.freq_rownorm Fri Aug 28 07:38:12 2015 -0400 |
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| @@ -0,0 +1,25 @@ +# BLOSUM Clustered Target Frequencies=qij +# Blocks Database = /data/blocks_5.0/blocks.dat +# Cluster Percentage: >= 62 +# Normalized frequencies (by row) from file: blosum62.qij +A R N D C Q E G H I L K M F P S T W Y V +0.2901 0.0310 0.0256 0.0297 0.0216 0.0256 0.0405 0.0783 0.0148 0.0432 0.0594 0.0445 0.0175 0.0216 0.0297 0.0850 0.0499 0.0054 0.0175 0.0688 +0.0446 0.3450 0.0388 0.0310 0.0078 0.0484 0.0523 0.0329 0.0233 0.0233 0.0465 0.1202 0.0155 0.0174 0.0194 0.0446 0.0349 0.0058 0.0174 0.0310 +0.0427 0.0449 0.3169 0.0831 0.0090 0.0337 0.0494 0.0652 0.0315 0.0225 0.0315 0.0539 0.0112 0.0180 0.0202 0.0697 0.0494 0.0045 0.0157 0.0270 +0.0410 0.0299 0.0690 0.3974 0.0075 0.0299 0.0914 0.0466 0.0187 0.0224 0.0280 0.0448 0.0093 0.0149 0.0224 0.0522 0.0354 0.0037 0.0112 0.0243 +0.0650 0.0163 0.0163 0.0163 0.4837 0.0122 0.0163 0.0325 0.0081 0.0447 0.0650 0.0203 0.0163 0.0203 0.0163 0.0407 0.0366 0.0041 0.0122 0.0569 +0.0559 0.0735 0.0441 0.0471 0.0088 0.2147 0.1029 0.0412 0.0294 0.0265 0.0471 0.0912 0.0206 0.0147 0.0235 0.0559 0.0412 0.0059 0.0206 0.0353 +0.0552 0.0497 0.0405 0.0902 0.0074 0.0645 0.2965 0.0350 0.0258 0.0221 0.0368 0.0755 0.0129 0.0166 0.0258 0.0552 0.0368 0.0055 0.0166 0.0313 +0.0783 0.0229 0.0391 0.0337 0.0108 0.0189 0.0256 0.5101 0.0135 0.0189 0.0283 0.0337 0.0094 0.0162 0.0189 0.0513 0.0297 0.0054 0.0108 0.0243 +0.0420 0.0458 0.0534 0.0382 0.0076 0.0382 0.0534 0.0382 0.3550 0.0229 0.0382 0.0458 0.0153 0.0305 0.0191 0.0420 0.0267 0.0076 0.0573 0.0229 +0.0471 0.0177 0.0147 0.0177 0.0162 0.0133 0.0177 0.0206 0.0088 0.2710 0.1679 0.0236 0.0368 0.0442 0.0147 0.0250 0.0398 0.0059 0.0206 0.1767 +0.0445 0.0243 0.0142 0.0152 0.0162 0.0162 0.0202 0.0213 0.0101 0.1154 0.3755 0.0253 0.0496 0.0547 0.0142 0.0243 0.0334 0.0071 0.0223 0.0962 +0.0570 0.1071 0.0415 0.0415 0.0086 0.0535 0.0708 0.0432 0.0207 0.0276 0.0432 0.2781 0.0155 0.0155 0.0276 0.0535 0.0397 0.0052 0.0173 0.0328 +0.0522 0.0321 0.0201 0.0201 0.0161 0.0281 0.0281 0.0281 0.0161 0.1004 0.1968 0.0361 0.1606 0.0482 0.0161 0.0361 0.0402 0.0080 0.0241 0.0924 +0.0338 0.0190 0.0169 0.0169 0.0106 0.0106 0.0190 0.0254 0.0169 0.0634 0.1142 0.0190 0.0254 0.3869 0.0106 0.0254 0.0254 0.0169 0.0888 0.0550 +0.0568 0.0258 0.0233 0.0310 0.0103 0.0207 0.0362 0.0362 0.0129 0.0258 0.0362 0.0413 0.0103 0.0129 0.4935 0.0439 0.0362 0.0026 0.0129 0.0310 +0.1099 0.0401 0.0541 0.0489 0.0175 0.0332 0.0524 0.0663 0.0192 0.0297 0.0419 0.0541 0.0157 0.0209 0.0297 0.2199 0.0820 0.0052 0.0175 0.0419 +0.0730 0.0355 0.0434 0.0375 0.0178 0.0276 0.0394 0.0434 0.0138 0.0533 0.0651 0.0454 0.0197 0.0237 0.0276 0.0927 0.2465 0.0059 0.0178 0.0710 +0.0303 0.0227 0.0152 0.0152 0.0076 0.0152 0.0227 0.0303 0.0152 0.0303 0.0530 0.0227 0.0152 0.0606 0.0076 0.0227 0.0227 0.4924 0.0682 0.0303 +0.0405 0.0280 0.0218 0.0187 0.0093 0.0218 0.0280 0.0249 0.0467 0.0436 0.0685 0.0312 0.0187 0.1308 0.0156 0.0312 0.0280 0.0280 0.3178 0.0467 +0.0700 0.0219 0.0165 0.0178 0.0192 0.0165 0.0233 0.0247 0.0082 0.1646 0.1303 0.0261 0.0316 0.0357 0.0165 0.0329 0.0494 0.0055 0.0206 0.2689 |
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| diff -r b1ac138f0287 -r d90f4809ccc6 Hammock/settings/settings-hhalign.txt --- a/Hammock/settings/settings-hhalign.txt Mon Jan 26 06:24:21 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -hhalignParameters=-realign -id 100 -diff inf -alt 1 -corr 0 -shift 0 -ssm 0 -nocontxt -pcm 2 -tags -nocons -nopred -nodssp -M a2m -alt 1 -sc 0 -v 0 -z 2 -Z 500000 -local -mact 0.0 -p 0 |
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| diff -r b1ac138f0287 -r d90f4809ccc6 Hammock/settings/settings.prop --- a/Hammock/settings/settings.prop Mon Jan 26 06:24:21 2015 -0500 +++ b/Hammock/settings/settings.prop Fri Aug 28 07:38:12 2015 -0400 |
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| @@ -14,13 +14,12 @@ #hmmDirectory= #hhDirectory= #hmmsearchOutDirectory= -#hhalignOutDirectory= #hhsearchOutDirectory= #fastaDatabaseFile= #Tool parameters. Generally, it is not recommended to change this section. clustalOmegaParameters= -hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino -hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 -hmmalignParameters=--outformat selex --amino +hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino --seed 42 +hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 --seed 42 +hmmalignParameters=--outformat selex --amino --seed 42 hhmakeParameters=-M a2m -id 100 -diff inf -pcm 3 -nocontxt -v 0 -hhsearchParameters=-norealign -alt 1 -corr 0 -shift 0 -ssm 0 -tags -nocons -nopred -nodssp -sc 0 -v 0 -z 2 -Z 500000 -local -p 0.0 -vit -b 100.0 -E 100.0 -e 100.0 -z 100 -BLOSUM65 +hhsearchParameters=-norealign -alt 1 -corr 0 -shift 0 -ssm 0 -tags -nocons -nopred -nodssp -sc 0 -v 0 -z 2 -Z 500000 -local -p 0.0 -vit -b 100.0 -E 100.0 -e 100.0 -z 100 |
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| diff -r b1ac138f0287 -r d90f4809ccc6 hammock.xml --- a/hammock.xml Mon Jan 26 06:24:21 2015 -0500 +++ b/hammock.xml Fri Aug 28 07:38:12 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="hammock_1.0" name="Hammock - cluster peptides"> +<tool id="hammock_1.0" name="Hammock - cluster peptides" version="1.0.2" hidden="false"> <description>Clusters short peptide sequences</description> @@ -15,6 +15,12 @@ #if $advanced_greedy_params.set_greedy_params == "set": -x $advanced_greedy_params.max_shift -p $advanced_greedy_params.shift_penalty + -R $advanced_greedy_params.set_order.order + + #if $advanced_greedy_params.set_order.order == "random": + -S $advanced_greedy_params.set_order.seed + #end if + -m \${MATRIX_PATH}${advanced_greedy_params.scoring_matrix}.txt #if $advanced_greedy_params.greedy_params.set_greedy == "set": -g $advanced_greedy_params.greedy_params.greedy_threshold @@ -103,6 +109,24 @@ <param name="shift_penalty" type="integer" value="0" label="Sequence shift penalty" help="Score penalty added to to each alignment score during greedy clustering. This penalty is added for every amino acid aligned towards a (trailing) gap. This value should typically be non-positive (With a positive value, sequences benefit from containing more gaps). See -p, --gap penalty in manual for details."/> + <conditional name="set_order"> + + <param name="order" type="select" label="Greedy clustering order" help="Select the order of sequences during the greedy clustering. See -R, --order in manual for details."> + <option value="size">Size</option> + <option value="alphabetic">Alphabetic</option> + <option value="random">Random</option> + </param> + + <when value="size" /> + <when value="alphabetic" /> + <when value="random"> + <param name="seed" type="integer" value="42" label="Seed for random number generation" help="Set a seed value for the pseudorandom sequence order. See -S, --seed in manual for details."/> + </when> + + </conditional> + + + <param name="scoring_matrix" type="select" label="Substitiution matrix schema." help="Select a substitution matrix to be used to score alignments during glreedy clustering. See -m, --matrix in manual for details."> <option value="blosum62">Blosum 62</option> <option value="blosum30">Blosum 30</option> |