1 | |
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2 | item:ClustalW automatic |
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3 | itemmeta: W |
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4 | itemmethod:(GOTO_LOCAL_DIR; \ |
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5 | tr '"%//' '>' <in1 >clus_in; \ |
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6 | RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align ; \ |
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7 | cat clus_in.pir | sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | sed "s/^\*$//g" >out1; )); \ |
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8 | RM_LOCAL_FILES(clus_in* in1)) |
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9 | |
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10 | itemhelp:clustalw.help |
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11 | |
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12 | |
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13 | in:in1 |
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14 | informat:flat |
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15 | insave: |
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16 | |
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17 | out:out1 |
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18 | outformat:flat |
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19 | |
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20 | // -------------------------------------------------------------------------------- |
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21 | |
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22 | item:Create ClustalW Profile 2 |
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23 | itemmeta: C |
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24 | itemmethod:(GOTO_LOCAL_DIR ; tr '"%//' '>' <in1 >../clus_prf ; RM_LOCAL_FILES(in1)) |
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25 | |
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26 | itemhelp:clustalw.help |
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27 | |
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28 | in:in1 |
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29 | informat:flat |
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30 | insave: |
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31 | |
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32 | // -------------------------------------------------------------------------------- |
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33 | |
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34 | item:ClustalW Profile Alignment |
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35 | itemmeta: P |
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36 | itemmethod:(GOTO_LOCAL_DIR; \ |
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37 | tr '"%//' '>' <in1 >clus_in; \ |
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38 | RUN_IN_WINDOW((clustalw -output=PIR -profile1=clus_in -profile2=../clus_prf -align ; \ |
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39 | cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >out1; )); \ |
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40 | RM_LOCAL_FILES(clus_in* in1)) |
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41 | |
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42 | itemhelp:clustalw.help |
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43 | |
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44 | |
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45 | in:in1 |
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46 | informat:flat |
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47 | insave: |
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48 | |
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49 | out:out1 |
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50 | outformat:flat |
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51 | |
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52 | // -------------------------------------------------------------------------------- |
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53 | |
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54 | item:ClustalW DNA Alignment (fast) |
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55 | seqtype: N |
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56 | itemmeta: N |
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57 | itemmethod:(GOTO_LOCAL_DIR; \ |
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58 | tr '"%//' '>' <in1 >clus_in ; \ |
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59 | RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \ |
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60 | -quicktree $INTERACTIVE \ |
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61 | -ktuple=$KTUPLE -topdiags=$TOPDIAGS \ |
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62 | -window=$WINDOW -pairgap=$PAIRGAP \ |
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63 | -score=$SCORE \ |
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64 | -type=DNA -transweight=$TRANSWEIGHT \ |
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65 | -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \ |
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66 | -dnamatrix=$DNAMATRIX; \ |
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67 | cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >out1; )) ; \ |
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68 | RM_LOCAL_FILES(clus_in* in1)) |
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69 | |
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70 | itemhelp:clustalw.help |
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71 | |
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72 | // parameters for fast pairwise alignment: |
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73 | |
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74 | arg:PAIRGAP |
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75 | arglabel:Gap penalty (pairwise ali) |
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76 | argtype:slider |
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77 | argmin:1 |
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78 | argmax:500 |
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79 | argvalue:5 |
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80 | |
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81 | arg:KTUPLE |
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82 | arglabel:K-tuple size |
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83 | argtype:slider |
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84 | argmin:1 |
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85 | argmax:4 |
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86 | argvalue:2 |
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87 | |
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88 | arg:TOPDIAGS |
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89 | arglabel:No. of top diagonals |
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90 | argtype:slider |
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91 | argmin:1 |
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92 | argmax:50 |
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93 | argvalue:4 |
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94 | |
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95 | arg:WINDOW |
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96 | arglabel:Window size |
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97 | argtype:slider |
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98 | argmin:1 |
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99 | argmax:50 |
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100 | argvalue:4 |
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101 | |
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102 | // parameters for multiple alignment: |
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103 | |
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104 | arg:DNAMATRIX |
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105 | argtype:choice_menu |
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106 | arglabel:Weighting matrix (multiple ali) |
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107 | argchoice:IUB:IUB |
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108 | argchoice:CLUSTALW:CLUSTALW |
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109 | |
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110 | arg:GOP |
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111 | argtype:slider |
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112 | arglabel:Gap Open Penalty |
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113 | argmin:0 |
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114 | argmax:100 |
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115 | argvalue:15 |
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116 | |
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117 | arg:GEP |
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118 | arglabel:Gap Extend Penalty |
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119 | argtype:slider |
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120 | argmin:0 |
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121 | argmax:10 |
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122 | argvalue:6.66 |
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123 | |
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124 | arg:MAXDIV |
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125 | arglabel:% identity for delay |
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126 | argtype:slider |
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127 | argmin:0 |
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128 | argmax:100 |
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129 | argvalue:30 |
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130 | |
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131 | arg:TRANSWEIGHT |
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132 | arglabel:Transition weight |
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133 | argtype:slider |
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134 | argmin:0.0 |
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135 | argmax:1.0 |
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136 | argvalue:0.5 |
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137 | |
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138 | arg:INTERACTIVE |
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139 | arglabel:Interactive |
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140 | argtype:choice_menu |
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141 | argchoice:No: |
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142 | argchoice:Yes:-interactive |
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143 | |
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144 | in:in1 |
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145 | informat:flat |
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146 | insave: |
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147 | |
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148 | out:out1 |
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149 | outformat:flat |
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150 | |
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151 | // -------------------------------------------------------------------------------- |
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152 | |
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153 | item:ClustalW DNA Alignment (slow & accurate) |
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154 | seqtype: N |
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155 | itemmeta: s |
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156 | itemmethod:(GOTO_LOCAL_DIR; \ |
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157 | tr '"%//' '>' <in1 >clus_in ; \ |
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158 | RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \ |
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159 | $INTERACTIVE \ |
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160 | -pwdnamatrix=$PWDNAMATRIX \ |
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161 | -pwgapopen=$PWGOP -pwgapext=$PWGEP \ |
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162 | -type=DNA -transweight=$TRANSWEIGHT \ |
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163 | -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \ |
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164 | -dnamatrix=$DNAMATRIX; \ |
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165 | cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >out1; )) ; \ |
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166 | RM_LOCAL_FILES(clus_in* in1)) |
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167 | |
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168 | itemhelp:clustalw.help |
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169 | |
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170 | // parameters for pairwise alignment: |
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171 | |
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172 | arg:PWDNAMATRIX |
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173 | argtype:choice_menu |
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174 | arglabel:Weighting matrix (pairwise ali) |
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175 | argchoice:IUB:IUB |
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176 | argchoice:CLUSTALW:CLUSTALW |
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177 | |
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178 | arg:PWGOP |
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179 | argtype:slider |
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180 | arglabel:Gap Open Penalty |
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181 | argmin:0 |
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182 | argmax:100 |
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183 | argvalue:15 |
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184 | |
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185 | arg:PWGEP |
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186 | arglabel:Gap Extend Penalty |
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187 | argtype:slider |
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188 | argmin:0 |
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189 | argmax:10 |
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190 | argvalue:6.66 |
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191 | |
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192 | // parameters for multiple alignment: |
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193 | |
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194 | arg:DNAMATRIX |
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195 | argtype:choice_menu |
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196 | arglabel:Weighting matrix (multiple ali) |
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197 | argchoice:IUB:IUB |
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198 | argchoice:CLUSTALW:CLUSTALW |
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199 | |
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200 | arg:GOP |
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201 | argtype:slider |
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202 | arglabel:Gap Open Penalty |
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203 | argmin:0 |
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204 | argmax:100 |
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205 | argvalue:15 |
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206 | |
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207 | arg:GEP |
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208 | arglabel:Gap Extend Penalty |
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209 | argtype:slider |
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210 | argmin:0 |
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211 | argmax:10 |
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212 | argvalue:6.66 |
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213 | |
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214 | arg:MAXDIV |
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215 | arglabel:% identity for delay |
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216 | argtype:slider |
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217 | argmin:0 |
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218 | argmax:100 |
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219 | argvalue:30 |
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220 | |
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221 | arg:TRANSWEIGHT |
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222 | arglabel:Transition weight |
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223 | argtype:slider |
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224 | argmin:0.0 |
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225 | argmax:1.0 |
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226 | argvalue:0.5 |
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227 | |
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228 | arg:INTERACTIVE |
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229 | arglabel:Interactive |
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230 | argtype:choice_menu |
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231 | argchoice:No: |
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232 | argchoice:Yes:-interactive |
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233 | |
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234 | in:in1 |
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235 | informat:flat |
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236 | insave: |
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237 | |
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238 | out:out1 |
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239 | outformat:flat |
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240 | |
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241 | // -------------------------------------------------------------------------------- |
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242 | |
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243 | item:ClustalW Protein Alignment (fast) |
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244 | seqtype: A |
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245 | itemmeta: o |
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246 | itemmethod:(GOTO_LOCAL_DIR; \ |
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247 | tr '"%//' '>' <in1 >clus_in ; \ |
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248 | RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \ |
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249 | -quicktree $INTERACTIVE \ |
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250 | -ktuple=$KTUPLE -topdiags=$TOPDIAGS \ |
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251 | -window=$WINDOW -pairgap=$PAIRGAP \ |
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252 | -score=$SCORE \ |
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253 | -type=PROTEIN -transweight=$TRANSWEIGHT \ |
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254 | -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \ |
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255 | -matrix=$MATRIX $NEGMATRIX; \ |
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256 | cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >out1; )) ; \ |
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257 | RM_LOCAL_FILES(clus_in* in1)) |
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258 | |
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259 | itemhelp:clustalw.help |
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260 | |
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261 | // parameters for fast pairwise alignment: |
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262 | |
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263 | arg:PAIRGAP |
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264 | arglabel:Gap penalty (pairwise ali) |
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265 | argtype:slider |
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266 | argmin:1 |
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267 | argmax:500 |
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268 | argvalue:3 |
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269 | |
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270 | arg:KTUPLE |
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271 | arglabel:K-tuple size |
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272 | argtype:slider |
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273 | argmin:1 |
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274 | argmax:2 |
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275 | argvalue:1 |
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276 | |
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277 | arg:TOPDIAGS |
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278 | arglabel:No. of top diagonals |
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279 | argtype:slider |
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280 | argmin:1 |
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281 | argmax:50 |
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282 | argvalue:5 |
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283 | |
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284 | arg:WINDOW |
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285 | arglabel:Window size |
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286 | argtype:slider |
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287 | argmin:1 |
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288 | argmax:50 |
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289 | argvalue:5 |
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290 | |
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291 | // parameters for multiple alignment: |
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292 | |
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293 | arg:MATRIX |
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294 | argtype:choice_menu |
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295 | arglabel:Weighting matrix (multiple ali) |
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296 | argchoice:Gonnet series:GONNET |
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297 | argchoice:Blosum series:BLOSUM |
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298 | argchoice:PAM series:PAM |
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299 | argchoice:ID matrix:ID |
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300 | |
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301 | arg:GOP |
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302 | argtype:slider |
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303 | arglabel:Gap Open Penalty |
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304 | argmin:0 |
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305 | argmax:100 |
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306 | argvalue:10 |
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307 | |
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308 | arg:GEP |
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309 | arglabel:Gap Extend Penalty |
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310 | argtype:slider |
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311 | argmin:0 |
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312 | argmax:10 |
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313 | argvalue:0.2 |
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314 | |
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315 | arg:MAXDIV |
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316 | arglabel:% identity for delay |
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317 | argtype:slider |
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318 | argmin:0 |
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319 | argmax:100 |
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320 | argvalue:30 |
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321 | |
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322 | arg:TRANSWEIGHT |
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323 | arglabel:Transition weight |
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324 | argtype:slider |
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325 | argmin:0.0 |
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326 | argmax:1.0 |
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327 | argvalue:0.5 |
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328 | |
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329 | arg:NEGMATRIX |
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330 | arglabel:Use negative matrix |
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331 | argtype:choice_menu |
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332 | argchoice:No: |
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333 | argchoice:Yes:-negative |
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334 | |
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335 | arg:INTERACTIVE |
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336 | arglabel:Interactive |
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337 | argtype:choice_menu |
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338 | argchoice:No: |
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339 | argchoice:Yes:-interactive |
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340 | |
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341 | in:in1 |
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342 | informat:flat |
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343 | insave: |
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344 | |
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345 | out:out1 |
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346 | outformat:flat |
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347 | |
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348 | // -------------------------------------------------------------------------------- |
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349 | |
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350 | item:ClustalW Protein Alignment (slow & accurate) |
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351 | seqtype: A |
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352 | itemmeta: l |
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353 | itemmethod:(GOTO_LOCAL_DIR; \ |
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354 | tr '"%//' '>' <in1 >clus_in ; \ |
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355 | RUN_IN_WINDOW((clustalw -output=PIR -infile=clus_in -align \ |
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356 | $INTERACTIVE \ |
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357 | -pwmatrix=$PWMATRIX \ |
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358 | -pwgapopen=$PWGOP -pwgapext=$PWGEP \ |
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359 | -type=PROTEIN -transweight=$TRANSWEIGHT \ |
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360 | -gapopen=$GOP -gapext=$GEP -maxdiv=$MAXDIV \ |
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361 | -matrix=$MATRIX $NEGMATRIX; \ |
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362 | cat clus_in.pir | arb_sed "s/^>DL;/#/g" | sed "s/^>P1;/%/g" | arb_sed "s/^\*$//g" >out1; )) ; \ |
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363 | RM_LOCAL_FILES(clus_in* in1)) |
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364 | |
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365 | itemhelp:clustalw.help |
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366 | |
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367 | // parameters for pairwise alignment: |
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368 | |
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369 | arg:PWMATRIX |
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370 | argtype:choice_menu |
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371 | arglabel:Weighting matrix (pairwise ali) |
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372 | argchoice:Gonnet series:GONNET |
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373 | argchoice:Blosum series:BLOSUM |
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374 | argchoice:PAM series:PAM |
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375 | argchoice:ID matrix:ID |
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376 | |
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377 | arg:PWGOP |
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378 | argtype:slider |
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379 | arglabel:Gap Open Penalty |
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380 | argmin:0 |
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381 | argmax:100 |
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382 | argvalue:10 |
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383 | |
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384 | arg:PWGEP |
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385 | arglabel:Gap Extend Penalty |
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386 | argtype:slider |
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387 | argmin:0 |
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388 | argmax:10 |
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389 | argvalue:0.1 |
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390 | |
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391 | // parameters for multiple alignment: |
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392 | |
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393 | arg:MATRIX |
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394 | argtype:choice_menu |
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395 | arglabel:Weighting matrix (multiple ali) |
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396 | argchoice:Gonnet series:GONNET |
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397 | argchoice:Blosum series:BLOSUM |
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398 | argchoice:PAM series:PAM |
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399 | argchoice:ID matrix:ID |
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400 | |
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401 | arg:GOP |
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402 | argtype:slider |
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403 | arglabel:Gap Open Penalty |
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404 | argmin:0 |
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405 | argmax:100 |
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406 | argvalue:10 |
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407 | |
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408 | arg:GEP |
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409 | arglabel:Gap Extend Penalty |
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410 | argtype:slider |
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411 | argmin:0 |
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412 | argmax:10 |
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413 | argvalue:0.2 |
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414 | |
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415 | arg:MAXDIV |
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416 | arglabel:% identity for delay |
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417 | argtype:slider |
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418 | argmin:0 |
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419 | argmax:100 |
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420 | argvalue:30 |
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421 | |
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422 | arg:TRANSWEIGHT |
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423 | arglabel:Transition weight |
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424 | argtype:slider |
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425 | argmin:0.0 |
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426 | argmax:1.0 |
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427 | argvalue:0.5 |
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428 | |
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429 | arg:NEGMATRIX |
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430 | arglabel:Use negative matrix |
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431 | argtype:choice_menu |
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432 | argchoice:No: |
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433 | argchoice:Yes:-negative |
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434 | |
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435 | arg:INTERACTIVE |
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436 | arglabel:Interactive |
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437 | argtype:choice_menu |
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438 | argchoice:No: |
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439 | argchoice:Yes:-interactive |
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440 | |
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441 | in:in1 |
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442 | informat:flat |
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443 | insave: |
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444 | |
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445 | out:out1 |
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446 | outformat:flat |
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447 | |
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448 | // -------------------------------------------------------------------------------- |
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449 | |
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450 | item:Assemble Contigs |
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451 | itemmeta: g |
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452 | itemmethod: ( GOTO_LOCAL_DIR; \ |
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453 | tr '"%//' '>' <in1 >in1.tmp; \ |
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454 | CAP2 in1.tmp $OVERLAP $PMATCH > out1; \ |
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455 | RM_LOCAL_FILES(in1 in1.tmp) ) |
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456 | itemhelp:CAP2.help |
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457 | |
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458 | arg:OVERLAP |
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459 | argtype:slider |
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460 | arglabel:Minimum overlap? |
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461 | argmin:5 |
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462 | argmax:100 |
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463 | argvalue:20 |
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464 | |
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465 | arg:PMATCH |
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466 | argtype:slider |
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467 | arglabel:Percent match required within overlap |
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468 | argmin:25 |
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469 | argmax:100 |
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470 | argvalue:90 |
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471 | |
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472 | in:in1 |
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473 | informat:flat |
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474 | |
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475 | out:out1 |
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476 | outformat:gde |
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477 | |
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