Mercurial > repos > bcclaywell > argo_navis

annotate pact.sh @ 2:7eaf6f9abd28 draft default tip

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b-dirty
author bcclaywell
date Mon, 12 Oct 2015 17:57:38 -0400
parents d67268158946
children
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1 #!/bin/bash
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2
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3 source $(dirname $0)/util.sh
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4 source $1
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5
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7
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8 # PRELIMINARY RUN OF PACT FOR TMRCA AND DEME MAP
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9 # ==============================================
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10
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11 PRELIM_DIR=prelim_dir
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12 mkdir $PRELIM_DIR
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14
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15 # First copy things over into our preliminary working dir
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16 cp $ARGO_TOOL_DIR/prelim_pact_params $PRELIM_DIR/in.param
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17 cp $TREEFILE $PRELIM_DIR/in.trees
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18
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19 # Go in and run; get out
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20 cd $PRELIM_DIR
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21 pact
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22 cd ..
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23
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24 # Get id -> seqname translation from nexus treefile translations
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25 ID_TRANSLATION=id_translation.csv
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26 extract_nexus_translations.py $TREEFILE $ID_TRANSLATION
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27
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28 # Translate the tree rules so we have some metadata to work with
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29 PRELIM_PARSED_PACT_TREE="prelim_parsed_pact_tree.csv"
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30 ls $PRELIM_DIR
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31 parse_pact_tree.py $PRELIM_DIR/out.rules $PRELIM_PARSED_PACT_TREE
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32
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33 # Join preliminary parsed pact tree data and id translation so we get metadata mapping seqname to deme
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34 METADATA="metadata.csv"
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35 csvjoin -c id,name $ID_TRANSLATION $PRELIM_PARSED_PACT_TREE | \
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36 csvcut -c id,sequence,label - | \
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37 sed '1 s/label/deme/' > $METADATA
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38
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39 # Extract average time to MRCA from the out.stats
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40 TMRCA=`csvgrep -t -c statistic -m tmrca $PRELIM_DIR/out.stats | csvcut -c mean | grep -v mean`
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41
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42
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43
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44 # INITIALIZE THINGS
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45 # =================
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46
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47 WORK_DIR=working_dir
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48 mkdir $WORK_DIR
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49
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50 # We're using arrays here to solve this problem:
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51 # http://stackoverflow.com/questions/12136948/in-bash-why-do-shell-commands-ignore-quotes-in-arguments-when-the-arguments-are
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52 # Can't really seem to get multiple deme or tip names in otherwise
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53 PACT_ARGS=($TREEFILE "-d" "deme" "-r" "-o" $WORK_DIR)
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54
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55
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56
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57 # SET UP TIP SELECTION
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58 # ====================
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59
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60 if [[ $TIP_SELECTION_METHOD == "demes" ]]
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61 then
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62 PACT_ARGS+=("-l" "\"$DEMES\"" "-m" $METADATA)
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63 elif [[ $TIP_SELECTION_METHOD == "names" ]]
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64 then
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65 PACT_ARGS+=("-t" "\"$TIP_NAMES\"")
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66 elif [[ $TIP_SELECTION_METHOD == "file" ]]
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67 then
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68 PACT_ARGS+=("-T" $TIP_FILE)
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69 fi
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70
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71
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72 # TIME RANGE SELECTION
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73 # ====================
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74
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75 if [[ $TIME_RANGE_SELECTOR == "custom" ]]
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76 then
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77 # Still have to write the --strim-start for this into the wrapper
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78 PACT_ARGS+=("-S" $TIME_RANGE_START)
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79 if [[ $TIME_RANGE_END != "" ]]
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80 then
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81 PACT_ARGS+=("-e" $TIME_RANGE_END)
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82 fi
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83 else
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84 PACT_ARGS+=("-s" $TMRCA)
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85 # Add custom logic for doing two prelim pact runs to get the tmrca for just focus tips
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86 fi
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87
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88
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89 # RUN IT
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90 # ======
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91
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92 # Again, as mentioned above, have to do this array thing to get arg list construction to work properly
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93 pact_wrapper.py "${PACT_ARGS[@]}"
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94 # XXX Stubbing code! Comment out the above, and in the below; or vice versa
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95 #echo "Would be calling PACT with args: $PACT_ARGS"
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96 #WORK_DIR=/home/matsengrp/working/csmall/galaxy-central/database/job_working_directory/000/62/working_dir
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97
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98
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99 OUT_RULES="$WORK_DIR/out.rules"
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100 OUT_STATS="$WORK_DIR/out.stats"
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101 OUT_SKYLINES="$WORK_DIR/out.skylines"
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102
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103
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104
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105 # PLOTTING RESULTS
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106 # ================
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107
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108 # Thread access to some shared plotting code
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109 COMMONR="$ARGO_TOOL_DIR/bin/common.R"
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110
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111 # First we're going to create a file with the deme list, for more predicatable coloring:
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112 FULL_DEME_LIST="full_deme_list"
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113 csvcut -t -c statistic $OUT_STATS | \
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114 csvgrep -c statistic -r "^pro_" | \
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115 sed s/pro_// | \
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116 sed '1 s/statistic/deme/' > $FULL_DEME_LIST
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117
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118 if [[ `grep _ $FULL_DEME_LIST` != "" ]]
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119 then
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120 echo "WARNING: Deme names with underscores ( '_' ) are not supported; You may get a bonkerz migration rate plot." > /dev/stderr
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121 fi
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122
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123
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124 # Specify colors
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125 COMMON_ARGS="$COMMONR -d $FULL_DEME_LIST"
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126 if [[ $COLOR_SELECTOR == "brewer" ]]
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127 then
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128 COMMON_ARGS="$COMMON_ARGS -b $COLOR_BREWER"
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129 else
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130 COMMON_ARGS="$COMMON_ARGS -c $COLOR_FILE"
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131 fi
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132
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133 # Parse the out.rules file and make a tree plots of it
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134 TREE_PLOT="tree_plot.svg"
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135 parse_pact_tree.py $OUT_RULES parsed_pact_tree.csv
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136 csvjoin --left -c name,id parsed_pact_tree.csv $ID_TRANSLATION > parsed_pact_tree.renamed.csv
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137
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138 plot_pact_tree.R $COMMON_ARGS parsed_pact_tree.renamed.csv $TREE_PLOT
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139
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140 # Make skyline plot
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141 SKYLINE_PLOT="skyline_plot.svg"
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142 plot_skyline_hist.R $COMMON_ARGS $OUT_SKYLINES $OUT_STATS $SKYLINE_PLOT
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143
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144 # Do migration rate plot
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145 MIGRATION_RATES_PLOT="migration_rates_plot.svg"
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146 plot_migration_rates.R $COMMON_ARGS $OUT_STATS $MIGRATION_RATES_PLOT
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147
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148 # Other stats extraction
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149 MISC_STATS="misc_stats.svg"
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150 grep -v mig $OUT_STATS | column -t | txt2svg -s 3.5 - $MISC_STATS
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151
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152 # Title SVG
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153 TITLE="title.svg"
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154 echo $FIGURES_TITLE | txt2svg -s 8 - $TITLE
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155
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156 # Start combining results using svgstack, and convert the final result to PDF w/ inkscape
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157 STATS="stats.svg"
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158 MAIN="main.svg"
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159 COMBINED_SVG="combined.svg"
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160 svg_stack.py --direction="v" $MIGRATION_RATES_PLOT $MISC_STATS > $STATS
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161 svg_stack.py --direction="h" $TREE_PLOT $SKYLINE_PLOT $STATS > $MAIN
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162 svg_stack.py --direction="v" $TITLE $MAIN > $COMBINED_SVG
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163 inkscape --without-gui --export-pdf=$FIGURES $COMBINED_SVG
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164
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165
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166 # Remove things we don't want in the dynamic outputs:
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167 rm $WORK_DIR/in.trees
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168
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169