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1 # Sourced by .bashrc and singularity runscript
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2
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3 cu ()
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4 {
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5 cvs update "$@" | egrep -v '^\?'
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6 }
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7
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8 lss ()
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9 {
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10 ls -F --color=auto -lS "$@" | {
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11 read one;
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12 if [ -n "$one" -a "${one::5}" \!= "total" ]; then
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13 echo "$one";
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14 fi;
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15 cat
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16 }
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17 }
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18
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19 ff ()
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20 {
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21 pat=$1;
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22 shift;
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23 find . -iname "*$pat*" $@
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24 }
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25
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26 typecat ()
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27 {
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28 tt=$(type $1);
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29 case $tt in
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30 *\ is\ hashed\ *)
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31 cat $(echo $tt | cut -f 4 -d ' ' | tr -d '()')
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32 ;;
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33 *\ is\ /*)
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34 cat $(echo $tt | cut -f 3 -d ' ' | tr -d '()')
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35 ;;
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36 *)
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37 type $1
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38 ;;
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39 esac
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40 }
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41
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42 sus ()
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43 {
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44 sort "$@" | uniq -c | sort -k1nr,1
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45 }
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46
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47 uz ()
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48 {
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49 igzip -dc "$@"
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50 }
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51
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52 function tot ()
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53 {
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54 awk '{sum+=$1} END {printf "%u\n",sum}'
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55 }
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56
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57 btot ()
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58 {
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59 python3 -c 'import sys
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60 multiCol = dostats = sample = False
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61 c = ""
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62 p = 0
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63 q = None
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64 d = 2
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65 ssq = 0
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66 while len(sys.argv)>1:
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67 if multiCol and sys.argv[1][0]!="-":
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68 p=1
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69 q=int(sys.argv.pop(1))
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70 elif sys.argv[1]=="-c":
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71 # add commas
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72 c = ","
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73 sys.argv.pop(1)
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74 elif sys.argv[1]=="-a":
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75 # do sum etc. for all columns [p]:q
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76 multiCol = True
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77 sys.argv.pop(1)
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78 try:
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79 q = int(sys.argv.pop(1))
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80 except IndexError:
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81 print("you must supply an N for multi-column")
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82 exit(1)
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83 elif sys.argv[1]=="-s":
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84 # include mean and sample stdev
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85 dostats = True
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86 sample = True
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87 sys.argv.pop(1)
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88 elif sys.argv[1]=="-p":
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89 # include mean and population stdev
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90 dostats = True
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91 sys.argv.pop(1)
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92 elif sys.argv[1]=="-d":
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93 sys.argv.pop(1)
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94 d=int(sys.argv.pop(1))
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95 else:
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96 break
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97 n=0
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98 if multiCol:
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99 w=q-p
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100 import numpy as np
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101 s=np.array([0]*w)
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102 n=np.array([0]*w)
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103 if dostats:
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104 ssq=np.array([0]*w)
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105 else:
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106 s=0
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107 if dostats:
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108 ssq=0
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109 import math
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110 for l in sys.stdin: # ["1 11\n","2 22\n"]:
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111 try:
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112 if multiCol:
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113 ll=l.split()[p:q]
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114 ii=np.array([(0 if i.startswith("NaN") else int(i)) for i in ll])
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115 s+=ii
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116 ssq+=ii*ii
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117 n+=np.array([(0 if i.startswith("NaN") else 1) for i in ll])
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118 else:
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119 if l[0]!="N":
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120 i=int(l)
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121 s+=i
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122 if dostats:
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123 ssq+=(i*i)
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124 n+=1
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125 except (NameError,ValueError) as e:
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126 print(l,e,file=sys.stderr)
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127 if dostats:
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128 if multiCol:
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129 m=s/n
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130 var=(ssq/n)-pow(m,2)
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131 if sample:
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132 var=(n/(n-1))*var
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133 sd=pow(var,0.5)
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134 else:
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135 m=float(s)/float(n)
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136 var=(float(ssq)/float(n))-pow(float(m),2)
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137 if sample:
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138 var=(float(n)/float(n-1))*var
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139 sd=math.sqrt(var)
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140 if dostats:
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141 if multiCol:
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142 print("\t".join(f"{i:{c}.{d}f}" for i in s))
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143 print("\t".join(f"{i:{c}.{d}f}" for i in m))
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144 print("\t".join(f"{i:{c}.{d}f}" for i in sd))
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145 else:
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146 print(f"{s:}\t{m:}\t{sd:}")
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147 else:
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148 if multiCol:
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149 print("\t".join(f"{i:}" for i in s))
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150 else:
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151 print(f"{s:}")
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152
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153 ' "$@"
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154 }
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155
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156 headtail ()
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157 {
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158 case "$1" in -*)
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159 n="$1"
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160 shift
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161 ;;
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162 *) n="-10"
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163 ;;
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164 esac
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165 cat "$@" | { sed -u ${n:1}q ; echo === ; tail $n ; }
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166 }
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167
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168 export -f cu lss ff typecat sus uz tot btot headtail
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