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comparison gecko/bin/workflow.sh @ 1:35af401890c0 draft

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author bitlab
date Thu, 13 Dec 2018 07:59:25 -0500
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0:ee6b15b409e5 1:35af401890c0
1 #!/bin/bash
2
3 FL=1000 # frequency limit
4
5 if [ $# != 8 ]; then
6 echo " ==== ERROR ... you called this script inappropriately."
7 echo ""
8 echo " usage: $0 seqXName seqYName lenght similarity WL fixedL output.frags output.csv"
9 echo ""
10 exit -1
11 fi
12
13 #{
14
15
16 MYRAND=$((( RANDOM % 10000000) +1))
17 MGDIR=${PWD}/${MYRAND}
18 echo "MGDIR $MGDIR"
19 mkdir -p ${MGDIR}
20
21 genoXname=$(basename "$1")
22 genoYname=$(basename "$2")
23 genoXname="${genoXname%.*}"
24 genoYname="${genoYname%.*}"
25
26
27 cp $1 $MGDIR/${genoXname}.fasta
28 cp $2 $MGDIR/${genoYname}.fasta
29 mkdir -p ${MGDIR}/dictionaries
30 mkdir -p ${MGDIR}/fragments
31
32 genoXExt="fasta"
33 genoYExt="fasta"
34
35
36
37 BINDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
38
39 length=${3}
40 similarity=${4}
41 WL=${5} # wordSize
42 fixedL=${6}
43 output=${7}
44 csv=${8}
45
46 mkdir ${MGDIR}/intermediateFiles
47
48 mkdir ${MGDIR}/intermediateFiles/${genoXname}-${genoYname}
49 mkdir ${MGDIR}/results
50 mkdir ${MGDIR}/intermediateFiles/dictionaries
51 mkdir ${MGDIR}/intermediateFiles/hits
52
53 # Copiamos los fastas
54 ln -s ${MGDIR}/${genoXname}.${genoXname} ${MGDIR}/intermediateFiles/${genoXname}-${genoYname}
55 ln -s ${MGDIR}/${genoYname}.${genoYname} ${MGDIR}/intermediateFiles/${genoYname}-${genoXname}
56
57 cd ${MGDIR}/intermediateFiles/${genoXname}-${genoYname}
58
59 ###############
60
61
62
63 echo "${BINDIR}/reverseComplement ${MGDIR}/${genoYname}.${genoXExt} ${genoYname}-revercomp.${genoYExt}"
64 ${BINDIR}/reverseComplement ${MGDIR}/${genoYname}.${genoYExt} ${MGDIR}/${genoYname}-revercomp.${genoYExt}
65
66 if [[ ! -f ../dictionaries/${genoXname}.d2hP ]]; then
67 echo "${BINDIR}/dictionary.sh ${MGDIR}/${genoXname}.${genoXExt} &"
68 ${BINDIR}/dictionary.sh ${MGDIR}/${genoXname}.${genoXExt} &
69 fi
70
71 if [[ ! -f ../dictionaries/${seqYName}.d2hP ]]; then
72 echo "${BINDIR}/dictionary.sh ${MGDIR}/${genoYname}.${genoYExt} &"
73 ${BINDIR}/dictionary.sh ${MGDIR}/${genoYname}.${genoYExt} &
74 fi
75
76 if [[ ! -f ../dictionaries/${genoYname}-revercomp.d2hP ]]; then
77 echo "${BINDIR}/dictionary.sh ${MGDIR}/${genoYname}-revercomp.${genoYExt} &"
78 ${BINDIR}/dictionary.sh ${MGDIR}/${genoYname}-revercomp.${genoYExt} &
79 fi
80
81 echo "Waiting for the calculation of the dictionaries"
82
83 for job in `jobs -p`
84 do
85 #echo $job
86 wait $job
87 done
88
89
90
91 mv ${genoXname}.d2hP ../dictionaries/
92 mv ${genoXname}.d2hW ../dictionaries/
93 mv ${genoYname}.d2hP ../dictionaries/
94 mv ${genoYname}.d2hW ../dictionaries/
95 mv ${genoYname}-revercomp.d2hP ../dictionaries/
96 mv ${genoYname}-revercomp.d2hW ../dictionaries/
97
98
99
100 # Hacemos enlace simbolico
101 ln -s ../dictionaries/${genoXname}.d2hP .
102 ln -s ../dictionaries/${genoXname}.d2hW .
103
104 ln -s ../dictionaries/${genoYname}.d2hP .
105 ln -s ../dictionaries/${genoYname}.d2hW .
106
107 ln -s ../dictionaries/${genoYname}-revercomp.d2hP .
108 ln -s ../dictionaries/${genoYname}-revercomp.d2hW .
109
110 echo "${BINDIR}/comparison.sh ${MGDIR}/${genoXname}.${genoXExt} ${MGDIR}/${genoYname}.${genoYExt} ${length} ${similarity} ${WL} ${fixedL} f &"
111 ${BINDIR}/comparison.sh ${MGDIR}/${genoXname}.${genoXExt} ${MGDIR}/${genoYname}.${genoYExt} ${length} ${similarity} ${WL} ${fixedL} f &
112
113 echo "${BINDIR}/comparison.sh ${MGDIR}/${genoXname}.${genoXExt} ${MGDIR}/${genoYname}-revercomp.${genoYExt} ${length} ${similarity} ${WL} ${fixedL} r &"
114 ${BINDIR}/comparison.sh ${MGDIR}/${genoXname}.${genoXExt} ${MGDIR}/${genoYname}-revercomp.${genoYExt} ${length} ${similarity} ${WL} ${fixedL} r &
115
116 echo "Waiting for the comparisons"
117
118 for job in `jobs -p`
119 do
120 #echo $job
121 wait $job
122 done
123
124
125 #echo "rm ${seqYName}-revercomp.${extensionY}"
126 #rm ${seqYName}-revercomp.${extensionY}
127
128
129 echo "${BINDIR}/combineFrags ${genoXname}-${genoYname}-sf.frags ${genoXname}-${genoYname}-revercomp-sr.frags ${genoXname}-${genoYname}.frags"
130 ${BINDIR}/combineFrags ${genoXname}-${genoYname}-sf.frags ${genoXname}-${genoYname}-revercomp-sr.frags ${genoXname}-${genoYname}.frags
131
132 #Borramos todo menos los frags y los diccionarios
133
134 # Get Info from frags
135 echo "${BINDIR}/getInfo ${genoXname}-${genoYname}.frags > ${genoXname}-${genoYname}.csv"
136 ${BINDIR}/getInfo ${genoXname}-${genoYname}.frags > ${genoXname}-${genoYname}.csv.tmp
137 cat ${genoXname}-${genoYname}.frags.INF ${genoXname}-${genoYname}.csv.tmp > ${genoXname}-${genoYname}.csv
138 rm -rf ${genoXname}-${genoYname}.csv.tmp
139
140 if [[ -L "../../${genoXname}.fasta" ]]
141 then
142 rm ../../${genoYname}.fasta
143 fi
144
145 if [[ -L "../../${genoXname}.fasta" ]]
146 then
147 rm ../../${genoYname}.fasta
148 fi
149
150 #Movemos los frags y los info
151 mv ${genoXname}-${genoYname}.frags $output
152 mv ${genoXname}-${genoYname}.csv $csv
153
154
155
156 #echo "Borrando ${seqXName}-${seqYName}"
157 cd ..
158
159 #rm -rf ${seqXName}-${seqYName}
160
161 cd ..
162
163
164 rm -r ${MGDIR}
165