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

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