Mercurial > repos > alvarofaure > bitlab

comparison chromeister/bin/index_chromeister_solo.sh @ 0:7fdf47a0bae8 draft

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author alvarofaure
date Wed, 12 Dec 2018 07:18:40 -0500
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-1:000000000000 0:7fdf47a0bae8
1 #!/usr/bin/env bash
2 DIR=$1
3 FASTAS1=$3
4 FASTAS2=$4
5 OUT=$2
6
7 echo "Computing index CSV..." > index.csv.temp
8
9 while [ "$(find . -size 0 | wc -l)" -ne 0 ]; do
10 sleep 10s
11 done
12
13
14 EXT="mat"
15 EXTSCORE="scr.txt"
16 EXTGENERAL=".fasta"
17
18 # data is like
19 # HOMSA.Chr.10.fasta
20
21
22
23 if [ $# != 4 ]; then
24 echo "***ERROR*** Use: $0 <directory> <out> <fastas_directory_1> <fastas_directory_2>"
25 exit -1
26 fi
27
28
29 rm $OUT
30
31 for elem in $(ls -d $DIR/*.$EXT | awk -F "/" '{print $NF}' | awk -F ".$EXT" '{print $1}')
32 do
33
34 IFS='-', read -a splits <<< "$elem" # yields MUSMU.Chr.8.fasta and MUSMU.Chr.Y.fasta
35 IFS='.', read -a getnum <<< "$elem" # yields MUSMU Chr 8 fasta and MUSMU Chr Y fasta
36
37 scorepath=$(basename $elem .mat).$EXTSCORE
38
39 sed -i "/X.*/d" $DIR/$scorepath
40 sed -i "s/\[1\]//g" $DIR/$scorepath
41
42 score=$( head -1 $DIR/$scorepath)
43 len1=$( head -1 $DIR/$elem.mat.events.txt | awk -F="," '{print $1}')
44 len2=$( head -1 $DIR/$elem.mat.events.txt | awk -F="," '{print $2}')
45
46
47
48 file1=${splits[0]}
49 file2=$(basename ${splits[1]} .mat)
50
51 ID1=$(head -1 $FASTAS1/$file1)
52 ID2=$(head -1 $FASTAS2/$file2)
53
54
55 #scorepath="$(basename $elem .mat).$EXTSCORE"
56 #score="$(head -1 $DIR/$scorepath)"
57
58 counter=0
59 numX=${getnum[2]}
60 numY=${getnum[5]}
61
62
63
64
65 echo "$(basename ${splits[0]} $EXTGENERAL),$(basename ${splits[1]} ${EXTGENERAL}),$ID1,$ID2,$elem.$EXT.filt.png,$numX,$numY,$score,$len1 $len2" >> $OUT
66
67 done
68
69 sort -k5,5n -k6,6n -o $OUT $OUT
70
71
72 sed -i '1iSpX, SpY, IDX, IDY, IMG, CHNumberX, CHNumberY, Score, LengthX, LengthY' $OUT
73
74 rm index.csv.temp
75