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updated script. Now the path of subscripts is automatically aquired. … #33

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merged 21 commits into from
Jan 9, 2019
Merged

updated script. Now the path of subscripts is automatically aquired. … #33

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694291c
updated script. Now the path of subscripts is automatically aquired. …
JannikHamp Jan 4, 2019
3ebb1b8
added some documentation
JannikHamp Jan 4, 2019
7d834a4
added collumn for strand information
JannikHamp Jan 4, 2019
7de9a1b
added column "strand"
JannikHamp Jan 4, 2019
1a49821
documentation
JannikHamp Jan 4, 2019
9b5b061
documentation
JannikHamp Jan 4, 2019
9ecba8a
documentation
JannikHamp Jan 4, 2019
58eff98
documentation
JannikHamp Jan 4, 2019
b1cab10
Update compareBed.sh
JannikHamp Jan 5, 2019
cca8ac4
Added check for \t at the end of lines in BED-file
renewiegandt Jan 6, 2019
f983d22
Remove header = false from fread
renewiegandt Jan 6, 2019
1134d74
merge.R: Set separator from auto to '\t' in fread
renewiegandt Jan 6, 2019
37c69e6
this r script is no more necessary, the other does its job
JannikHamp Jan 8, 2019
6802d72
New updated version. Faster and more robust
JannikHamp Jan 8, 2019
b787d14
updated version.. make unique updated, more robust in general
JannikHamp Jan 8, 2019
becfeae
added information for logfile
JannikHamp Jan 8, 2019
c55e8ff
added dicumentation and parameter for .stats output file
JannikHamp Jan 8, 2019
4acc20f
documentation changes
JannikHamp Jan 9, 2019
90c8c05
updated check for trailing tabs in motiffiles
JannikHamp Jan 9, 2019
1a35ce5
removed echo from testing
JannikHamp Jan 9, 2019
530627c
more documentation, replce =, <-
JannikHamp Jan 9, 2019
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20 changes: 9 additions & 11 deletions bin/1.2_filter_motifs/compareBed.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ fa=false
mi=false
ma=false
ou=false
pa=false
he=false

if [ $# -eq 0 ]
Expand Down Expand Up @@ -70,6 +71,7 @@ case $key in
;;
-p|--path)
path="$2"
pa=true
shift
shift
;;
Expand Down Expand Up @@ -120,6 +122,7 @@ then
echo " -max --max maximum size of footprints; default is 80"
echo " -o --output output path/file ; default dir is workdir and filename is newMotifs.bed and newMotifs.bed.fasta"
echo " -h --help shows this help message"
echo " -p --path the path where the required scripts merge.R and maxScore.R are stored. Default: same path as this scripts path"
exit 0
fi

Expand All @@ -133,6 +136,7 @@ echo min: $mi
echo max: $ma
echo output: $ou
echo help: $he
echo path of scripts: $pa

if [ $da == false ] || [ $mo == false ] || [ $fa == false ]
then
Expand All @@ -143,12 +147,8 @@ fi

if [ $wo == false ]
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You should set $workdir in the beginning to './' and overwrite it if necessary. This would save you this whole if statement + an additional $wo variable.

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Looking a bit further I think that most if not all of your if statements in this part are overcomplicated. You should set default values at the beginning of your script. This would enable you to discard most of the if statements and leave you only with the required parameters. These should be checked for their existence or in other words whether they were set (https://stackoverflow.com/questions/3601515/how-to-check-if-a-variable-is-set-in-bash).

then
#if [ ! -d workdir1337 ]
#then
# mkdir workdir1337
#fi
wo=true
workdir=$path
workdir=$PWD
fi

if [ $ou == false ]
Expand All @@ -169,9 +169,10 @@ then
ma=true
fi

if [ ! -d $workdir ]
if [ $pa == false ]
then
mkdir $workdir
path=`echo $0 | sed 's/\/[^\/]*$/\//g'`
pa=true
fi

#1. first filter. no overlap vs. overlap
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"Filter for sequences without overlap" would be a nicer comment.

Expand Down Expand Up @@ -268,8 +269,5 @@ fi
Rscript --vanilla $path/merge.R $min $max $workdir $data

#5. add fasta sequences to bed and create fasta file
bedtools getfasta -fi $fasta -bed "$workdir"/merged.bed -bedOut > $output
bedtools getfasta -fi $fasta -bed $workdir/merged.bed -bedOut > $output
bedtools getfasta -name -fi $fasta -bed "$output" -fo "$output".fasta

#6 clean up
#rm "$workdir"/pass1Fa.bed "$workdir"/pass1Tr.bed "$workdir"/pass2Tr.bed "$workdir"/merged.bed "$workdir"/pass1FaHelp.bed "$workdir"/pass1TrHelp.bed