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corrected the wrong stats output of number of footprints after filter #75

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merged 4 commits into from
Jan 18, 2019
Merged

corrected the wrong stats output of number of footprints after filter #75

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f6a7c27
Merge pull request #65 from loosolab/dev
renewiegandt Jan 13, 2019
a999fb5
Merge pull request #69 from loosolab/dev
HendrikSchultheis Jan 14, 2019
eeb5727
corrected the wrong stats output of number of footprints after filter
JannikHamp Jan 16, 2019
654c5f8
this should fix the 1 off count of footprins discrepacy
JannikHamp Jan 18, 2019
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4 changes: 2 additions & 2 deletions bin/1.2_filter_motifs/compareBed.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -279,7 +279,7 @@ then
# add some final values to the log file
fp_initial=`cat $data | wc -l`
fp_initial=`expr $fp_initial - 1`
fp_final=`cat "$workdir"/filtered.bed | wc -l`
fp_final=`cat "$workdir"/filtered_flagged.bed | wc -l`
fp_final=`expr $fp_final - 1`
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Please remove the -1 from line 283. Since you are not writing a header to this temp-file you do not need to subtract 1.

echo $fp_initial | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
echo $fp_final | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
Expand All @@ -288,7 +288,7 @@ else
rm -f $output
# add some final values to the log file
cat $data | wc -l | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
cat "$workdir"/filtered.bed | wc -l | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
cat "$workdir"/filtered_flagged.bed | wc -l | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
fi

# add fasta sequences to bed and create fasta file
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