mars-update-pipeline's People
mars-update-pipeline's Issues
bed2chipseq.sh
`#!/usr/bin/env bash
function get_fasta(){
#check the size of the input sequence of reduce the processing time form large files (assumes sorted file)
lenbed=$(wc -l $bed_in | cut -f1 -d " ")
lenuse=$(($lenbed/10))
if [ "$lenbed" -gt 5000 ];
then
cut -f 1,2,3 $bed_in | head -$lenuse | bed-widen -width $len >$bed_wide.bed
else
cut -f 1,2,3 $bed_in | bed-widen -width 100 >$bed_wide.bed
fi
#Extract negative bed and the fasta
python extractnegative.py $bed_wide.bed $bed_wide.negbed 500
fastaFromBed -tab -fi $hg -bed $bed_wide.bed -fo $bed_wide.fas
fastaFromBed -tab -fi $hg -bed $bed_wide.negbed -fo $bed_wide.negfas
cut -f 4 $bed_in >/tmp/f1
cut -f 1 $bed_wide.fas >/tmp/f2
cut -f 2 $bed_wide.fas >/tmp/f3
paste /tmp/f2 /tmp/f1 /tmp/f3 >$bed_wide.fas
cut -f 4 $bed_in >/tmp/f1
cut -f 1 $bed_wide.negfas >/tmp/f2
cut -f 2 $bed_wide.negfas >/tmp/f3
paste /tmp/f2 /tmp/f1 /tmp/f3 >$bed_wide.negfas
python removemasked.py $bed_wide.fas $bed_wide.fa
python removemasked.py $bed_wide.negfas $bed_wide.negfa
# use the length of the available sequences to determine the size of test and negative sequences
lenfa=$(wc -l $bed_wide.fa | cut -f1 -d " ")
len_negfa=$(wc -l $bed_wide.negfa | cut -f1 -d " ")
lenuse=$(($lenbed/20))
if [ $lenuse -gt 500 ];
then
lenuse=$lenuse
else
lenuse=500
fi
if [ "$lenfa" -gt $lenuse ] && [ "$len_negfa" -gt $lenuse ];
then
cutoff=$lenuse
elif [ "$lenfa" -lt "$len_negfa" ] ;
then
cutoff=$lenfa
else
cutoff=$len_negfa
fi
head -$cutoff $bed_wide.fa >$bed_wide.posneg
head -$cutoff $bed_wide.negfa >>$bed_wide.posneg
#clean up the temporary files
#rm $bed_wide.neg*
#rm $bed_wide.fa*
rm /tmp/f*
}
bed_in=$1
bed_wide=$2
hg=$3
len=${4:-100} #Use a default f 100 if not provided
get_fasta`
Centrimo Output
I can see so much has changed on MEME Suite, but here is n old output. https://www.dropbox.com/t/cIiJCzNkI04JJAxW
You can also find sample outputs in the older versions: http://web.mit.edu/meme_v4.11.4/share/doc/examples/centrimo_example_output_files/centrimo.html
Database update
Hi @kipkurui, I have managed to write an sql script of the database here.
Kindly review it and give feedback. I hope you should be able to run it well from your side.
Description
The script starts with the sql commands for building the database and the required tables then this is followed by inserting the data into the tables which takes in majority of the script.
Challenge
I have found a challenge in updating the foreign key and and constrains which have run me into multiple errors.
I ended up commenting them out of the code. Kindly help me address this problem and updating all the required and necessary keys & constrains into the script.
A quick question on PBM_Data
table I didnt understand what PBM_DEBRU
meant...
Looking forward to hearing from you.
Fnyasimi/Msc_Project#22
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