I have written a bash script that consists of multiple Unix commands and Python scripts. The goal is to make a pipeline for detecting long non coding RNA from a certain input. Ultimately I would like to turn this into an 'app' and host it on some bioinformatics website. One problem I am facing is using getopt
tools in bash. I couldn't find a good tutorial that I understand clearly. In addition any other comments related to the code is appreciated.
#!/bin/bash
if [ "$1" == "-h" ]
then
echo "Usage: sh $0 cuffcompare_output reference_genome blast_file"
exit
else
wget https://github.com/TransDecoder/TransDecoder/archive/2.0.1.tar.gz && tar xvf 2.0.1 && rm -r 2.0.1
makeblastdb -in $3 -dbtype nucl -out $3.blast.out
grep '"u"' $1 | \
gffread -w transcripts_u.fa -g $2 - && \
python2.7 get_gene_length_filter.py transcripts_u.fa transcripts_u_filter.fa && \
TransDecoder-2.0.1/TransDecoder.LongOrfs -t transcripts_u_filter.fa
sed 's/ .*//' transcripts_u_filter.fa | grep ">" | sed 's/>//' > transcripts_u_filter.fa.genes
cd transcripts_u_filter.fa.transdecoder_dir
sed 's/|.*//' longest_orfs.cds | grep ">" | sed 's/>//' | uniq > longest_orfs.cds.genes
grep -v -f longest_orfs.cds.genes ../transcripts_u_filter.fa.genes > longest_orfs.cds.genes.not.genes
sed 's/^/>/' longest_orfs.cds.genes.not.genes > temp && mv temp longest_orfs.cds.genes.not.genes
python ../extract_sequences.py longest_orfs.cds.genes.not.genes ../transcripts_u_filter.fa longest_orfs.cds.genes.not.genes.fa
blastn -query longest_orfs.cds.genes.not.genes.fa -db ../$3.blast.out -out longest_orfs.cds.genes.not.genes.fa.blast.out -outfmt 6
python ../filter_sequences.py longest_orfs.cds.genes.not.genes.fa.blast.out longest_orfs.cds.genes.not.genes.fa.blast.out.filtered
grep -v -f longest_orfs.cds.genes.not.genes.fa.blast.out.filtered longest_orfs.cds.genes.not.genes.fa > lincRNA_final.fa
fi
Here is how I run it:
sh test.sh cuffcompare_out_annot_no_annot.combined.gtf /mydata/db/Brapa_sequence_v1.2.fa TE_RNA_transcripts.fa
If you wanted the call to be :
test -c cuffcompare_output -r reference_genome -b blast_file
You would have something like :
#!/bin/bash
while getopts ":b:c:hr:" opt; do
case $opt in
b)
blastfile=$OPTARG
;;
c)
comparefilefile=$OPTARG
;;
h)
echo "USAGE : test -c cuffcompare_output -r reference_genome -b blast_file"
;;
r)
referencegenome=$OPTARG
;;
\?)
echo "Invalid option: -$OPTARG" >&2
exit 1
;;
:)
echo "Option -$OPTARG requires an argument." >&2
exit 1
;;
esac
done
In the string ":b:c:hr:", - the first ":" tells getopts that we'll handle any errors, - subsequent letters are the allowable flags. If the letter is followed by a ':', then getopts will expect that flag to take an argument, and supply that argument as $OPTARG
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