scripts/Pcitri_assembly1_IPS_commands.txt

Version 1

#InterProScan soft filtered transcriptome non-mapped contigs
# interproscan.properties file change: binary.getorf.parser.filtersize=3 #(Default 12)
# precalc server lookup disabled because these are nonpublished sequences!
#run on bufo

cd /DATA/markop/Pcitri_rnaspades

mkdir IPS_softfiltered_unmapped

#translate nt -> aa
mkdir transeq
/DATA/markop/my_interproscan/interproscan-5.32-71.0/bin/nucleotide/translate -i ./STAR_mapSpadesTRtoGenome/PcSpadesTRsofttoGenome_STARlong_Unmapped.out.mate1 -o ./transeq/PcSpadesTRsofttoGenome_STARlong_Unmapped.out.mate1.pep

#filter to longest 3 orfs per contig
python3 /DATA/markop/my_interproscan/interproscan-5.32-71.0/bin/nucleotide/parseOrfs.py 3 ./transeq/PcSpadesTRsofttoGenome_STARlong_Unmapped.out.mate1.pep ./transeq/PcSpadesTRsofttoGenome_STARlong_Unmapped.out.mate1.pep.filtered

#IPS run on translated aa seqs without precalc queries
/DATA/markop/my_interproscan/interproscan-5.32-71.0/interproscan.sh \
--applications Pfam \
--seqtype p \
-i ./transeq/PcSpadesTRsofttoGenome_STARlong_Unmapped.out.mate1.pep.filtered \
--output-dir IPS_softfiltered_unmapped \
--cpu 32 \
--disable-precalc \
--formats TSV,GFF3,HTML



#IPS all soft-filtered contigs from spades

#translate nt -> aa
/DATA/markop/my_interproscan/interproscan-5.32-71.0/bin/nucleotide/translate -i ./output/soft_filtered_transcripts.fasta -o ./transeq/soft_filtered_transcripts.pep

#filter to longest 3 orfs per contig
python3 /DATA/markop/my_interproscan/interproscan-5.32-71.0/bin/nucleotide/parseOrfs.py 3 ./transeq/soft_filtered_transcripts.pep ./transeq/soft_filtered_transcripts.pep.filtered

#IPS run on translated aa seqs without precalc queries
mkdir IPS_softfiltered_all
/DATA/markop/my_interproscan/interproscan-5.32-71.0/interproscan.sh \
--applications Pfam \
--seqtype p \
-i ./transeq/soft_filtered_transcripts.pep.filtered \
--output-dir IPS_softfiltered_all \
--disable-precalc \
--formats TSV