Parsing the InterProScan results
InterProScan is a powerful and useful protein identifier explorer.However, the result of it is not easy to handle. For example, the example of it have many columns and duplicated rows. Here, we are going to use script to merge the same gene ID to one lines. So the script is called interproscan_to_one_line.py. Please find the difference before and after using the script on the TAIR 10 data. The Homo_sapiens data is at the bottom of the page.
Before:
AT1G11750.1 e35d0d54d5d209033484e31afc0ff009 271 Coils Coil Coil 210 230 - T 27-09-2021 - - AT1G11750.1 e35d0d54d5d209033484e31afc0ff009 271 Hamap MF_00444 ATP-dependent Clp protease proteolytic subunit [clpP]. 84 270 33.141739 T 27-09-2021 IPR001907 ATP-dependent Clp protease proteolytic subunit GO:0004176|GO:0004252|GO:0006508 - AT1G11750.1 e35d0d54d5d209033484e31afc0ff009 271 CDD cd07017 S14_ClpP_2 96 264 3.96818E-88 T 27-09-2021 IPR001907 ATP-dependent Clp protease proteolytic subunit GO:0004176|GO:0004252|GO:0006508 - AT1G11750.1 e35d0d54d5d209033484e31afc0ff009 271 ProSitePatterns PS00382 Endopeptidase Clp histidine active site. 189 202 - T 27-09-2021 IPR033135 ClpP, histidine active site - - AT1G11750.1 e35d0d54d5d209033484e31afc0ff009 271 Pfam PF00574 Clp protease 96 269 3.7E-65 T 27-09-2021 IPR023562 Clp protease proteolytic subunit /Translocation-enhancing protein TepA - MetaCyc: PWY-7884
After:
AT1G11750.1 PF00574 Clp protease AT5G53350.1 PF10431,PF07724 C-terminal, D2-small domain, of ClpB protein,AAA domain (Cdc48 subfamily) AT4G17040.1 PF00574 Clp protease AT5G15450.1 PF10431,PF17871,PF02861,PF02861,PF07724,PF00004 C-terminal, D2-small domain, of ClpB protein,AAA lid domain,Clp amino terminal domain, pathogenicity island component,Clp amino terminal domain, pathogenicity island component,AAA domain (Cdc48 subfamily),ATPase family associated with various cellular activities (AAA) AT5G51070.1 PF07724,PF10431,PF02861,PF02861,PF00004,PF17871 AAA domain (Cdc48 subfamily),C-terminal, D2-small domain, of ClpB protein,Clp amino terminal domain, pathogenicity island component,Clp amino terminal domain, pathogenicity island component,ATPase family associated with various cellular activities (AAA),AAA lid domain
Because we only displayed the one contain “Pfam” protein patterns.User can change the parameters: Pfam to others e.g., CDD, Hamap to filter out the others.
- Step One: Running the InterProScan with your interested protein fasta files.
>/interproscan.sh -i proteins_of_your_genome.fasta -f tsv -dp
If you are new to InterProScan, please find detailed usage at the Step #6 in (Zhang et.al 2021)(https://doi.org/10.1016/j.xpro.2021.100619)
- Step Two: Run the interproscan_to_one_line.py script which can be found via (https://github.com/zx0223winner/InterProScan_Parser)
python3 interproscan_to_one_line.py test_data.tsv out.txt Pfam
InterproScan data result for human-being
Homo_sapiens: GCF_000001405.39_GRCh38.p13_protein.faa
1. This protein includes alternative splicing transcripts translated proteins (e.g.,XX.t1, XX.t2, XX.t3) Use this script (isoform2one https://github.com/zx0223winner/isoform2one) to select the primary transcript protein sequence (longest transcript)
2. Then run the Interproscan analysis. Results documented here: /misc/scratch2/xizhang/HSDatabase/Results/Interproscan_
<Last updated by Xi Zhang on Oct 8th,2021>