-
Notifications
You must be signed in to change notification settings - Fork 0
/
04a-CDS_extract_BLAST_July2020.sh
70 lines (49 loc) · 4.24 KB
/
04a-CDS_extract_BLAST_July2020.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
#############################################
# CDS EXTRACTION FROM BRAKER.GTF
#############################################
cd BRAKER2_analysis/STAR_map_DmercJuly2020/headerEditMap_Unmasked
mkdir BLAST_analysis
gffread -g Dmercatorum/reference_July2020/dmerc.ctg.polished1.fa -x BRAKER2_analysis/STAR_map_DmercJuly2020/headerEditMap_Unmasked/BLAST_analysis/dmerc.BRAKER_CDS_gffread.fasta BRAKER2_analysis/STAR_map_DmercJuly2020/headerEditMap_Unmasked/braker_mergeBam/braker.gtf
#############################################
# BLAST 2.10.1
#############################################
cd
mkdir Dmel_reference/blast_gi/
esearch -db nuccore -query "Drosophila melanogaster [organism]" | efetch -db nuccore -format uid > Dmel_reference/blast_gi/Dmel_gilist_July2020.gi
esearch -db protein -query "Drosophila melanogaster [organism]" | efetch -db protein -format uid > Dmel_reference/blast_gi/Dmel_gilist_protein_July2020.gi
cd
mkdir all_Droso_accessions
esearch -db protein -query "Drosophila [organism]" | efetch -db protein -format uid > all_Droso_accessions/All_Drosophila_gilist_proteins_Sept2020.gi
cd
update_blastdb.pl --showall [*]
update_blastdb.pl --decompress nr
# BLASTx of extracted CDS vs Dmelanogaster protein databank
blastx -query BRAKER2_analysis/STAR_map_DmercJuly2020/headerEditMap_Unmasked/BLAST_analysis/dmerc.BRAKER_CDS_gffread.fasta -db nr -num_threads 60 -outfmt '6 qseqid stitle qlen slen length qcovs qcovhsp evalue bitscore pident sacc sseqid sscinames' -gilist Dmel_reference/blast_gi/Dmel_gilist_protein_July2020.gi -max_target_seqs 137871 -out BRAKER2_analysis/STAR_map_DmercJuly2020/headerEditMap_Unmasked/BLAST_analysis/dmerc.BRAKER_CDS_gffread_BLASTx.txt
sed 's/ /_/g' dmerc.BRAKER_CDS_gffread_BLASTx.txt | sed 's/\,//g' | sed 's/\_\[Drosophila\_melanogaster\]//g' | cut -f1,2,3,4,5,6,7,8,9,10,11,12 > dmerc.BRAKER_CDS_gffread_BLASTx_edit.txt
##################################
# ADD FBGN TO BLAST HITS MAPPING FILE
##################################
# Download and edit Fbgn file from flybase
cd Dmel_reference
wget ftp://ftp.flybase.net/releases/current/precomputed_files/genes/fbgn_NAseq_Uniprot_fb_2020_03.tsv.gz
zcat Dmel_reference/fbgn_NAseq_Uniprot_fb_2020_03.tsv.gz > Dmel_reference/fbgn_NAseq_Uniprot_fb_2020_03.tsv
sed 's/## gene_symbol/gene_symbol/g' Dmel_reference/fbgn_NAseq_Uniprot_fb_2020_03.tsv | grep -v '^#' | sed 's/primary_FBgn\#/primary_FBgn/g' | sed 's/\t/,/g' > Dmel_reference/fbgn_NAseq_Uniprot_fb_2020_03_edit.csv
Rscript fbgn_accession_file_edit_2020_03.R # to get fbgn_NAseq_Uniprot_fb_2020_03_edit_final.txt (see scripts folder on github)
# filter blast output and add FBgns
cd BRAKER2_analysis/STAR_map_DmercJuly2020/headerEditMap_Unmasked/BLAST_analysis
mkdir fbgn2blast_out_strict_pident35
Rscript BRAKER2_analysis/add_fbgn_to_blast_strict_pident35.R 30 BRAKER2_analysis/STAR_map_DmercJuly2020/headerEditMap_Unmasked/braker_mergeBam/all_gene_ids.txt dmerc.BRAKER_CDS_gffread_BLASTx_edit.txt fbgn_NAseq_Uniprot_fb_2020_03_edit_final.txt fbgn2blast_out_strict_pident35/
############################
# REVERSE BLAST DMEL CDS TO DMERC WITH TBLASTX
############################
# Makeblastdb
cd blast/
mkdir blast/Dmerc_CDS
makeblastdb -in BRAKER2_analysis/STAR_map_DmercJuly2020/headerEditMap_Unmasked/BLAST_analysis/dmerc.BRAKER_CDS_gffread.fasta -title Dmerc_CDS -dbtype nucl -out blast/Dmerc_CDS -hash_index
blastdbcmd -db blast/Dmerc_CDS -info
sed 's/ type.*//g' Dmel_reference/dmel-all-CDS-r6.35.fasta > Dmel_reference/dmel-all-CDS-r6.35_edit.fasta
tblastx -query Dmel_reference/dmel-all-CDS-r6.35_edit.fasta -db blast/Dmerc_CDS -num_threads 20 -outfmt '6 qseqid stitle qlen slen length qcovs qcovhsp evalue bitscore pident sacc sseqid sscinames' -max_target_seqs 18313 -out BRAKER2_analysis/STAR_map_DmercJuly2020/headerEditMap_Unmasked/BLAST_analysis/Dmel_to_Dmerc_tblastx/mel_CDS_to_Dmerc_CDS_gffread_tBLASTx.txt
cd BRAKER2_analysis/STAR_map_DmercJuly2020/headerEditMap_Unmasked/BLAST_analysis/Dmel_to_Dmerc_tblastx
sed 's/ /\_/g' mel_CDS_to_Dmerc_CDS_gffread_tBLASTx.txt | awk '$6>50 && $8<1e-10 && $10>35' | cut -f1,2 | sort | uniq | sed 's/\_gene\=/\t/g' | cut -f1,3 | sort | uniq > mel_CDS_to_Dmerc_CDS_gffread_tBLASTx_qcov50_eval1e10_pident35.txt
# Get forward & reverse orthologs
Rscript create_tblastx_map_file.R # (see scripts folder on github)