ENH update 06_Compare_with_other_datasets

Author: cocodyq

General_Scripts/06_Compare_with_other_datasets/02_filter_sp_dedup.py

@@ -11,11 +11,7 @@ def filter_dedup(infile,outfile):
                     out.write(f'>{header}\n{seq}\n')
                     seqset.add(seq)
 
-infile1 = '~/refseq/arc/refseq_arc.faa.gz'
-outfile1 = '~/refseq/arc/refseq_sp_arc_dedup.faa'
+infile1 = 'database.faa'
+outfile1 = 'database_dedup.faa'
 
-infile2 = '~/refseq/bac/refseq_bac.faa.gz'
-outfile2 = '~/refseq/bac/refseq_sp_bac_dedup.faa'
-
-filter_dedup(infile1,outfile1)
-filter_dedup(infile2,outfile2)
+filter_dedup(infile1,outfile1)

General_Scripts/06_Compare_with_other_datasets/03_align.sh

@@ -3,10 +3,4 @@
 # Concept: 
 # Use Diamond to align sequences to GMSC
 
-diamond blastp -q refseq_sp_arc_dedup.faa -d 100AA_GMSC.dmnd -o refseq_arc.tsv --more-sensitive -e 0.00001 --outfmt 6 qseqid sseqid full_qseq full_sseq qlen slen pident length evalue qcovhsp scovhsp -p 64
-
-diamond blastp -q refseq_sp_bac_dedup.faa -d 100AA_GMSC.dmnd -o refseq_bac.tsv --more-sensitive -e 0.00001 --outfmt 6 qseqid sseqid full_qseq full_sseq qlen slen pident length evalue qcovhsp scovhsp -p 64
-
-diamond blastp -q cluster.faa -d 100AA_GMSC.dmnd -o cluster.tsv --more-sensitive -e 0.00001 --outfmt 6 qseqid sseqid full_qseq full_sseq qlen slen pident length evalue qcovhsp scovhsp -p 64
-
-diamond blastp -q family.faa -d 100AA_GMSC.dmnd -o family.tsv --more-sensitive -e 0.00001 --outfmt 6 qseqid sseqid full_qseq full_sseq qlen slen pident length evalue qcovhsp scovhsp -p 64
+diamond blastp -q database_dedup.faa -d 100AA_GMSC.dmnd -o database.tsv --more-sensitive -e 0.00001 --outfmt 6 qseqid sseqid full_qseq full_sseq qlen slen pident length evalue qcovhsp scovhsp -p 64