Skip to content

name BLAST database as ./data/VB12_2020 #3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
kenscripts wants to merge 3 commits into
base: main
Choose a base branch
from
Open

name BLAST database as ./data/VB12_2020 #3

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
40cb58f
name BLAST database as /data/VB12_2020
kenscripts May 4, 2022
3552d4e
truncate target sequence labels from usearch
kenscripts May 7, 2022
0154097
add faa filetype
kenscripts May 7, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions VB12Path_FunctionProfiler.PL
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ my $diamond = "./bin/diamond";
my $diamond_parameters = "-k 1 -e 1e-4 -p 20 --sensitive";
##usearch https://www.drive5.com/usearch/download.html
my $usearch = "./bin/usearch8.1.1861_i86linux32";
my $usearch_parameters = "-id 0.3"; ##identity cutoff for search_global
my $usearch_parameters = "-id 0.3 -trunclabels"; ##identity cutoff for search_global

my ($workdir, $method, $outfile, $seqtype, $filetype, $sampleinfo,
$randomsampling);
Expand All @@ -36,7 +36,7 @@ if ( !defined $workdir
|| !defined $seqtype
|| !defined $sampleinfo
|| $method !~ /^diamond|usearch|blast$/
|| $filetype !~ /^fastq|fastq.gz|fasta|fasta.gz|fq|fq.gz|fa|fa.gz$/)
|| $filetype !~ /^fastq|fastq.gz|fasta|fasta.gz|fq|fq.gz|fa|fa.gz|faa$/)
{
&PrintHelp();
die;
Expand Down Expand Up @@ -105,7 +105,7 @@ if ($method eq "diamond") {
die "Only fasta files are supported by blast program!";
}
@files = glob("$workdir/*$filetype");
system("$formatdb -i ./data/VB12_2020.faa -p T");
system("$formatdb -i ./data/VB12_2020.faa -p T -n ./data/VB12_2020");
foreach my $file (@files) {
my $out = $file;
$out =~ s/$filetype/blast/;
Expand Down Expand Up @@ -246,7 +246,7 @@ sub PrintHelp() {
print
"perl VB12Path_FunctionProfiler.PL -d <workdir> -m <diamond|usearch|blast> -f <filetype> -s <seqtype> -si <sample size info file> -rs <random sampling size> -o <outfile>\n";
print "-m diamond|usearch|blast\n";
print "-f fastq, fastq.gz, fasta,fasta.gz, fq, fq.gz, fa, fa.gz\n";
print "-f fastq, fastq.gz, fasta, fasta.gz, fq, fq.gz, fa, fa.gz, faa\n";
print "-s sequence type, nucl or prot \n";
print "-si tab delimited file for sequence number in each file\n";
print "-rs random sampling size\n";
Expand Down