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comparison PGAP-1.2.1/PGAP.pl @ 4:70b7a5270968 draft

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Uploaded
author dereeper
date Thu, 24 Jun 2021 16:15:34 +0000
parents 83e62a1aeeeb
children d8c5bea1cce2
comparison
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3:bbb2c473664c 4:70b7a5270968
1 #!/usr/bin/perl 1 #!/usr/bin/perl
2 use strict; 2 use strict;
3 use warnings; 3 use warnings;
4 use Getopt::Long; 4 use Getopt::Long;
5 use File::Basename;
6
7 use lib dirname(__FILE__);
5 8
6 ### programs from BLAST 9 ### programs from BLAST
7 my $formatdb="formatdb"; 10 my $formatdb=`which formatdb`;
8 my $blastall="blastall"; 11 chomp($formatdb);
12
13 my $blastall=`which blastall`;
14 chomp($blastall);
9 15
10 ### programs from mcl 16 ### programs from mcl
11 my $mcl="mcl"; 17 my $mcl=`which mcl`;
18 chomp($mcl);
12 19
13 ### programs from mafft 20 ### programs from mafft
14 my $mafft="mafft"; 21 my $mafft=`which mafft`;
22 chomp($mafft);
15 23
16 ### programs from PHYLIP 24 ### programs from PHYLIP
17 my $seqboot="seqboot"; 25 my $seqboot=`which seqboot`;chomp($seqboot);
18 my $neighbor="neighbor"; 26 my $neighbor=`which neighbor`;chomp($neighbor);
19 my $consense="consense"; 27 my $consense=`which consense`;chomp($consense);
20 my $dnaml="dnaml"; 28 my $dnaml=`which dnaml`;chomp($dnaml);
21 my $dnadist="dnadist"; 29 my $dnadist=`which dnadist`;chomp($dnadist);
22 my $dnapars="dnapars"; 30 my $dnapars=`which dnapars`;chomp($dnapars);
23 31
24 my $count_tree=0; 32 my $count_tree=0;
25 33
26 my $sampleSize=8000; # when calculate the pan-genome size, we will sample $sampleSize combinations 34 my $sampleSize=8000; # when calculate the pan-genome size, we will sample $sampleSize combinations
27 # if the total combination number is larger than $sampleSize for specific genomes 35 # if the total combination number is larger than $sampleSize for specific genomes