Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

comparison alignment/mafft.pl @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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-1:000000000000 0:5b9a38ec4a39
1 #!/usr/bin/perl
2
3 my $strategy = $ARGV[0];
4 my $input = $ARGV[1];
5 my $output = "seqs_aligned.fasta";
6
7 if($strategy eq "Auto") {
8 my $run = qx/mafft --auto $input > $output 2>log.txt/;
9 }
10 elsif($strategy eq "FFT-NS-1") {
11 my $run = qx/mafft --retree 1 $input > $output 2>log.txt/;
12 }
13 elsif($strategy eq "FFT-NS-2") {
14 my $run = qx/mafft --retree 2 $input > $output 2>log.txt/;
15 }
16 elsif($strategy eq "FFT-NS-i") {
17 my $run = qx/mafft-fftnsi $input > $output 2>log.txt/;
18 }
19 elsif($strategy eq "E-INS-i") {
20 my $run = qx/mafft-einsi $input > $output 2>log.txt/;
21 }
22 elsif($strategy eq "L-INS-i") {
23 my $run = qx/mafft-linsi $input > $output 2>log.txt/;
24 }
25 elsif($strategy eq "G-INS-i") {
26 my $run = qx/mafft-ginsi $input > $output 2>log.txt/;
27 }
28 elsif($strategy eq "Q-INS-i") {
29 my $run = qx/mafft-qinsi $input > $output 2>log.txt/;
30 }
31
32 print $run;