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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/perl
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 use strict;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 no warnings; #genbank produces annoying warning if no sequence is found
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 #use FindBin;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 #use lib "$FindBin::Bin/lib";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 use Bio::DB::GenBank;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 use Bio::SeqIO;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 use Bio::Root::Exception;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 use Error qw(:try);
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11
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 my $datafile = $ARGV[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 my $datatype = $ARGV[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 my $outtype = $ARGV[2];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 my $outfile = $ARGV[3];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 my $nodata = $ARGV[4];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 my $accessions;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 my @accnums;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 open (FILE,"<$datafile") or die "Cannot open file containing accession numbers\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 open (OUT,">$outfile") or die "Cannot open outfile\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 close OUT; #This overwrites old file if it exists
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25 open (ND,">$nodata") or die "Cannot open file\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 my $fh = Bio::SeqIO->newFh(-format=>$outtype, -file=>">>$outfile");
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27
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28
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29 while (<FILE>)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 chomp;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 next unless ($_);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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33 push(@accnums, $_);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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34 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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35 close FILE;
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36
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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37 my $countnames = 0;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 foreach (@accnums){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 #Should check input for one word per line and throw error if not, which is not done
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40
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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41 $accessions = $_;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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42 chomp;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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43 if($accessions eq ""){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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44 die "Put spaces between accession numbers. No Empty Lines allowed.\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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45 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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46 my $qry_string .= $accessions."[organism]"." ";
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47
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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48 # my $GBseq;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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49 my $gb = new Bio::DB::GenBank;
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50 my $query = Bio::DB::Query::GenBank->new
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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51 (-query =>$qry_string,
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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52 -db =>$datatype);
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53
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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54 my $seqio;
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55
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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56 if (eval {$gb->get_Stream_by_query($query)}){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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57 $seqio = $gb->get_Stream_by_query($query);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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58 while( my $GBseq = $seqio->next_seq ) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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59 my $sequence = $GBseq; # read a sequence object
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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60 print $fh $sequence; # write a sequence object
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61 }
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62 }else{
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63 print ND "$accessions\n";
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64 }
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65 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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66 exit;
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67
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