hyphaltip

#Here is code for parsing 
use strict;
use warnings;
my $hmmertable = shift @ARGV;
open(HMMERTABLE, $hmmertable) || die "$hmmertable: $!";
while(<HMMERTABLE>){
    chomp;
    next if /^\#/ || /^\s+$/;
    my ($domain,$domacc,$tlen,$qname,$qacc,$qlen, $fullevalue,$fullscore,$fullbias,

hyphaltip

#!/usr/bin/perl
use strict;
use warnings;
use Bio::TreeIO;

my ($treefile,$taxon_name) = @ARGV;
my $in = Bio::TreeIO->new(-format => 'newick', -file => $treefile);
my $tree = $in->next_tree;
if( ! $tree ) {
 die "cannot parse treefile $treefile and find a valid tree";

hyphaltip

#!env perl
use strict;
use warnings;

use Bio::DB::GenBank;
use Bio::SeqIO;
use Getopt::Long;

# remote retrieval of sequences from GenBank
my $db = Bio::DB::GenBank->new;

hyphaltip

#!env perl
use strict;
use warnings;

my $dir = shift || "marker_files";
my $odir = shift || "marker_hmm";
mkdir($odir) unless -d $odir;
opendir(DIR,$dir)|| die "cannot open $dir: $!";
my $locusct =1;
for my $file ( readdir(DIR) ) {

hyphaltip

>vividMutant
ATGAGCCATACCGTGAACTCGAGCACCATGAACCCATGGGAGGTTGAGGC
GTAACAGCAATACCACTATGACCCTCGAACCGCGCCCACGGCCAACCCTC
TCTTCTTCCATACGCTCTACGCTCCCGGCGGTTATGACATTATGGGCTAT
CTGATTCAGATTATGAACAGGCCAAACCCCCAAGTAGAACTGGGACCTGT
TGACACGTCATGCGCTCTGATTCTGTGCGACCTGAAGCAAAAAGACACGC
CAATTGTGTACGCCTCGGAAGCTTTTCTCTATATGACAGGATACAGCAAT
GCGGAGGTCTTGGGGAGAAACTGCCGTTTTCTTCAGTCACCCGACGGAAT
GGTCAAGCCGAAATCGACAAGGAAGTACGTCGACTCCAACACGATCAATA
CGATGAGGAAAGCGATTGATAGGAACGCCGAGGTGCAGGTTGAGGTGGTC

hyphaltip

gene_id	bundle_id	chr	left	right	FPKM	FPKM_conf_lo	FPKM_conf_hi	status
NCU10129	18585	supercont10.1	1166	2603	50.9314	36.6581	65.2046	OK
NCU09901	18586	supercont10.1	3197	4838	15.5736	7.68094	23.4663	OK
NCU11134	18588	supercont10.1	15929	16647	0	0	0	OK
NCU09904	18589	supercont10.1	17889	19368	67.7417	51.2807	84.2028	OK
NCU09903	18587	supercont10.1	9603	13334	31.5378	20.3061	42.7695	OK
NCU09908	18592	supercont10.1	43708	44551	0	0	0	OK
NCU09907	18591	supercont10.1	40949	42632	0	0	0	OK
NCU09906	18590	supercont10.1	35915	39245	139.627	115.994	163.26	OK
NCU09910	18594	supercont10.1	49271	51866	22.6875	13.1612	32.2138	OK

hyphaltip

>MLOC_42952.1 cdna:novel contig:220312v1:morex_contig_2669042:2:251:-1 gene:MLOC_42952 transcript:MLOC_42952.1
GAGCTACTCGGGACTCCGCCGCCGCAGTCTTTCTCGATGGCCTTCTGTTTTTTCATACCC
TTGACCTTGAATATCATGATTGCATAGCTGCGGTGGACACCAAGGGAGAGACNNGCCTGA
TATTCAGGGTCCCTGGTGGTCAGGTTTATGATTTTGGCCAGGCTGATGACTTTGTTCAAC
ACGTCTTATTCAAGGTTCCTGGTGGTCGGTTTCATTATTTTGGTGTGGCTCATGGTTAAG
GTAAAGGAAG
>MLOC_42947.1 cdna:novel contig:220312v1:morex_contig_2668822:118:275:1 gene:MLOC_42947 transcript:MLOC_42947.1
CCCTTGGGCTCGCCGGGTTTCAGCACCGACCGGGTGCCTCCCAACACCACCACCAGCCGC
GGCGCCACCGACCCATCCTCCTACTCGGACGACGATGGCGAGGCGGAGGTCGACCCCAAT
GTGCACCCCGAGGACGACGGCACCACCGTTATCCTCGA

hyphaltip

# would be additional tests in t/LocalDB/DBFasta.t
# test out writing the Bio::PrimarySeq::Fasta objects with SeqIO

$db = Bio::DB::Fasta->new($test_dbdir, -reindex => 1);
my $out = Bio::SeqIO->new(-format => 'genbank');
# works
$primary_seq = Bio::Seq->new(-primary_seq => $db->get_Seq_by_acc('AW057119'));
# fails
#$primary_seq = $db->get_Seq_by_acc('AW057119');

hyphaltip

# concat multiple nexus formatted files into one nexus format file
# assuming sequence IDs are the same across all files
# and data is all aligned and all seqs are present in all files

use Bio::AlignIO;
use Bio::SimpleAlign;
use strict;
my %seqs;
for my $file ( @ARGV ) {
 my $in = Bio::AlignIO->new(-format=> 'nexus', -file => $file);

hyphaltip

#!/usr/bin/perl -w
# Jason Stajich jason<at>bioperl.org
use strict;
use Bio::DB::GenPept;
use Bio::DB::GenBank;
use Bio::SeqIO;

#  get the FASTA formatted header for BLAST database
my $db = Bio::DB::GenBank->new(-format => 'fasta');
my $out = Bio::SeqIO->new(-format => 'fasta');