pcantalupo

Hello,

I found a very simple bug in 'download_query_genbank.PLS'. Here is the 'git diff':

$ git diff -- download_query_genbank.PLS
diff --git a/scripts/utilities/download_query_genbank.PLS b/scripts/utilities/do
index 803f438..e1ede38 100755
--- a/scripts/utilities/download_query_genbank.PLS
+++ b/scripts/utilities/download_query_genbank.PLS
@@ -59,7 +59,7 @@ GetOptions(

pcantalupo

commit cd0e4415fbed27a6e8362d124f857e1edc78c88e
Author: Paul Cantalupo <[email protected]>
Date:   Fri Nov 16 12:56:19 2012 -0500

    fixing bug 3376

diff --git a/Bio/SearchIO/hmmer2.pm b/Bio/SearchIO/hmmer2.pm
index 9ef726c..b0ced06 100644
--- a/Bio/SearchIO/hmmer2.pm
+++ b/Bio/SearchIO/hmmer2.pm

pcantalupo

Running tests in bioperl-live without searchio-writer-bsmlresultwriter gave essentially same result as when removing blastxml files from bioperl-live:

$ diff prove.blastxml prove.bsmlresultwriter
6c6
<   (Missing operator before t?)
---
>   (Missing operator before t?)
726c726
< Files=339, Tests=22070, 147 wallclock secs ( 3.79 usr  1.28 sys + 130.78 cusr 13.28 csys = 149.13 CPU)
---

pcantalupo

=head2 monofreq

 Title   : monofreq
 Usage   : $seq = Bio::SeqUtils->monofreq($seq)
 Function: Method for determining the mononucleotide frequencies of
           a DNA sequence

 Returns : Array of mononucleotide frequencies T, C, G, A
 Args    : none

pcantalupo

#!/usr/bin/env perl

# Based on scripts and discussion found in http://seqanswers.com/forums/showthread.php?t=1425
# and https://www.biostars.org/p/43855/

# This script changes the color space sequence on the 2nd line of each fastq
# to base space.  It does not convert the qual string since SOLID qual is
# already in Sanger format.  The first base and quality value (primer) are
# discarded.

pcantalupo

#!/bin/bash

# get annotations
wget ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.genomic.gbff.gz
gunzip viral.1.genomic.gbff.gz
wget ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.protein.gpff.gz
gunzip viral.1.protein.gpff.gz

# download and create BLAST databases for viral refseq genomic
wget ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.1.genomic.fna.gz

pcantalupo

#!/usr/bin/env perl

my $base  = "ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/";

my @files = qw/gi_taxid_nucl.dmp.gz
               gi_taxid_prot.dmp.gz
               taxdump.tar.gz
               taxcat.tar.gz/;

foreach my $file (@files) {

pcantalupo

#!perl
# Author:  Jason Stajich <[email protected]>
# Purpose: Retrieve the NCBI Taxa ID for organism(s)

# TODO: add rest of POD
#

use LWP::UserAgent;
use XML::Twig;
use strict;

pcantalupo

>p53_NM000546 203..1384
atggaggagccgcagtcagatcctagcgtcgagccccctctgagtcaggaaacattttcagacctatggaaactacttcctgaaaacaacgttctgtcccccttgccgtcccaagcaatggatgatttgatgctgtccccggacgatattgaacaatggttcactgaagacccaggtccagatgaagctcccagaatgccagaggctgctccccccgtggcccctgcaccagcagctcctacaccggcggcccctgcaccagccccctcctggcccctgtcatcttctgtcccttcccagaaaacctaccagggcagctacggtttccgtctgggcttcttgcattctgggacagccaagtctgtgacttgcacgtactcccctgccctcaacaagatgttttgccaactggccaagacctgccctgtgcagctgtgggttgattccacacccccgcccggcacccgcgtccgcgccatggccatctacaagcagtcacagcacatgacggaggttgtgaggcgctgcccccaccatgagcgctgctcagatagcgatggtctggcccctcctcagcatcttatccgagtggaaggaaatttgcgtgtggagtatttggatgacagaaacacttttcgacatagtgtggtggtgccctatgagccgcctgaggttggctctgactgtaccaccatccactacaactacatgtgtaacagttcctgcatgggcggcatgaaccggaggcccatcctcaccatcatcacactggaagactccagtggtaatctactgggacggaacagctttgaggtgcgtgtttgtgcctgtcctgggagagaccggcgcacagaggaagagaatctccgcaagaaaggggagcctcaccacgagctgcccccagggagcactaagcgagcactgcccaacaacaccagctcctctccccagccaaagaagaaaccactggatggagaatatttcacccttcagatccgtg

pcantalupo

>contig_13
ACCTCCATCAGAGCTGATTCAGTTATTCAACTATACCACCATCATCAAGGACATCCGTTAGTGTAACAACGTGTATGCTTTCACGTTGACGAGCGCGTCGGCCAGAGTTAATAATCCCGTACGTTTACACGAGGCTGTTGCTACTGGTAGGAATGTAACTACCATATCCTGGGAGCACTTTGTCGCCGCATCGGTTCCCTGACAAAACTACCTGGACGTGCGCCTTCAATCGCTCAGTTATACTTTTATGACTGCAGTGATGGTTACTACTACAACGCTATGCTGGAGACTTGTCCATCTGGGCGGGTTAGGATCGGTTCATCGTGTTGATCTTGCAACGTGTTTTCACAGACAACATCTTTTTGGCGGAGTTATTTAAGAACGCGTACGAGCGAACATCTGCGAACATCTCGTATCGAAGGTGTTGATCAACGTCGGTAAAACCGGCCGTCGGTGGCATGAATAGAAGGGCTATTGATCAACGGACAAACTGCATCAGTCGAGACCTATTGGTGCAGACCCGTAATACTGGGAGGTTAGTGTAATAAGCAA
>contig_20
TGGCGAAGAAATAGATCTTCATATTGAGTCACTTTTCGTTACAGACTTTCGATTTCTTGGCAATATATTTCACTAAAAAAACAATTCCTATTTGCCAAAAAACTTAATTCACCAAGGTCATTTACTAATCGGTCGATGATTTGTTCGAATTTGACATAACTCAAGCCACATTCCGGAATTGTCTATCGCACCTATGGACCTCGAAGTCCATGTTAACGATGAATATTCACTAATCACTAGGTATAAGGCTGGAACGCGATATTTTTAAATTAAGATTGCTTAGAGCCTAGTTTATTCCAAAATATTACTGATTACTGTGAAAAAATCCATTTGTATGAATCATCATCGTCAGTACAAAGGGCCCTTTTTGTAATTGATCCAGGGTTTAGTAGTATAATTGATATTTGTCCAAAGTGGGCACAACCGGACTGCTAAAATGTCGAAAGTAT