standage

/*
Copyright (c) 2013-2014, Daniel S. Standage <daniel.standage@gmail.com>

Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.

THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR

standage

#!/usr/bin/env perl

# Copyright (c) 2013, Daniel S. Standage <daniel.standage@gmail.com>
#
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF

standage

#!/usr/bin/env perl
use strict;
use Bio::SeqIO;
use Getopt::Long;

# Given a set of transcript or protein alignments in GeneSeqer or GenomeThreader
# format, retrieve all sequences that map to the specified genomic region
#
# Example: perl gsq-select.pl Chr1:100001-200000 tair-ests.fa est-alignments.gsq

standage

#!/usr/bin/env perl

# Copyright (c) 2012-2013, Daniel S. Standage <daniel.standage@gmail.com>
#
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF

standage

#!/usr/bin/env perl
use strict;

my %alignments;
my @exon_scores;
my $align_score;
while(my $line = <STDIN>)
{
  if($line =~ m/ Exon +\d+.+; score: (.+)/)
  {

standage

#!/usr/bin/env perl

# Copyright (c) 2013, Daniel S. Standage <daniel.standage@gmail.com>
#
# input:  two columns of data in tab-delimited format, mapping from a key
#         (column 1) to a value (column 2);
# output: also two columns of data in tab delimited format, but all values
#         sharing the same key are printed on a single line; that is, each key
#         corresponds to a comma-separated list of associated values

standage

##gff-version   3
##sequence-region   PdomScaf0001 252075 255869
PdomScaf0001  maker	mRNA	252075	255869	.	-	.	ID=PdomMRNAr1.1-00022.1;_AED=0.29;_eAED=0.29;_QI=0|0.5|0.33|1|1|1|3|893|923
PdomScaf0001	maker	exon	252075	255370	118	-	.	Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	maker	stop_codon	252968	252970	.	-	.	Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	.	CDS	252968	255370	.	-	.	ID=myCDS;Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	maker	exon	255453	255790	35.2	-	.	Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	.	CDS	255453	255790	.	-	.	ID=myCDS;Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	maker	exon	255839	255869	9.8	-	.	Parent=PdomMRNAr1.1-00022.1
PdomScaf0001	.	CDS	255839	255869	.	-	.	ID=myCDS;Parent=PdomMRNAr1.1-00022.1

standage

>gi|94449065|gb|DQ473580.1| Ricinus communis plastid Tic40 mRNA, complete cds; nuclear gene for plastid product
ACGT
>gi|94449065|gb|DQ473580.1|abcdefghijk Ricinus communis plastid Tic40 mRNA, complete cds; nuclear gene for plastid product
ACGT
>gb|DQ473580.1| Ricinus communis plastid Tic40 mRNA, complete cds; nuclear gene for plastid product
ACGT
>gb|DQ473580.1|abcdefghijk Ricinus communis plastid Tic40 mRNA, complete cds; nuclear gene for plastid product
ACGT
>gi|61556715|ref|NM_001013027.1| Danio rerio ba1 globin, like (ba1l), mRNA
ACGT

standage

#!/usr/bin/env python
import sys
import re

aedgt = 0
eaedgt = 0
perfect = 0
nosupport = 0
for line in sys.stdin:
  if "\tmRNA\t" in line:

standage

#include <stdio.h>

int main()
{
  int frequency[26];
  int ch;

  for (ch = 0; ch < 26; ch++)
    frequency[ch] = 0;