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arty
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#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use Getopt::Long;
use lib "$FindBin::RealBin/../lib";
#--------------------------------------------------------------------------------
#----------------------------------- MAIN ---------------------------------------
#--------------------------------------------------------------------------------
my $usage = "
Description:
arty - a suite of tools for hacking genomics data
Commands:
help Show this message and exit.
### File Formats
fasta Work with Fasta files. Not yet implimented.
";
# bed Work with BED files. Not yet implimented.
#
# fastq Work with Fastq files. Not yet implimented.
#
# gff3 Work with GFF3 files. Not yet implimented.
#
# vcf Work with VCF files. Not yet implimented.
#
# ### Data Sources
#
# clinvar Work with ClinVar data.
#
# dbsnp Work with dbSNP data. Not yet implimented.
#
# go Work with data Gene Onology data. Not yet implimented.
#
# hgnc Work with data HGNC data. Not yet implimented.
#
# hpo Work with Human Phenotype Ontology data. Not yet implimented.
#
# omim Work with OMIM data. Not yet implimented.
#
# so Work with Sequence Ontology data. Not yet implimented.
# Dispatch command
#--------------------------------------------------------------------------------
my $command = shift @ARGV || '';
if (! $command) {
die "$usage\n\nFATAL : missing_command : You must provide a command to ugp_db2\n";
}
elsif ($command eq 'bed') {
command_bed();
}
elsif ($command eq 'fasta') {
command_fasta();
}
elsif ($command eq 'fastq') {
command_fastq();
}
elsif ($command eq 'gff3') {
command_gff3();
}
elsif ($command eq 'vcf') {
command_vcf();
}
elsif ($command eq 'clinvar') {
command_clinvar();
}
elsif ($command eq 'dbsnp') {
command_dbsnp();
}
elsif ($command eq 'go') {
command_go();
}
elsif ($command eq 'hgnc') {
command_hgnc();
}
elsif ($command eq 'hpo') {
command_hpo();
}
elsif ($command eq 'omim') {
command_omim();
}
elsif ($command eq 'so') {
command_so();
}
else {
die "$usage\n\nFATAL : unknown_command : $command\n";
}
#--------------------------------------------------------------------------------
#---------------------------------- Commands ------------------------------------
#--------------------------------------------------------------------------------
sub command_bed {
my $usage = "
Synopsis:
arty bed
Description:
Work with bed data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty bed\n";
}
#--------------------------------------------------------------------------------
sub command_fasta {
my $usage = "
Synopsis:
arty fasta rev_comp sequence.fa
arty fasta translate sequence.fa
arty fasta m50 sequence.fa
Description:
Work with fasta data. The `arty fasta` tool provides a variety
of methods to manipulate and report on sequence data in fasta
format.
Functions:
chunk <integer>
Split a single multi-fasta file into the given number of sub
files specified by chunks.
split
Split a multi-fasta into individual files. One for each fasta
record.
break <integer>
Break the sequence from a single-fasta file into a multi-fasta
file with subsequences of the given size.
eval_code <code>
Run the given code on (\$seq_obj, \$seq or \$header). If
the code block returns a positive value then the sequence is
printed. This can be used to build complex and custom filters.
eval_all <code>
Run the given code on (\$seq_obj, \$seq or \$header).
Prints all sequences regardless of the return value of the
evaled code. This can but used to perform operations (e.g. soft
to hard masking with s/[a-z]/N/g, but still print every sequence
even if it's unaltered.
extract_ids <id_file.txt>
Extract all of the sequences who's IDs are found in the given
file.
grep_header <pattern>
Grep through a multi fasta file and print out only the fasta
sequences that have a match in the header. Use grepv_header for
negation.
grep_seq <pattern>
Grep through a multi fasta file and print out only the fasta
sequences that have a match in the sequence. Use grepv_seq for
negation.
wrap <integer>
Wrap the sequence output to a given number of columns.
translate <string>
Translate a given nucleotide sequence to protein sequence.
Accepts 0,1,2 (for the phase) or 'maker' if you want to use the
frame from MAKER produced headers
trim_maker_utr
Prints MAKER produced transcipts without the leading and
trailing UTR sequence
seq_only
Print only the sequence (without the header) to STDOUT. This
can also be accomplished with grep -v '>' fasta_file.
nt_count
Print the number and percentage of every nt/aa found in the
sequence.
length
Print the length of each sequence.
mapable_length
Print the mapable length (remove all Ns) of each sequence.
total_length
Print the total length of all sequences.
n50
Calculate the N-50 (http://en.wikipedia.org/wiki/N50_statistic)
of the sequences in the file.
tab
Print the header and sequence on the same line separated by a
tab.
table
Print in table format rather than fasta format.
print
Print the sequence. Use in conjuction with 'wrap' or other
formatting commands to reformat the sequence.
reverse
Reverse the order of the sequences in a fasta file.
rev_seq
Reverse the sequence (the order of the nt/aa).
comp_seq
Complement the nucleotide sequence.
rev_comp
Reverse compliment a sequence. Same as --rev_seq && --comp_seq
together.
uniq
Print only uniq sequences. This method only compares complete
sequences.
uniq_sub
Print only uniq sequences, but also check that shorter sequences
are not perfect substrings of longer sequences.
shuffle_order
Randomize the order of the sequences in a multi-fasta file.
shuffle_seq
Randomize the sequence (the order of the nt/aa).
shuffle_codon
Randomize the order of the codons in a nucleotide sequence.
shuffle_pick
Pick a given number of sequences from a multi-fasta file.
select
Pass in a file with IDs and return sequences with these IDs.
remove
Pass in a file with IDs and remove sequences with these IDs.
map_ids
Pass in a file with two columns of IDs and map the IDs in the
fasta headers from the first column of the ID file to the second
column of the ID file. If an ID in the fasta header is not
found in the first column of the ID file then issue a warning,
but leave the ID unmapped.
fix_prot
Fix protein fasta files for use as blast database. Removes spaces
and '*' and replaces any non amino acid codes with C.
subseq
Grab a sub-sequence from a fasta file based on coordinates. The
requested coordinates are in the form seqid:start-end;
filter_horter
Filter (remove) entries shorter than the filter. IE \"--filter_shorter 800\"
will filter all sequences <= 800 basepairs long.
filter_longer
Filter (remove entries longer than the filter. IE \"--filter_longer 800\"
will filter all sequences > 800 basepairs long.
mask_fasta
Masks the genome using coordinates from a gff3 file
";
# Dispatch command
#--------------------------------------------------------------------------------
my $command = shift @ARGV || '';
if (! $command) {
die "$usage\n\nFATAL : missing_command : You must provide a command to ugp_db2\n";
}
elsif ($command eq 'help') {
print "$usage\n";
}
elsif ($command eq 'chunk') {
command_fasta_chunk();
}
elsif ($command eq 'split') {
command_fasta_split();
}
elsif ($command eq 'break') {
command_fasta_break();
}
elsif ($command eq 'eval_code') {
command_fasta_eval_code();
}
elsif ($command eq 'eval_all') {
command_fasta_eval_all();
}
elsif ($command eq 'extract_ids') {
command_fasta_extract_ids();
}
elsif ($command eq 'grep_header') {
command_fasta_grep_header();
}
elsif ($command eq 'grep_seq') {
command_fasta_grep_seq();
}
elsif ($command eq 'wrap') {
command_fasta_wrap();
}
elsif ($command eq 'translate') {
command_fasta_translate();
}
elsif ($command eq 'trim_maker_utr') {
command_fasta_trim_maker_utr();
}
elsif ($command eq 'seq_only') {
command_fasta_seq_only();
}
elsif ($command eq 'nt_count') {
command_fasta_nt_count();
}
elsif ($command eq 'length') {
command_fasta_length();
}
elsif ($command eq 'mapable_length') {
command_fasta_mapable_length();
}
elsif ($command eq 'total_length') {
command_fasta_total_length();
}
elsif ($command eq 'n50') {
command_fasta_n50();
}
elsif ($command eq 'tab') {
command_fasta_tab();
}
elsif ($command eq 'table') {
command_fasta_table();
}
elsif ($command eq 'print') {
command_fasta_print();
}
elsif ($command eq 'reverse') {
command_fasta_reverse();
}
elsif ($command eq 'rev_seq') {
command_fasta_rev_seq();
}
elsif ($command eq 'comp_seq') {
command_fasta_comp_seq();
}
elsif ($command eq 'rev_comp') {
command_fasta_rev_comp();
}
elsif ($command eq 'uniq') {
command_fasta_uniq();
}
elsif ($command eq 'uniq_sub') {
command_fasta_uniq_sub();
}
elsif ($command eq 'shuffle_order') {
command_fasta_shuffle_order();
}
elsif ($command eq 'shuffle_seq') {
command_fasta_shuffle_seq();
}
elsif ($command eq 'shuffle_codon') {
command_fasta_shuffle_codon();
}
elsif ($command eq 'shuffle_pick') {
command_fasta_shuffle_pick();
}
elsif ($command eq 'select') {
command_fasta_select();
}
elsif ($command eq 'remove') {
command_fasta_remove();
}
elsif ($command eq 'map_ids') {
command_fasta_map_ids();
}
elsif ($command eq 'fix_prot') {
command_fasta_fix_prot();
}
elsif ($command eq 'subseq') {
command_fasta_subseq();
}
elsif ($command eq 'filter_shorter') {
command_fasta_filter_shorter();
}
elsif ($command eq 'filter_longer') {
command_fasta_filter_longer();
}
elsif ($command eq 'mask_fasta') {
command_fasta_mask_fasta();
}
else {
die "$usage\n\nFATAL : unknown_command : $command\n";
}
}
#--------------------------------------------------------------------------------
sub command_fasta_chunk {
my $usage = "
Synopsis:
arty fasta chunk
Description:
Apply the chunk function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty fastq\n";
}
#--------------------------------------------------------------------------------
sub command_fasta_split {
my $usage = "
Synopsis:
arty fasta split
Description:
Apply the split function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty fastq\n";
}
#--------------------------------------------------------------------------------
sub command_fasta_break {
my $usage = "
Synopsis:
arty fasta break
Description:
Apply the break function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty fastq\n";
}
#--------------------------------------------------------------------------------
sub command_fasta_eval_code {
my $usage = "
Synopsis:
arty fasta eval_code
Description:
Apply the eval_code function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty fastq\n";
}
#--------------------------------------------------------------------------------
sub command_fasta_eval_all {
my $usage = "
Synopsis:
arty fasta eval_all
Description:
Apply the eval_all function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty fastq\n";
}
#--------------------------------------------------------------------------------
sub command_fasta_extract_ids {
my $usage = "
Synopsis:
arty fasta extract_ids
Description:
Apply the extract_ids function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty fastq\n";
}
#--------------------------------------------------------------------------------
sub command_fasta_grep_header {
my $usage = "
Synopsis:
arty fasta grep_header
Description:
Apply the grep_header function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty fastq\n";
}
#--------------------------------------------------------------------------------
sub command_fasta_grep_seq {
my $usage = "
Synopsis:
arty fasta grep_seq
Description:
Apply the grep_seq function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty fastq\n";
}
#--------------------------------------------------------------------------------
sub command_fasta_wrap {
my $usage = "
Synopsis:
arty fasta wrap
Description:
Apply the wrap function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty fastq\n";
}
#--------------------------------------------------------------------------------
sub command_fasta_translate {
my $usage = "
Synopsis:
arty fasta translate
Description:
Apply the translate function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty fastq\n";
}
#--------------------------------------------------------------------------------
sub command_fasta_trim_maker_utr {
my $usage = "
Synopsis:
arty fasta trim_maker_utr
Description:
Apply the trim_maker_utr function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty fastq\n";
}
#--------------------------------------------------------------------------------
sub command_fasta_seq_only {
my $usage = "
Synopsis:
arty fasta seq_only
Description:
Apply the seq_only function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,
);
my $opt_success = GetOptions(\%opt,
'help|h',
);
if ($help) {
print $usage;
exit(0);
}
die $usage if ! $opt_success;
die "FATAL : function_not_yet_implimented : arty fastq\n";
}
#--------------------------------------------------------------------------------
sub command_fasta_nt_count {
my $usage = "
Synopsis:
arty fasta nt_count
Description:
Apply the nt_count function on fasta data.
Options:
--option, -o [default]
This options does something.
";
my ($help);
my %opt = (help => \$help,