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annotate pseudogenome.pl @ 0:47b586ab4729 draft default tip

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author nml
date Fri, 06 Apr 2018 14:29:17 -0400
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0
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1 #!/usr/bin/env perl
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2 use strict;
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3 use warnings;
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4 use autodie qw(:all);
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5 use Bio::SeqIO;
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6 use Readonly;
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7 use File::Basename;
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8 use Getopt::Long;
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9 use Pod::Usage;
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10 Getopt::Long::Configure('bundling');
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11
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12 =head1 NAME
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13
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14 nml_pseudogenome.pl - To create a single pseudo genome out of multiple contigs provided in a single fasta file. Contig are combined in order of appearances in file
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15
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16 =head1 SYNOPSIS
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17
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18 nml_pseudogenome.pl -i F<file_name.fna> -n 100 -c X -o F<filename.fna>
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19
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20 =head1 OPTIONS
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21
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22 =over
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23
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24 =item B<-i>, B<--input>
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25
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26 Multiple fasta file
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27
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28 =item B<-n>, B<--number>
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29
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30 Number of filler base pairs to be added, default : 10
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31
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32 =item B<-c>, B<--chars>
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33
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34 Character to be used as the 'glue' between contigs, default : 'N'
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35
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36 =item B<--id>
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37
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38 Name of fasta file to be used default: pseudogenome
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39
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40 =item B<-o>, B<--output>
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41
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42 Output file name, default : Same as input
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43
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44 =item B<-s>, B<--stitch>
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45
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46 Add the stitch pattern between contigs only
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47
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48 =item B<-h>, B<--help>
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49
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50 Print this help
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51
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52 =item EXAMPLE
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53
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54 nml_pseudogenome.pl -i multiple_fasta.fna -n 100 -c X -o pseudo.fna
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55
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56 nml_pseudogenome.pl -i another_multiple.fna
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57
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58 =back
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59
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60 =head1 DESCRIPTION
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61
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62 To create a single pseudo genome out of multiple contigs provided in a single fasta file. Contig are combined in order of appearances in file.
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63
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64 =cut
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65
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66 # Nonsub perlcode
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67
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68 Readonly my $DEFAULT_NUM_CHAR => 10;
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69 Readonly my $stitch_pattern => 'NNNNNCACACACTTAATTAATTAAGTGTGTGNNNNN';
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70 Readonly my $DEFAULT_CHAR => 'N';
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71 my ( $input,$id, $number, $char, $output,$stitch, $help );
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72
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73 GetOptions(
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74 'i|input=s' => \$input,
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75 'n|number=s' => \$number,
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76 'c|char=s' => \$char,
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77 'o|output=s' => \$output,
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78 'h|help' => \$help,
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79 's|stitch' => \$stitch,
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80 'id=s' => \$id
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81 );
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82 ($input,$id,$number,$char,$output) =check_inputs( $input, $number, $char,$output, $help,$stitch );
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83
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84
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85
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86 my $in = Bio::SeqIO->new(-file=>$input,-format=>'fasta');
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87
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88 my $sequence;
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89
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90 #go thru every sequence and append to main sequence
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91 while (my $seq = $in->next_seq()) {
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92 if ($stitch) {
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93 $sequence .= $seq->seq . $stitch_pattern;
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94 }
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95 else {
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96 $sequence .= $seq->seq . ($char x $number );
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97 }
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98
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99 }
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100
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101 my $main = Bio::Seq->new(-display_id=>$id,-seq=>$sequence);
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102
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103 my $out = Bio::SeqIO->new(-file => ">$output" ,-format=>'fasta');
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104 $out->write_seq($main);
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105
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106 exit;
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107
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108 =begin HTML
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109
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110 =head2 check_inputs
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111
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112 Title : check_inputs
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113 Usage : check_inputs($fasta,$num,$filler,$out_to,$usage);
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114 Function: check arguments provided by the user to see if they are usable and more or less correct
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115 Returns : Return 1 if all is correct,otherwise 0
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116 Args : $query: Query that we are looking for in the database. Could be accession number or locus_tag
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117 $db: Name of database we are looking for using the query provided
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118 $format: Ensure that format was given by user and is valid format
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119 $usage: If true, return usage description
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120 Throws : none
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121
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122 =cut
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123
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124 sub check_inputs {
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125 my ( $fasta, $num, $filler, $out_to, $usage,$use_stitch ) = @_;
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126
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127 if ( $help || !( $fasta || $num || $filler || $out_to ) ) {
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128 pod2usage();
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129 exit;
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130 }
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131
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132 if ( !($fasta) || !( -e $fasta ) ) {
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133 print STDERR "Error: Input file not given or does not exist\n";
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134 pod2usage();
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135 exit;
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136 }
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137
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138 if ($use_stitch) {
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139 print "Using stitch pattern\n";
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140
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141 }
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142 else {
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143 if ( !$num ) {
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144 $num = $DEFAULT_NUM_CHAR;
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145 print STDERR "Number of character not given, using $num\n";
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146 }
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147 elsif ( !( $num =~ /^\d+$/xms ) ) {
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148 print STDERR "Error: Number of character was not a number\n";
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149 pod2usage();
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150 exit;
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151 }
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152
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153 if ( !$filler ) {
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154 $filler = $DEFAULT_CHAR;
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155 print STDERR "No filler character given, using 'N'\n";
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156 }
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157
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158 }
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159
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160 if ( !($out_to) ) {
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161 $out_to = fileparse($fasta) . ".pseudogenome";
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162 print
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163 "Output file was not given. Result will be written to '$out_to'\n";
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164 }
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165 if ( ! $id) {
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166 $id = 'pseudogenome';
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167 }
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168
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169 return ( $fasta,$id, $num, $filler, $out_to );
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170 }
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171
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172 =end HTML
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173
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174 =head1 SEE ALSO
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175
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176 No related files.
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177
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178 =head1 AUTHOR
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179
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180 Philip Mabon, <philip.mabon@canada.ca>
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181
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182 =head1 BUGS
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183
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184 None reported.
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185
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186 =head1 COPYRIGHT & LICENSE
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187
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188 Copyright (C) 2018 by Public Health Agency of Canada
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189
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190 This program is free software; you can redistribute it and/or modify
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191 it under the same terms as Perl itself, either Perl version 5.8.2 or,
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192 at your option, any later version of Perl 5 you may have available.
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193
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194 =head1 DEVELOPER PAGE
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195
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196 No developer documentation.
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197
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198 =cut