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| 1 : | golsen | 1.1 | ######################################################################## |
| 2 : | # -*- perl -*- | ||
| 3 : | # | ||
| 4 : | golsen | 1.3 | # Copyright (c) 2003-2007 University of Chicago and Fellowship |
| 5 : | golsen | 1.1 | # for Interpretations of Genomes. All Rights Reserved. |
| 6 : | # | ||
| 7 : | # This file is part of the SEED Toolkit. | ||
| 8 : | # | ||
| 9 : | # The SEED Toolkit is free software. You can redistribute | ||
| 10 : | # it and/or modify it under the terms of the SEED Toolkit | ||
| 11 : | # Public License. | ||
| 12 : | # | ||
| 13 : | # You should have received a copy of the SEED Toolkit Public License | ||
| 14 : | # along with this program; if not write to the University of Chicago | ||
| 15 : | # at info@ci.uchicago.edu or the Fellowship for Interpretation of | ||
| 16 : | # Genomes at veronika@thefig.info or download a copy from | ||
| 17 : | # http://www.theseed.org/LICENSE.TXT. | ||
| 18 : | # | ||
| 19 : | |||
| 20 : | # collect_related_sequences [options] dbfile seqfile | ||
| 21 : | |||
| 22 : | # use Data::Dumper; | ||
| 23 : | use strict; | ||
| 24 : | use gjoseqlib; | ||
| 25 : | use collect_related_sequences; | ||
| 26 : | |||
| 27 : | golsen | 1.3 | my $min_coverage = 0.80; |
| 28 : | my $tmp_dir; | ||
| 29 : | my $max_e_value = 0.001; | ||
| 30 : | my $fids; | ||
| 31 : | my $min_identity = 0.25; | ||
| 32 : | my $merge = 1; | ||
| 33 : | my $nr = 0; | ||
| 34 : | my $tmp; | ||
| 35 : | my $extra_ends = 10; | ||
| 36 : | golsen | 1.2 | |
| 37 : | my $usage =<<"End_of_Usage"; | ||
| 38 : | golsen | 1.1 | |
| 39 : | Usage: collect_related_sequences [options] dbfile seqfile | ||
| 40 : | |||
| 41 : | Options: | ||
| 42 : | |||
| 43 : | golsen | 1.3 | -c min_coverage # fraction of exemplar coverged (D=$min_coverage) |
| 44 : | golsen | 1.1 | -d tmp_dir # name of temporary directory |
| 45 : | golsen | 1.3 | -e max_e_value # required match significance (D=$max_e_value) |
| 46 : | -f 'fid ...' # use exemplar(s) from SEED (instead of seqfile) | ||
| 47 : | -i min_identity # required similarity to exemplar (D=$min_identity) | ||
| 48 : | golsen | 1.2 | -m # do NOT merge queries with found sequences |
| 49 : | -n # use SEED nr database (instead of dbfile) | ||
| 50 : | golsen | 1.1 | -t tmp # place for temporary directory |
| 51 : | golsen | 1.3 | -x extra_ends # extra length at ends (D=$extra_ends residues) |
| 52 : | golsen | 1.1 | |
| 53 : | End_of_Usage | ||
| 54 : | |||
| 55 : | while ( $ARGV[0] =~ /^-/ ) | ||
| 56 : | { | ||
| 57 : | $_ = shift; | ||
| 58 : | if ( s/^-c// ) { $min_coverage = $_ || shift } | ||
| 59 : | elsif ( s/^-d// ) { $tmp_dir = $_ || shift } | ||
| 60 : | elsif ( s/^-e// ) { $max_e_value = $_ || shift } | ||
| 61 : | golsen | 1.3 | elsif ( s/^-f// ) { $fids = $_ || shift } |
| 62 : | golsen | 1.1 | elsif ( s/^-i// ) { $min_identity = $_ || shift } |
| 63 : | golsen | 1.2 | elsif ( s/^-m// ) { $merge = 0 } |
| 64 : | golsen | 1.3 | elsif ( s/^-n// ) { $nr = 1 } |
| 65 : | golsen | 1.1 | elsif ( s/^-t// ) { $tmp = $_ || shift } |
| 66 : | elsif ( s/^-x// ) { $extra_ends = $_ || shift } | ||
| 67 : | else | ||
| 68 : | { | ||
| 69 : | usage( "Bad command flag '$_'\n" ); | ||
| 70 : | } | ||
| 71 : | } | ||
| 72 : | |||
| 73 : | golsen | 1.3 | my $dbfile = shift @ARGV if ! $nr; |
| 74 : | $nr || -f $dbfile || usage( "Cannot locate database file '$dbfile'." ); | ||
| 75 : | golsen | 1.2 | |
| 76 : | golsen | 1.3 | my @seq; |
| 77 : | my @fids = (); | ||
| 78 : | golsen | 1.1 | |
| 79 : | golsen | 1.2 | if ( $fids ) |
| 80 : | { | ||
| 81 : | golsen | 1.3 | @fids = ref( $fids ) eq 'ARRAY' ? @$fids |
| 82 : | : split /[,\s]+/, $fids; | ||
| 83 : | golsen | 1.2 | } |
| 84 : | else | ||
| 85 : | { | ||
| 86 : | my $seqfile = shift @ARGV; | ||
| 87 : | @seq = read_fasta( $seqfile ); | ||
| 88 : | @seq or usage( "Failed to read sequences from '$seqfile'." ); | ||
| 89 : | } | ||
| 90 : | golsen | 1.1 | |
| 91 : | my $options = | ||
| 92 : | golsen | 1.3 | { max_e_value => $max_e_value, |
| 93 : | min_coverage => $min_coverage, | ||
| 94 : | golsen | 1.1 | min_identity => $min_identity, |
| 95 : | extra_ends => $extra_ends | ||
| 96 : | }; | ||
| 97 : | golsen | 1.2 | |
| 98 : | golsen | 1.3 | $options->{ exemplars } = \@seq if ! $fids; |
| 99 : | $options->{ fids } = \@fids if $fids; | ||
| 100 : | $options->{ no_merge } = 1 if ! $merge; | ||
| 101 : | $options->{ nr } = 1 if $nr; | ||
| 102 : | $options->{ seq_db } = $dbfile if ! $nr; | ||
| 103 : | $options->{ tmp } = $tmp if $tmp; | ||
| 104 : | $options->{ tmp_dir } = $tmp_dir if $tmp_dir; | ||
| 105 : | golsen | 1.2 | |
| 106 : | golsen | 1.3 | my $found = collect_related_sequences::collect_related_sequences( $options ); |
| 107 : | golsen | 1.2 | |
| 108 : | golsen | 1.3 | print_alignment_as_fasta( $found ) if $found; |
| 109 : | golsen | 1.1 | |
| 110 : | exit; | ||
| 111 : | |||
| 112 : | |||
| 113 : | sub usage | ||
| 114 : | { | ||
| 115 : | print STDERR join( "\n", @_, $usage ); | ||
| 116 : | exit; | ||
| 117 : | } |
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