osiris_phylogenetics: phyloconversion/seqConverterG.pl annotate

author	osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date	Tue, 11 Mar 2014 12:19:13 -0700
parents
children

rev	line source
0 5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	1 #!/usr/bin/perl -w
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	2 #
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	3 # seqConverter.pl v1.2
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	4 # Last modified August 12, 2010 21:09
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	5 # Minor modifications for running in Galaxy by TH Oakley Jan 2012
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	6 # (c) Olaf R.P. Bininda-Emonds
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	7 #
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	8 # Input:
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	9 # Sequence data in any of fasta, GenBank, nexus, (classic or extended) phylip,
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	10 # or Se-Al formats
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	11 #
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	12 # Output:
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	13 # Sequence data in any of fasta, nexus, (classic or extended) phylip, and/or
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	14 # Se-Al formats.
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	15 #
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	16 # Usage: seqConverter.pl -d<filename> -o<f\|n\|pc\|pe\|s> [-a] [-c<number>] [-g]
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	17 # [-G] [-H] [-i<f\|g\|n\|p\|s>] [-j] [-l<number>] [-n] [-r<a\|i>] [-s] [-t]
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	18 # [-u] [-v] [-h]
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	19 # [-O]<outfile> specify outfile
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	20 # options: -a = print out accession numbers instead of taxon labels for nexus
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	21 # and phylip output
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	22 # -c<number> = global genetic code (to be used for translation unless
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	23 # otherwise specified) (default = standard code; end
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	24 # with * to override local settings)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	25 # -d<filename> = file containing raw sequence information; * = batch
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	26 # convert all specified file types in working
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	27 # directory (suffixes must be .fasta / .fas, .gb,
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	28 # .nexus / .nex, .phylip / .ph, or .seal as
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	29 # appropriate)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	30 # -g = do not convert ~ gap characters (e.g., from BioEdit) to -
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	31 # -G = convert flanking gaps to Ns
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	32 # -H = convert sequence data to haplotype data
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	33 # -i<f\|g\|n\|p\|s> = format of sequence file (fasta (f), GenBank (g),
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	34 # nexus (n), phylip (p), or Se-Al (s)); default =
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	35 # autodetect
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	36 # -j = produce jackknifed data sets each with a single sequence
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	37 # deleted
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	38 # -l<number> = interleave nexus- and/or phylip-formatted output
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	39 # (default = sequential) with specified sequence length
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	40 # (between 10 and 100 inclusive; default = 80);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	41 # NOTE: also sets default interleave length for fasta
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	42 # output
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	43 # -n = convert ambiguous nucleotides to Ns
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	44 # -o<f\|n\|pc\|pe\|s> = output results in any or all of fasta (f), nexus
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	45 # (n), classic or extended phylip (pc or pe),
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	46 # and/or Se-Al (s) formats (NOTE: flag can be
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	47 # invoked multiple times)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	48 # -r<a\|i> = order sequences in final output alphabetically by name
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	49 # (a; default) or in input order from file (i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	50 # -s = split data set into individual partitions according to nexus
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	51 # charset statements
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	52 # -t = translate sequences into amino acids
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	53 # -u = interactive user-input mode
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	54 # -h = print this message and quit
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	55 # -v = verbose output
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	56
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	57 use strict;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	58 use POSIX;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	59 #THO added ability for Galaxy -G to specify outfile name
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	60 my $OutFile;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	61
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	62 # Set user-input defaults and associated parameters
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	63 # Data set variables
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	64 my $inputType = ""; # Options are "fasta", "GenBank", "nexus", "phylip", and "Se-Al"
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	65 my ($readFile, @seqFiles);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	66 my $dataSource;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	67 my $seqType = "nucleotide";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	68 my $globalGenCode = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	69 my $globalOverride = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	70
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	71 my (@accNum, %nameLabel, %sequence, %geneticCode, %accPresent);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	72 my (@charsetList, %charsetStart, %charsetEnd);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	73 my (%deletedSeq, %finalSeq);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	74 my $seqCount;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	75 my $ntax;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	76 my $nameClean = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	77 my $skipDuplicates = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	78
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	79 # User input variables
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	80 my $seqOrder = "alphabetical"; # Options are "alphabetical" (default) and "input"
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	81 my $seqSplit = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	82 my $jackknife = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	83 my $gapChange = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	84 my $ambigChange = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	85 my $translateSeqs = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	86 my $haploTyping = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	87 my $haploFile;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	88 my $flankGap = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	89
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	90 # Translation variables and genetic codes
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	91 my %transTable = ('1' => 'standard',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	92 '2' => 'vertebrate mitochondrial',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	93 '3' => 'yeast mitochondrial',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	94 '4' => 'mold, protozoan and colenterate mitochondrial and mycoplasam/spiroplasma',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	95 '5' => 'invertebrate mitochondrial',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	96 '6' => 'ciliate, dasycladacean and hexamita nuclear',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	97 '9' => 'echinoderm mitochondrial',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	98 '10' => 'euplotid nuclear',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	99 '11' => 'bacterial and plant plastid',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	100 '12' => 'alternative yeast nuclear',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	101 '13' => 'ascidian mitochondrial',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	102 '14' => 'alternative flatworm mitochondrial',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	103 '15' => 'Blepharisma nuclear',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	104 '16' => 'chlorophycean mitochondrial',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	105 '21' => 'trematode mitochondrial',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	106 '22' => 'Scenedesmus obliquus mitochondrial',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	107 '23' => 'Thraustochytrium mitochondrial');
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	108 my %gb2seal = ('1' => '0',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	109 '2' => '1',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	110 '3' => '2',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	111 '4' => '3',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	112 '4' => '4',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	113 '5' => '5',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	114 '6' => '6',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	115 '9' => '7',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	116 '10' => '8',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	117 '11' => '9',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	118 '12' => '10',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	119 '13' => '11',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	120 '14' => '12',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	121 '15' => '13',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	122 '16' => '1',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	123 '21' => '1',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	124 '22' => '1',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	125 '23' => '1');
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	126 my %seal2gb = ('0' => '1',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	127 '1' => '2',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	128 '2' => '3',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	129 '3' => '4',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	130 '4' => '4',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	131 '5' => '5',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	132 '6' => '6',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	133 '7' => '9',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	134 '8' => '10',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	135 '9' => '11',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	136 '10' => '12',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	137 '11' => '13',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	138 '12' => '14',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	139 '13' => '15');
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	140 my %genCodes;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	141 foreach my $code (qw(0 1 2 3 4 5 6 9 10 11 12 13 14 15 16 21 22 23))
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	142 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	143 $genCodes{$code} = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	144 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	145 my %DNAtoAA;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	146 my @ambigList = qw(A C G T M R W S Y K V H D B N);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	147 my %ambigCode = ('A' => 'A', 'C' => 'C', 'G' => 'G', 'T' => 'T',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	148 'AC' => 'M', 'AG' => 'R', 'AT' => 'W', 'CG' => 'S', 'CT' => 'Y', 'GT' => 'K',
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	149 'ACG' => 'V', 'ACT' => 'H', 'AGT' => 'D', 'CGT' => 'B', 'ACGT' => 'N');
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	150 my (%constitNTlist);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	151 while (my ($nt, $code) = each %ambigCode) # Where $nt = key and $code = value
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	152 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	153 push @{$constitNTlist{$code}}, $_ foreach (split("",$nt));
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	154 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	155
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	156 # Output variables
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	157 my $maxLength;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	158 my $fastaPrint = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	159 my $fastaOut;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	160 my $nexusPrint = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	161 my $nexusOut;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	162 my ($phylipTradPrint, $phylipExtPrint) = (0, 0);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	163 my $phylipOut;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	164 my $sealPrint = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	165 my $sealOut;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	166 my $outFormat = "sequential";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	167 my $interleaveLength = 80;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	168 my $fastaLength = 80;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	169 my $accPrint = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	170
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	171 # Miscellaneous variables
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	172 my $verbose = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	173 my $debug = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	174 my $perlScript = "seqConverterG.pl";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	175 my $version = "1.2";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	176
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	177 # Read in user input
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	178 if (not @ARGV or join(' ', @ARGV) =~ /\s-u/ or $ARGV[0] =~ /^-u/) # Enter interactive user-input mode
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	179 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	180 print "Entering interactive user-input mode. Type \"q\" at any prompt to exit program.\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	181
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	182 # Get print format
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	183 my $defaultAcc = ($accPrint) ? "y" : "n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	184 undef $accPrint;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	185 until (defined $accPrint)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	186 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	187 print "\tPrint out accession numbers only to nexus- and/or phylip output (y\|n) [$defaultAcc]: ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	188 $accPrint = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	189 chomp ($accPrint);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	190 exit(0) if ($accPrint eq "q");
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	191 if (substr($accPrint, 0, 1) =~ /^n/i or $accPrint eq "")
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	192 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	193 $accPrint = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	194 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	195 elsif (substr($accPrint, 0, 1) =~ /^y/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	196 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	197 $accPrint = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	198 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	199 else
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	200 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	201 print "\t\tInvalid input ($accPrint)\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	202 undef $accPrint;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	203 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	204 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	205
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	206 # Get datafile
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	207 until (defined $readFile)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	208 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	209 print "\tEnter name of data file (* = batch convert): ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	210 $readFile = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	211 chomp ($readFile);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	212 exit(0) if ($readFile eq "q");
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	213 unless (-e $readFile or $readFile eq "*")
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	214 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	215 print "\t\tFile '$readFile' does not exist\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	216 undef $readFile;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	217 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	218 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	219 push @seqFiles, $readFile;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	220
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	221 # Get format of datafile
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	222 my $defaultInput = "autodetect";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	223 undef $inputType;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	224 until (defined $inputType)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	225 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	226 print "\tEnter format of file $readFile (fasta\|GenBank\|nexus\|phylip\|Se-Al) [$defaultInput]: ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	227 $inputType = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	228 chomp ($inputType);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	229 exit(0) if ($inputType =~ /^q/i);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	230 if (substr($inputType, 0, 1) =~ /^a/i or $inputType eq "")
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	231 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	232 $inputType = "autodetect";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	233 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	234 elsif (substr($inputType, 0, 1) =~ /^f/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	235 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	236 $inputType = "fasta";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	237 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	238 elsif (substr($inputType, 0, 1) =~ /^g/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	239 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	240 $inputType = "GenBank";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	241 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	242 elsif (substr($inputType, 0, 1) =~ /^n/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	243 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	244 $inputType = "nexus";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	245 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	246 elsif (substr($inputType, 0, 1) =~ /^p/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	247 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	248 $inputType = "phylip";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	249 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	250 elsif (substr($inputType, 0, 1) =~ /^s/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	251 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	252 $inputType = "Se-Al";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	253 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	254 else
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	255 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	256 print "\t\tInvalid input ($inputType)\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	257 undef $inputType;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	258 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	259 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	260 $inputType = "" if ($inputType eq "autodetect");
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	261
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	262 # Get whether or not to clean sequence labels
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	263 my $defaultClean = ($nameClean) ? "y" : "n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	264 undef $nameClean;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	265 until (defined $nameClean)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	266 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	267 print "\tClean sequence labels by changing non-alphanumeric characters to underscores (y\|n)? [$defaultClean]: ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	268 $nameClean = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	269 chomp ($nameClean);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	270 exit(0) if ($nameClean =~ /^q/i);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	271 if (substr($nameClean, 0, 1) =~ /^y/i or $nameClean eq "")
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	272 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	273 $nameClean = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	274 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	275 elsif (substr($nameClean, 0, 1) =~ /^n/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	276 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	277 $nameClean = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	278 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	279 else
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	280 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	281 print "\t\tInvalid input ($seqSplit)\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	282 undef $nameClean;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	283 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	284 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	285
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	286 # Get whether or not to split sequences
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	287 my $defaultSplit = ($seqSplit) ? "y" : "n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	288 undef $seqSplit;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	289 until (defined $seqSplit)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	290 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	291 print "\tSplit into individual partitions following charset statements (y\|n)? [$defaultSplit]: ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	292 $seqSplit = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	293 chomp ($seqSplit);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	294 exit(0) if ($seqSplit =~ /^q/i);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	295 if (substr($seqSplit, 0, 1) =~ /^n/i or $seqSplit eq "")
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	296 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	297 $seqSplit = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	298 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	299 elsif (substr($seqSplit, 0, 1) =~ /^y/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	300 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	301 $seqSplit = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	302 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	303 else
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	304 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	305 print "\t\tInvalid input ($seqSplit)\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	306 undef $seqSplit;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	307 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	308 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	309
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	310 # Get whether or not to jackknife sequences
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	311 my $defaultJack = ($jackknife) ? "y" : "n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	312 undef $jackknife;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	313 until (defined $jackknife)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	314 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	315 print "\tProduce replicate, jackknifed data sets (y\|n)? [$defaultJack]: ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	316 $jackknife = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	317 chomp ($jackknife);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	318 exit(0) if ($jackknife =~ /^q/i);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	319 if (substr($jackknife, 0, 1) =~ /^n/i or $jackknife eq "")
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	320 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	321 $jackknife = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	322 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	323 elsif (substr($jackknife, 0, 1) =~ /^y/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	324 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	325 $jackknife = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	326 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	327 else
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	328 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	329 print "\t\tInvalid input ($jackknife)\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	330 undef $jackknife;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	331 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	332 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	333
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	334 # Get whether or not to convert gaps
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	335 my $defaultGaps = ($gapChange) ? "y" : "n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	336 undef $gapChange;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	337 until (defined $gapChange)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	338 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	339 print "\tConvert ~ gap characters to - (y\|n)? [$defaultGaps]: ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	340 $gapChange = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	341 chomp ($gapChange);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	342 exit(0) if ($gapChange =~ /^q/i);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	343 if (substr($gapChange, 0, 1) =~ /^n/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	344 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	345 $gapChange = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	346 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	347 elsif (substr($gapChange, 0, 1) =~ /^y/i or $gapChange eq "")
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	348 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	349 $gapChange = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	350 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	351 else
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	352 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	353 print "\t\tInvalid input ($gapChange)\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	354 undef $gapChange;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	355 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	356 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	357
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	358 # Get whether or not to convert flanking gaps
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	359 my $defaultFlank = ($flankGap) ? "y" : "n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	360 undef $flankGap;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	361 until (defined $flankGap)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	362 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	363 print "\tConvert flanking gap characters to Ns (y\|n)? [$defaultFlank]: ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	364 $flankGap = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	365 chomp ($flankGap);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	366 exit(0) if ($flankGap =~ /^q/i);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	367 if (substr($flankGap, 0, 1) =~ /^n/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	368 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	369 $flankGap = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	370 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	371 elsif (substr($flankGap, 0, 1) =~ /^y/i or $flankGap eq "")
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	372 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	373 $flankGap = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	374 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	375 else
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	376 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	377 print "\t\tInvalid input ($flankGap)\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	378 undef $flankGap;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	379 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	380 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	381
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	382 # Get whether or not to convert ambiguous nucleotides
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	383 my $defaultAmbig = ($ambigChange) ? "y" : "n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	384 undef $ambigChange;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	385 until (defined $ambigChange)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	386 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	387 print "\tConvert ambiguous nucleotides to Ns (y\|n)? [$defaultAmbig]: ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	388 $ambigChange = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	389 chomp ($ambigChange);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	390 exit(0) if ($ambigChange =~ /^q/i);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	391 if (substr($ambigChange, 0, 1) =~ /^n/i or $ambigChange eq "")
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	392 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	393 $ambigChange = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	394 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	395 elsif (substr($ambigChange, 0, 1) =~ /^y/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	396 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	397 $ambigChange = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	398 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	399 else
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	400 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	401 print "\t\tInvalid input ($ambigChange)\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	402 undef $ambigChange;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	403 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	404 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	405
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	406 # Get output order of sequences
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	407 my $defaultOrder = $seqOrder;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	408 undef $seqOrder;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	409 until (defined $seqOrder)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	410 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	411 print "\tEnter output order for sequences (alphabetical\|clustal\|input file) [$defaultOrder]: ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	412 $seqOrder = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	413 chomp ($seqOrder);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	414 exit(0) if ($seqOrder =~ /^q/i);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	415 if (substr($seqOrder, 0, 1) =~ /^i/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	416 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	417 $seqOrder = "input";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	418 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	419 elsif (substr($seqOrder, 0, 1) =~ /^a/i or $seqOrder eq "")
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	420 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	421 $seqOrder = "alphabetical";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	422 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	423 else
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	424 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	425 print "\t\tInvalid input ($seqOrder)\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	426 undef $seqOrder;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	427 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	428 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	429
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	430 # Get whether or not to convert to haplotypes
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	431 my $defaultHaplo = ($haploTyping) ? "y" : "n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	432 undef $haploTyping;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	433 until (defined $haploTyping)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	434 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	435 print "\tConvert sequence data to haplotypes (y\|n)? [$defaultHaplo]: ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	436 $haploTyping = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	437 chomp ($haploTyping);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	438 exit(0) if ($haploTyping =~ /^q/i);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	439 if (substr($haploTyping, 0, 1) =~ /^n/i or $haploTyping eq "")
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	440 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	441 $haploTyping = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	442 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	443 elsif (substr($haploTyping, 0, 1) =~ /^y/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	444 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	445 $haploTyping = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	446 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	447 else
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	448 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	449 print "\t\tInvalid input ($haploTyping)\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	450 undef $haploTyping;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	451 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	452 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	453
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	454 # Get whether or not to convert to amino acids
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	455 my $defaultTranslate = ($translateSeqs) ? "y" : "n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	456 undef $translateSeqs;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	457 until (defined $translateSeqs)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	458 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	459 print "\tConvert sequence data to amino acids (y\|n)? [$defaultTranslate]: ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	460 $translateSeqs = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	461 chomp ($translateSeqs);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	462 exit(0) if ($translateSeqs =~ /^q/i);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	463 if (substr($translateSeqs, 0, 1) =~ /^n/i or $translateSeqs eq "")
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	464 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	465 $translateSeqs = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	466 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	467 elsif (substr($translateSeqs, 0, 1) =~ /^y/i)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	468 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	469 $translateSeqs = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	470 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	471 else
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	472 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	473 print "\t\tInvalid input ($translateSeqs)\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	474 undef $translateSeqs;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	475 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	476 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	477
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	478 # Get genetic code for translation
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	479 my $defaultCode = $globalGenCode;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	480 $globalGenCode = 99;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	481 print "\tGenetic codes available for protein translation:\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	482 foreach my $code (qw(1 2 3 4 5 6 9 10 11 12 13 14 15 16 21 22 23))
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	483 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	484 print "\t\t$code: $transTable{$code}";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	485 print "\n";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	486 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	487 until (defined $genCodes{$globalGenCode})
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	488 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	489 $globalOverride = 0;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	490 print "\tEnter global genetic code to be applied (0 = no translation; follow with an * to override local code) [$defaultCode]: ";
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	491 $globalGenCode = <stdin>;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	492 chomp ($globalGenCode);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	493 exit(0) if ($globalGenCode =~ /^q/i);
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	494 $globalGenCode = $defaultCode if ($globalGenCode eq "");
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	495 if ($globalGenCode =~ /\*$/)
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	496 {
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	497 $globalOverride = 1;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	498 $globalGenCode =~ s/\*$//;
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	499 }
5b9a38ec4a39 First commit of old repositories osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> parents: diff changeset	500 print "\t\tInvalid input ($globalGenCode)\n" unless (defined $genCodes{$globalGenCode} or $globalGenCode == 0);

0

5b9a38ec4a39 First commit of old repositories