diff external_tools/darwin/lib/hh/scripts/splitfasta.pl @ 6:2277dd59b9f9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/external_tools/darwin/lib/hh/scripts/splitfasta.pl	Wed Nov 01 05:54:28 2017 -0400
@@ -0,0 +1,129 @@
+#! /usr/bin/env perl
+# splitfasta.pl 
+# Split a file with multiple, FASTA formatted sequences into many single-sequence FASTA files
+#
+# (C) Johannes Soeding, 2012
+#
+#     HHsuite version 2.0.15 (June 2012)
+#
+#     Reference: 
+#     Remmert M., Biegert A., Hauser A., and Soding J.
+#     HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.
+#     Nat. Methods, epub Dec 25, doi: 10.1038/NMETH.1818 (2011).
+
+#     This program is free software: you can redistribute it and/or modify
+#     it under the terms of the GNU General Public License as published by
+#     the Free Software Foundation, either version 3 of the License, or
+#     (at your option) any later version.
+
+#     This program is distributed in the hope that it will be useful,
+#     but WITHOUT ANY WARRANTY; without even the implied warranty of
+#     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#     GNU General Public License for more details.
+
+#     You should have received a copy of the GNU General Public License
+#     along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+#     We are very grateful for bug reports! Please contact us at [e-mail]
+
+use lib $ENV{"HHLIB"}."/scripts";
+use HHPaths;   # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+use strict;
+use warnings;
+
+my $ext="seq";
+my $usage="
+splitfasta.pl from HHsuite $VERSION  
+Split a file with multiple, FASTA formatted sequences into multiple single-sequence FASTA files.
+Write files into current directory and name each file by the first word after \">\" in the name line. 
+
+Usage: splitfasta.pl infile [option]
+Option:
+-fam       : use family-based name (for SCOP/ASTRAL sequences
+-name      : use sequence name as file name (default)
+-ext <ext> : extension for sequence files (default=$ext)
+\n";
+
+if (@ARGV<1) {die $usage;;}
+
+my $line;
+my $infile=$ARGV[0];
+my $outfile;
+my $sequence="";
+my $options="";
+my $fam=0;             # option -fam?
+my $famid="";
+my %numfams=(); 
+my $n=0;               # number of name lines read in so far
+
+if (@ARGV>1) {
+    $options.=join(" ",@ARGV[1..$#ARGV]);
+}
+
+# Set number of cpus to use
+if ($options=~s/-fam//g)         {$fam=1;}
+if ($options=~s/-name//g)        {$fam=0;}
+if ($options=~s/-ext\s+(\S+)//g) {$ext=$1;}
+
+
+open (INFILE,"<$infile") || die("ERROR: Can't open $infile: $!\n");
+
+if ($fam) {
+
+    while ($line=<INFILE>) {
+	if ($line=~/^>(\S+)\s+(\S+)/) {
+	    $famid=$2;
+	    if ($n) {
+		open (OUTFILE,">$outfile") || die("ERROR: Can't open $outfile: $!\n");
+		print(OUTFILE $sequence);
+		close(OUTFILE);
+	    }
+	    if (defined $numfams{$fam}) {$numfams{$fam}++;} else {$numfams{$fam}=1};
+	    $outfile="$fam.".$numfams{$fam}.".seq";
+	    $sequence=$line;
+	    $n++;
+	} else {
+	    $sequence.=$line;
+	}
+    }
+    if ($n) {
+	open (OUTFILE,">$outfile") || die("ERROR: Can't open $outfile: $!\n");
+	print(OUTFILE $sequence);
+	close(OUTFILE);
+    }
+
+} else {
+
+    my %exists=();
+    while ($line=<INFILE>) {
+	if ($line=~/^>(\S+)/) {
+	    if ($n) {
+		open (OUTFILE,">$outfile") || die("ERROR: Can't open $outfile: $!\n");
+		print(OUTFILE $sequence);
+		close(OUTFILE);
+	    }
+	    if ($exists{$1}) {print("\nWarning: id $1 appears more than once in $infile\n");}
+	    $exists{$1}=1;
+	    my $tmp = $1;
+	    $tmp =~ s/\|/_/g;
+	    $tmp =~ s/\./_/g;
+	    $outfile="$tmp.seq";
+	    $sequence=$line;
+	    $n++;
+	} else {
+	    $sequence.=$line;
+	}
+    }
+    if ($n) {
+	open (OUTFILE,">$outfile") || die("ERROR: Can't open $outfile: $!\n");
+	print(OUTFILE $sequence);
+	close(OUTFILE);
+    }
+}
+
+
+close(INFILE);
+printf("Created %i sequence files\n",$n);
+
+
+