gclib/scripts/pexo_srvrun.psx

#!/usr/bin/perl
use strict;
use Getopt::Std;
use Cwd qw(realpath cwd chdir);
use File::Basename;

my $usage = q/Usage:

 gridx [other_gridx_opts] -U -i <proteins.mfa> pexo_srvrun.psx <fastadb_esi_fullpath> [<port>]

 Start a local exonerate server and run exonerate for each protein sequence 
 in <proteins.mfa>, one sequence at a time.  Default port is 3834.
/;
umask 0002;
#so for pvmsx to consider the task was successful, $file must be deleted!
#============== 
# 1 is the name of the fasta sequence input file
# 2 is the # of sequences in ${1} should = 1 for this script
# 3 is the slice no. being processed by sx
# 4 is 0 if not the last file, 1 if the last file
# 5 is the # of sequences skipped initially
# 6 is the # of sequences to be processed (-1 = ALL)
# 7.. user parameters
#     1        2        3         4          5       6      7        8
my ($qmfa, $numpass, $slice_num, $last, $skipped, $total, $esidb,  $port )=@ARGV;

my $cwd=cwd();
$cwd=~s/\/$//;
die("$usage\n") unless $esidb;
die ($usage."Error locating file $esidb from current directory $cwd\n")
 unless -f $esidb;
$port=3834 unless $port;
my $srv="localhost:$port";
$esidb=realpath($esidb);
my $esidir=getFDir($esidb);
$esidir=~s/\/$//;
my $esifile=getFName($esidb);
$esidir='' if (-f $esifile) && ($esidir eq $cwd);
my $srvpid=0;

startServer();

open(MFA, $qmfa) || die ($usage."Error opening query file!\n");
#my $esibase=$esifile;
#$esibase=~s/\.esi$//i;
#$esibase=~s/\.[trans]+$//i;
#$esibase=~s/\.[mp]*fa*$//i;
my $outfile=$qmfa.'.exout';
#open(FOUT, '>'.$outfile) || die ("Error creating output file $outfile !\n");

my $params = '-V 0 --model p2g --percent 20 -n 11 --showalignment no --showtargetgff yes --showvulgar no'.
' --maxintron 450000 --seedrepeat 2 --saturatethreshold 80 --geneseed 60 -x 50 --proteinwordlen 4 '.
q/--ryo '%ti\t%qi\tmap_end\t%r\t%ql|%qab-%qae\t%ps\t%g\t%qd\n' /;
my $host=$ENV{'HOST'} || $ENV{'HOSTNAME'};
($host)=($host=~m/^(\w+)/);
my $username=$ENV{'USER'} || $ENV{'LOGNAME'};

unless ($username) { $username = $ENV{'USERNAME'} || 'user'; }
my $tmpqn=$host.'_'.$username.'_'.$$;
my $qno=1;
my ($qdefline, $qseq, $qseqlen, $qname);
while (<MFA>) {
  if (m/^>/) {
    my $d=$_;
    qSeqFa(); #uses $qseq, $qdefline, $qno, $outfile
    $qdefline=$d;
    ($qname)=($d=~m/^>(\S+)/);
    $qseqlen=0;
    }
   else {
    $qseq.=$_;
    chomp;
    $qseqlen+=length($_);
    }
}
qSeqFa();
close(MFA);
kill(15, $srvpid); # sending kill signal to server
exit 0;


#================ SUBROUTINES ============

sub getFName {
 return basename($_[0]);
}

sub getFDir {
 return dirname($_[0]);
}

sub qSeqFa {
 return unless $qdefline && $qseqlen>3;
 my $qnstr=sprintf('%06d', $qno);
 my $qfname=$tmpqn.'_'.$qnstr.'.qfa';
 open(QFA, '>'.$qfname) || die("Error creating tmp qry file $qfname !\n");
 print QFA $qdefline.$qseq;
 close(QFA);
 my $qfout=$qfname.'.exout';
 my $s=int($qseqlen/10);
 if ($s<150) { $s=60; }
   elsif ($s<250) { $s=100 }
   elsif ($s>1000) { $s=1000 }
 my $rparams=$params;  
 $rparams=~s/geneseed\s+\d+/geneseed $s/;
 my $ecmd="exonerate $rparams $qfname $srv > $qfout";
 print STDERR ">q_$qnstr [$qname, $qseqlen] : $ecmd\n";
 my $retry=0;
 QRETRY:
 if (runClient($ecmd, $qfname, $qfout)) { 
    print STDERR "   ..ran ok, wait for connection cleanup..\n";
    my $sl;
    do { $sl=<SRVLOG> } until ($sl=~m/cleaning up connection/);
    print STDERR "<q_$qnstr done.\n";
    # append qfout to outfile
    if (-s $qfout) {
       system("cat $qfout >> $outfile") &&
       die("Error at appending $qfout to $outfile !\n");
       }
    unlink($qfname);
    # read the server output, otherwise it gets suspended!
    } #no error
   else { #error detected
    unless (srvRunning()) { 
        #server not alive, restart it
        #close(SRVLOG);
        startServer();
        }
    $retry++;    
    if ($retry<2) {
       print STDERR " ..retrying $ecmd\n";
       sleep(5);
       goto QRETRY;
       }
      else { #giving up on this slice:
       print STDERR "Failed ($qno): $qfname vs $esifile\n";
       }
    }
 $qno++;
 $qseq='';
 $qseqlen=0;
 $qdefline=''; 
 unlink($qfout);
}

sub srvRunning() {
 my $s=`ps -h -o pid,ppid,cmd -p $srvpid`;
 my ($pid, $ppid, $cmd)=split(' ',$s,3);
 return ($pid==$srvpid && $ppid==$$);
}

sub runClient {
my ($docmd, $qname, $qdel) = @_;
my $errmsg = `($docmd) 2>&1`;
if ($? || ($errmsg=~/Error|Segmentation|Failed|Fatal|Invalid|Abort/si)) {
  #print STDERR "!Error at: $docmd\n";
  print STDERR " Error detected for $qname vs $esifile\n";
  print STDERR " Error msg : $errmsg\n";
  unlink($qdel);
  return 0;
  }
 return 1; 
}


sub startServer {
 if ($esidir) {
   chdir($esidir);
   }
 my $cmd='exonerate-server --proteinwordlen 4 --port '.$port.' '.$esifile;
 print STDERR "  Starting server (in $cwd): $cmd \n";
 $srvpid=open(SRVLOG, $cmd.' 2>&1 |');
 do {
   $_=<SRVLOG>;
   print STDERR $_;
   } until m/listening/i;
 #close(SRVLOG); -- no good, this will wait for the process to close! 
 if ($esidir) {
   chdir($cwd);
   }
}
Revision:	24
Committed:	Tue Jul 26 21:46:39 2011 UTC (13 years, 1 month ago) by gpertea
File size:	5004 byte(s)
Log Message:
Line	File contents
1	#!/usr/bin/perl
2	use strict;
3	use Getopt::Std;
4	use Cwd qw(realpath cwd chdir);
5	use File::Basename;
6
7	my $usage = q/Usage:
8
9	gridx [other_gridx_opts] -U -i <proteins.mfa> pexo_srvrun.psx <fastadb_esi_fullpath> [<port>]
10
11	Start a local exonerate server and run exonerate for each protein sequence
12	in <proteins.mfa>, one sequence at a time. Default port is 3834.
13	/;
14	umask 0002;
15	#so for pvmsx to consider the task was successful, $file must be deleted!
16	#==============
17	# 1 is the name of the fasta sequence input file
18	# 2 is the # of sequences in ${1} should = 1 for this script
19	# 3 is the slice no. being processed by sx
20	# 4 is 0 if not the last file, 1 if the last file
21	# 5 is the # of sequences skipped initially
22	# 6 is the # of sequences to be processed (-1 = ALL)
23	# 7.. user parameters
24	# 1 2 3 4 5 6 7 8
25	my ($qmfa, $numpass, $slice_num, $last, $skipped, $total, $esidb, $port )=@ARGV;
26
27	my $cwd=cwd();
28	$cwd=~s/\/$//;
29	die("$usage\n") unless $esidb;
30	die ($usage."Error locating file $esidb from current directory $cwd\n")
31	unless -f $esidb;
32	$port=3834 unless $port;
33	my $srv="localhost:$port";
34	$esidb=realpath($esidb);
35	my $esidir=getFDir($esidb);
36	$esidir=~s/\/$//;
37	my $esifile=getFName($esidb);
38	$esidir='' if (-f $esifile) && ($esidir eq $cwd);
39	my $srvpid=0;
40
41	startServer();
42
43	open(MFA, $qmfa) \|\| die ($usage."Error opening query file!\n");
44	#my $esibase=$esifile;
45	#$esibase=~s/\.esi$//i;
46	#$esibase=~s/\.[trans]+$//i;
47	#$esibase=~s/\.[mp]fa$//i;
48	my $outfile=$qmfa.'.exout';
49	#open(FOUT, '>'.$outfile) \|\| die ("Error creating output file $outfile !\n");
50
51	my $params = '-V 0 --model p2g --percent 20 -n 11 --showalignment no --showtargetgff yes --showvulgar no'.
52	' --maxintron 450000 --seedrepeat 2 --saturatethreshold 80 --geneseed 60 -x 50 --proteinwordlen 4 '.
53	q/--ryo '%ti\t%qi\tmap_end\t%r\t%ql\|%qab-%qae\t%ps\t%g\t%qd\n' /;
54	my $host=$ENV{'HOST'} \|\| $ENV{'HOSTNAME'};
55	($host)=($host=~m/^(\w+)/);
56	my $username=$ENV{'USER'} \|\| $ENV{'LOGNAME'};
57
58	unless ($username) { $username = $ENV{'USERNAME'} \|\| 'user'; }
59	my $tmpqn=$host.'_'.$username.'_'.$$;
60	my $qno=1;
61	my ($qdefline, $qseq, $qseqlen, $qname);
62	while (<MFA>) {
63	if (m/^>/) {
64	my $d=$_;
65	qSeqFa(); #uses $qseq, $qdefline, $qno, $outfile
66	$qdefline=$d;
67	($qname)=($d=~m/^>(\S+)/);
68	$qseqlen=0;
69	}
70	else {
71	$qseq.=$_;
72	chomp;
73	$qseqlen+=length($_);
74	}
75	}
76	qSeqFa();
77	close(MFA);
78	kill(15, $srvpid); # sending kill signal to server
79	exit 0;
80
81
82	#================ SUBROUTINES ============
83
84	sub getFName {
85	return basename($_[0]);
86	}
87
88	sub getFDir {
89	return dirname($_[0]);
90	}
91
92	sub qSeqFa {
93	return unless $qdefline && $qseqlen>3;
94	my $qnstr=sprintf('%06d', $qno);
95	my $qfname=$tmpqn.'_'.$qnstr.'.qfa';
96	open(QFA, '>'.$qfname) \|\| die("Error creating tmp qry file $qfname !\n");
97	print QFA $qdefline.$qseq;
98	close(QFA);
99	my $qfout=$qfname.'.exout';
100	my $s=int($qseqlen/10);
101	if ($s<150) { $s=60; }
102	elsif ($s<250) { $s=100 }
103	elsif ($s>1000) { $s=1000 }
104	my $rparams=$params;
105	$rparams=~s/geneseed\s+\d+/geneseed $s/;
106	my $ecmd="exonerate $rparams $qfname $srv > $qfout";
107	print STDERR ">q_$qnstr [$qname, $qseqlen] : $ecmd\n";
108	my $retry=0;
109	QRETRY:
110	if (runClient($ecmd, $qfname, $qfout)) {
111	print STDERR " ..ran ok, wait for connection cleanup..\n";
112	my $sl;
113	do { $sl=<SRVLOG> } until ($sl=~m/cleaning up connection/);
114	print STDERR "<q_$qnstr done.\n";
115	# append qfout to outfile
116	if (-s $qfout) {
117	system("cat $qfout >> $outfile") &&
118	die("Error at appending $qfout to $outfile !\n");
119	}
120	unlink($qfname);
121	# read the server output, otherwise it gets suspended!
122	} #no error
123	else { #error detected
124	unless (srvRunning()) {
125	#server not alive, restart it
126	#close(SRVLOG);
127	startServer();
128	}
129	$retry++;
130	if ($retry<2) {
131	print STDERR " ..retrying $ecmd\n";
132	sleep(5);
133	goto QRETRY;
134	}
135	else { #giving up on this slice:
136	print STDERR "Failed ($qno): $qfname vs $esifile\n";
137	}
138	}
139	$qno++;
140	$qseq='';
141	$qseqlen=0;
142	$qdefline='';
143	unlink($qfout);
144	}
145
146	sub srvRunning() {
147	my $s=`ps -h -o pid,ppid,cmd -p $srvpid`;
148	my ($pid, $ppid, $cmd)=split(' ',$s,3);
149	return ($pid==$srvpid && $ppid==$$);
150	}
151
152	sub runClient {
153	my ($docmd, $qname, $qdel) = @_;
154	my $errmsg = `($docmd) 2>&1`;
155	if ($? \|\| ($errmsg=~/Error\|Segmentation\|Failed\|Fatal\|Invalid\|Abort/si)) {
156	#print STDERR "!Error at: $docmd\n";
157	print STDERR " Error detected for $qname vs $esifile\n";
158	print STDERR " Error msg : $errmsg\n";
159	unlink($qdel);
160	return 0;
161	}
162	return 1;
163	}
164
165
166	sub startServer {
167	if ($esidir) {
168	chdir($esidir);
169	}
170	my $cmd='exonerate-server --proteinwordlen 4 --port '.$port.' '.$esifile;
171	print STDERR " Starting server (in $cwd): $cmd \n";
172	$srvpid=open(SRVLOG, $cmd.' 2>&1 \|');
173	do {
174	$_=<SRVLOG>;
175	print STDERR $_;
176	} until m/listening/i;
177	#close(SRVLOG); -- no good, this will wait for the process to close!
178	if ($esidir) {
179	chdir($cwd);
180	}
181	}