Improved user CLI interface

CONVERTF/example.perl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 # $parfile = "par.ANCESTRYMAP.EIGENSTRAT";
   $parfile = "par.EIGENSTRAT.PED"; 

CONVERTF/ind2pheno.perl

@@ -1,10 +1,26 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
+
+sub usage {
+    my $message = "@_";
+    die "
+Usage: ind2pheno.perl infile outfile
+
+Required Arguments:
+  infile  : input .ind file
+  outfile : output .pheno file
+
+$message
+
+";
+}
+
+unless (@ARGV == 2) {usage("OOPS unexpected number of arguments")}
 
 $in = $ARGV[0]; # .ind file
 $out = $ARGV[1]; # .pheno file
 
-open(IN,$in) || die("COF");
-open(OUT,">$out") || die("COF");
+open(IN,$in) || die("Cannot open file: $in");
+open(OUT,">$out") || die("Cannot open file: $out");
 
 while($line = <IN>)
 {

EIGENSTRAT/example.QTL.perl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $ENV{'PATH'} = "../bin:$ENV{'PATH'}"; 
 # MUST put smartpca bin directory in path for smartpca.perl to work

EIGENSTRAT/example.oldstyle.perl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $ENV{'PATH'} = "../bin:$ENV{'PATH'}"; 
 # MUST put pca bin directory in path for smartpca.perl to work

EIGENSTRAT/example.perl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $ENV{'PATH'} = "../bin:$ENV{'PATH'}"; 
 # MUST put smartpca bin directory in path for smartpca.perl to work

POPGEN/elldemo/doplot

@@ -1,4 +1,6 @@
-#!/usr//bin/perl  -w 
+#!/usr/bin/env perl
+
+use warnings;
 
 system "ploteig -i sicaa.evec -c 1:2  -g aaa  -p  test4 -x -k  -r ctable -e ell4aa.out -t \" Sicily EBA projected conf: 0.95\"" ;
 

POPGEN/elldemo/rescale_ell

@@ -1,7 +1,8 @@
-#!/usr//bin/perl  -w 
+#!/usr/bin/env perl
 
 ## rescale -i infile -o outfile -a inscale -b outscale 
 
+use warnings ;
 use Getopt::Std ;
 use File::Basename ;
 
@@ -82,9 +83,6 @@ sub critchi {
 
 }
 
-sub usage { 
-
-print "rescale_ell -i infile -o outfile -s outscale [-a inscale]\n"  ; 
-exit 0 ; 
-
+sub usage {
+    die "Usage: rescale_ell -i infile -o outfile -s outscale [-a inscale]\n"  ; 
 }

POPGEN/example.perl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $ENV{'PATH'} = "../bin:$ENV{'PATH'}";
 

POPGEN/twexample.perl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $command = "../bin/twstats";
 $command .= " -t twtable ";

bin/evec2pca-ped.perl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 ### translate .evec file to .pca file expected by eigenstrat program
 ### Note: .evec file does not contain entries for outliers
@@ -10,6 +10,26 @@
 # ----- indiv names are not found in the .evec file, try the 
 # ----- familyname:indivname combination.  
 
+sub usage {
+    my $message = "@_";
+    die "
+Usage: evec2pca-ped.perl k example.evec example.ind example.pca
+
+Required Arguments:
+  k            : the number of principal components in example.evec
+                 file (e.g. 10)
+  example.evec : file of principal components produced by smartpca
+  example.ind  : individual file
+  example.pca  : file of principal components in file needed by
+                 eigenstrat
+
+$message
+
+"
+}
+
+unless (@ARGV == 4) {usage("OOPS unexpected number of arguments")}
+
 $k = $ARGV[0];
 $evec = $ARGV[1]; 
 $ind = $ARGV[2];  

bin/evec2pca.perl

@@ -1,9 +1,29 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 ### translate .evec file to .pca file expected by eigenstrat program
 ### Note: .evec file does not contain entries for outliers
 ###       .pca  file does contain entries (set to all 0.0) for outliers
 
+sub usage {
+    my $message = "@_";
+    die "
+Usage: evec2pca.perl k example.evec example.ind example.pca
+
+Required Arguments:
+  k            : the number of principal components in example.evec 
+                 file (e.g. 10)
+  example.evec : file of principal components produced by smartpca
+  example.ind  : individual file
+  example.pca  : file of principal components in file needed by 
+                 eigenstrat
+
+$message
+
+"
+}
+
+unless (@ARGV == 4) {usage("OOPS unexpected number of arguments")}
+
 $k = $ARGV[0];
 $evec = $ARGV[1]; 
 $ind = $ARGV[2];  

bin/gc.perl

@@ -1,11 +1,37 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
+
+sub usage {
+    my $message = "@_";
+    die "
+Usage: gc.perl infile outfile
+
+Required Arguments:
+  infile  : input file of chisq statistics produced by eigenstrat
+            program. It contains both uncorrected and EIGENSTRAT 
+            statistics for each SNP.
+  outfile : output file. It lists lambda inflation values (for 
+            both uncorrected and EIGENSTRAT) chisq statistics 
+            after scaling by lambda (uncorrected and EIGENSTRAT)
+
+Computation of lambda is as described in Devlin and Roeder 1999.
+A lambda above 1 indicates inflation in chisq statistics.
+By definition, lambda is not allowed to be less than 1.
+
+Running time of the gc.perl program is very fast.
+
+$message
+
+"
+}
+
+unless(@ARGV == 2) {usage("OOPS unexpected number of arguments")}
 
 $P = $ARGV[0];
 $out = $ARGV[1];
 
 # get data
 $m=0;
-open(P,"$P") || die("COF");
+open(P,"$P") || die("Cannot open file: $P");
 while($line = <P>) { if($line =~ /Chisq/) { last; } } # header lines
 while($line = <P>)
 {
@@ -66,7 +92,7 @@
 if($lambda2 < 1) { $lambda2 = 1; } # not allowed to be less than 1
 
 # output
-open(OUT,">$out") || die("COF");
+open(OUT,">$out") || die("Cannot open file: $out");
 print OUT ("Chisq EIGENSTRAT\n");
 printf OUT ("lambda=%.03f lambda=%.03f\n",$lambda1,$lambda2);
 for($m=0; $m<$nSNP; $m++)

bin/ploteig

@@ -1,6 +1,7 @@
-#!/usr/local/bin/perl  -w 
+#!/usr/bin/env perl 
 
 ### ploteig -i eigfile -p pops -c a:b [-t title] [-s stem] [-g gstem] [-o outfile] [-x] [-k]  [-y] [-z sep] -r colorstring -m xmul -n ymul 
+use warnings ;
 use Getopt::Std ;
 use File::Basename ;
 
@@ -41,8 +42,7 @@ if (defined $opts{"i"}) {
  $infile = $opts{"i"} ;
 }
 else {
- usage() ;
- exit 0 ;
+ usage("OOPS -i parameter compulsory");
 }
 
 open (FF, $infile) || die "can't open $infile\n" ;
@@ -63,7 +63,7 @@ if (defined $opts{"p"}) {
  $pops = $opts{"p"} ;
 }
 else {
- die "p parameter compulsory\n" ;
+ usage("OOPS -p parameter compulsory");
 }
 
 $popsname = setpops ($pops) ;
@@ -142,7 +142,7 @@ $psfile = "$stem.ps" ;
   $psfile  =~ s/xtxt/ps/ ;
  }
 system "gnuplot < $gnfile > $psfile" ;
-system "/home/np29/bin/fixgreen  $psfile" ;
+#system "/home/np29/bin/fixgreen  $psfile" ;
 system "ps2pdf  $psfile " ;
 }
 unlink (@T) unless $keepflag ;
@@ -172,25 +172,38 @@ sub setcolor {
 }
 
 sub usage { 
-
-print "ploteig -i eigfile -p pops -c a:b [-t title] [-s stem] [-o outfile] [-x] [-k] -c colorstringh [-m xmul] [-n ymul]\n" ;  
-print "-i eigfile     input file first col indiv-id last col population\n" ;
-print "## as output by smartpca in outputvecs \n" ;
-print "-c a:b         a, b columns to plot.  1:2 would be common and leading 2 eigenvectors\n" ;
-print "-p pops        Populations to plot.  : delimited.   eg  -p Bantu:San:French\n" ;
-print "## pops can also be a filename.  List populations 1 per line\n" ;
-print "[-s stem]      stem will start various output files\n"  ;
-print "[-o ofile]     ofile will be gnuplot control file.  Should have xtxt suffix\n"; 
-print "[-x]           make ps and pdf files\n" ; 
-print "[-k]           keep various intermediate files although  -x set\n" ;
-print "## necessary if .xtxt file is to be hand edited\n" ;
-print "[-r colorstringpairs or colorstringfile]\n" ;
-print "[-g gstem]     make gstem.xtxt gstem.ps  gstem.pdf  \n" ;
-print "[-y]           put key at top right inside box (old mode)\n" ;
-print "[-t]           title (legend)\n" ;
-
-print "The xtxt file is a gnuplot file and can be easily hand edited.  Intermediate files
-needed if you want to make your own plot\n" ;
+    my $message = "@_";
+
+#       10       20       30       40       50       60       70       80       90
+#---+----|---+----|---+----|---+----|---+----|---+----|---+----|---+----|---+----|
+    die "
+Usage: ploteig [FLAGS]
+
+Required Flags:
+  -i eigfile   : input file first col indiv-id last col population
+                 as output by smartpca in outputvecs
+  -p pops      : Populations to plot.  : delimited.   eg  -p Bantu:San:French
+                 pops can also be a filename.  List populations 1 per line
+
+Optional Flags:
+  -c a:b       : a, b columns to plot.  1:2 would be common and leading 2 
+                 eigenvectors
+  -s stem      : stem will start various output files
+  -o ofile     : ofile will be gnuplot control file.  Should have xtxt suffix
+  -x           : make ps and pdf files
+  -k           : keep various intermediate files, although setting -x is
+                 necessary if .xtxt file is to be hand edited
+  -r cfile     : colorstringpairs or colorstringfile
+  -g gstem     : make gstem.xtxt gstem.ps gstem.pdf
+  -y           : put key at top right inside box (old mode)
+  -t           : title (legend)
+
+The xtxt file is a gnuplot file and can be easily hand edited. Intermediate
+files needed if you want to make your own plot
+
+$message
+
+" ;
 
 }
 sub setpops {      

bin/rescale_ell

@@ -1,7 +1,8 @@
-#!/usr//bin/perl  -w 
+#!/usr/bin/env perl
 
 ## rescale -i infile -o outfile -a inscale -b outscale 
 
+use warnings ;
 use Getopt::Std ;
 use File::Basename ;
 
@@ -82,9 +83,6 @@ sub critchi {
 
 }
 
-sub usage { 
-
-print "rescale_ell -i infile -o outfile -s outscale [-a inscale]\n"  ; 
-exit 0 ; 
-
+sub usage {
+    die "Usage: rescale_ell -i infile -o outfile -s outscale [-a inscale]\n"  ; 
 }