Commit d671a8a5 authored by Brandi Cantarel's avatar Brandi Cantarel
Browse files

add scripts from blcproject

parent 8706de70
miscscripts @ cdb3b452
Subproject commit cdb3b452854a8862d5d071c1275fc00094c95a1f
curl https://clinicaltrials.gov/ct2/show/NCT02674568?displayxml=true > NCT02674568.xml
curl https://clinicaltrials.gov/ct2/show/NCT01926197?displayxml=true > NCT01926197.xml
curl https://clinicaltrials.gov/ct2/show/NCT02176967?displayxml=true > NCT02176967.xml
curl https://clinicaltrials.gov/ct2/show/NCT02879643?displayxml=true > NCT02879643.xml
curl https://clinicaltrials.gov/ct2/show/NCT02601937?displayxml=true > NCT02601937.xml
curl https://clinicaltrials.gov/ct2/show/NCT01349881?displayxml=true > NCT01349881.xml
curl https://clinicaltrials.gov/ct2/show/NCT03072238?displayxml=true > NCT03072238.xml
curl https://clinicaltrials.gov/ct2/show/NCT02477878?displayxml=true > NCT02477878.xml
curl https://clinicaltrials.gov/ct2/show/NCT02411448?displayxml=true > NCT02411448.xml
curl https://clinicaltrials.gov/ct2/show/NCT01744223?displayxml=true > NCT01744223.xml
curl https://clinicaltrials.gov/ct2/show/NCT02554812?displayxml=true > NCT02554812.xml
curl https://clinicaltrials.gov/ct2/show/NCT02677922?displayxml=true > NCT02677922.xml
curl https://clinicaltrials.gov/ct2/show/NCT02445391?displayxml=true > NCT02445391.xml
curl https://clinicaltrials.gov/ct2/show/NCT02357836?displayxml=true > NCT02357836.xml
curl https://clinicaltrials.gov/ct2/show/NCT02289144?displayxml=true > NCT02289144.xml
curl https://clinicaltrials.gov/ct2/show/NCT02201992?displayxml=true > NCT02201992.xml
curl https://clinicaltrials.gov/ct2/show/NCT02659020?displayxml=true > NCT02659020.xml
curl https://clinicaltrials.gov/ct2/show/NCT03038100?displayxml=true > NCT03038100.xml
curl https://clinicaltrials.gov/ct2/show/NCT02152982?displayxml=true > NCT02152982.xml
curl https://clinicaltrials.gov/ct2/show/NCT01818986?displayxml=true > NCT01818986.xml
curl https://clinicaltrials.gov/ct2/show/NCT02065869?displayxml=true > NCT02065869.xml
curl https://clinicaltrials.gov/ct2/show/NCT02465060?displayxml=true > NCT02465060.xml
curl https://clinicaltrials.gov/ct2/show/NCT02154490?displayxml=true > NCT02154490.xml
curl https://clinicaltrials.gov/ct2/show/NCT01101451?displayxml=true > NCT01101451.xml
curl https://clinicaltrials.gov/ct2/show/NCT02562755?displayxml=true > NCT02562755.xml
curl https://clinicaltrials.gov/ct2/show/NCT02524119?displayxml=true > NCT02524119.xml
curl https://clinicaltrials.gov/ct2/show/NCT01674140?displayxml=true > NCT01674140.xml
curl https://clinicaltrials.gov/ct2/show/NCT02163356?displayxml=true > NCT02163356.xml
curl https://clinicaltrials.gov/ct2/show/NCT00980954?displayxml=true > NCT00980954.xml
curl https://clinicaltrials.gov/ct2/show/NCT02677116?displayxml=true > NCT02677116.xml
curl https://clinicaltrials.gov/ct2/show/NCT02424617?displayxml=true > NCT02424617.xml
curl https://clinicaltrials.gov/ct2/show/NCT02922777?displayxml=true > NCT02922777.xml
curl https://clinicaltrials.gov/ct2/show/NCT02064673?displayxml=true > NCT02064673.xml
curl https://clinicaltrials.gov/ct2/show/NCT02407054?displayxml=true > NCT02407054.xml
curl https://clinicaltrials.gov/ct2/show/NCT02514031?displayxml=true > NCT02514031.xml
curl https://clinicaltrials.gov/ct2/show/NCT02477826?displayxml=true > NCT02477826.xml
curl https://clinicaltrials.gov/ct2/show/NCT02637687?displayxml=true > NCT02637687.xml
curl https://clinicaltrials.gov/ct2/show/NCT01878617?displayxml=true > NCT01878617.xml
curl https://clinicaltrials.gov/ct2/show/NCT02667587?displayxml=true > NCT02667587.xml
curl https://clinicaltrials.gov/ct2/show/NCT02811783?displayxml=true > NCT02811783.xml
curl https://clinicaltrials.gov/ct2/show/NCT01602666?displayxml=true > NCT01602666.xml
curl https://clinicaltrials.gov/ct2/show/NCT02557854?displayxml=true > NCT02557854.xml
curl https://clinicaltrials.gov/ct2/show/NCT02667873?displayxml=true > NCT02667873.xml
curl https://clinicaltrials.gov/ct2/show/NCT02466971?displayxml=true > NCT02466971.xml
curl https://clinicaltrials.gov/ct2/show/NCT02516423?displayxml=true > NCT02516423.xml
curl https://clinicaltrials.gov/ct2/show/NCT02193282?displayxml=true > NCT02193282.xml
curl https://clinicaltrials.gov/ct2/show/NCT02401542?displayxml=true > NCT02401542.xml
curl https://clinicaltrials.gov/ct2/show/NCT02773849?displayxml=true > NCT02773849.xml
curl https://clinicaltrials.gov/ct2/show/NCT02834013?displayxml=true > NCT02834013.xml
curl https://clinicaltrials.gov/ct2/show/NCT02617589?displayxml=true > NCT02617589.xml
curl https://clinicaltrials.gov/ct2/show/NCT02513667?displayxml=true > NCT02513667.xml
curl https://clinicaltrials.gov/ct2/show/NCT02580448?displayxml=true > NCT02580448.xml
curl https://clinicaltrials.gov/ct2/show/NCT02688608?displayxml=true > NCT02688608.xml
curl https://clinicaltrials.gov/ct2/show/NCT00632853?displayxml=true > NCT00632853.xml
curl https://clinicaltrials.gov/ct2/show/NCT02781506?displayxml=true > NCT02781506.xml
curl https://clinicaltrials.gov/ct2/show/NCT02194738?displayxml=true > NCT02194738.xml
curl https://clinicaltrials.gov/ct2/show/NCT02902484?displayxml=true > NCT02902484.xml
curl https://clinicaltrials.gov/ct2/show/NCT02098343?displayxml=true > NCT02098343.xml
curl https://clinicaltrials.gov/ct2/show/NCT01962896?displayxml=true > NCT01962896.xml
curl https://clinicaltrials.gov/ct2/show/NCT02155920?displayxml=true > NCT02155920.xml
curl https://clinicaltrials.gov/ct2/show/NCT02562443?displayxml=true > NCT02562443.xml
curl https://clinicaltrials.gov/ct2/show/NCT02180867?displayxml=true > NCT02180867.xml
curl https://clinicaltrials.gov/ct2/show/NCT00887146?displayxml=true > NCT00887146.xml
curl https://clinicaltrials.gov/ct2/show/NCT02115282?displayxml=true > NCT02115282.xml
curl https://clinicaltrials.gov/ct2/show/NCT01503632?displayxml=true > NCT01503632.xml
curl https://clinicaltrials.gov/ct2/show/NCT01953588?displayxml=true > NCT01953588.xml
curl https://clinicaltrials.gov/ct2/show/NCT02003222?displayxml=true > NCT02003222.xml
curl https://clinicaltrials.gov/ct2/show/NCT03067610?displayxml=true > NCT03067610.xml
curl https://clinicaltrials.gov/ct2/show/NCT02492711?displayxml=true > NCT02492711.xml
curl https://clinicaltrials.gov/ct2/show/NCT00392327?displayxml=true > NCT00392327.xml
curl https://clinicaltrials.gov/ct2/show/NCT02228096?displayxml=true > NCT02228096.xml
curl https://clinicaltrials.gov/ct2/show/NCT03036488?displayxml=true > NCT03036488.xml
curl https://clinicaltrials.gov/ct2/show/NCT02240238?displayxml=true > NCT02240238.xml
curl https://clinicaltrials.gov/ct2/show/NCT00492778?displayxml=true > NCT00492778.xml
curl https://clinicaltrials.gov/ct2/show/NCT01979536?displayxml=true > NCT01979536.xml
curl https://clinicaltrials.gov/ct2/show/NCT02306161?displayxml=true > NCT02306161.xml
curl https://clinicaltrials.gov/ct2/show/NCT02101853?displayxml=true > NCT02101853.xml
curl https://clinicaltrials.gov/ct2/show/NCT02502266?displayxml=true > NCT02502266.xml
curl https://clinicaltrials.gov/ct2/show/NCT02883049?displayxml=true > NCT02883049.xml
curl https://clinicaltrials.gov/ct2/show/NCT02112916?displayxml=true > NCT02112916.xml
curl https://clinicaltrials.gov/ct2/show/NCT02595944?displayxml=true > NCT02595944.xml
curl https://clinicaltrials.gov/ct2/show/NCT02484443?displayxml=true > NCT02484443.xml
curl https://clinicaltrials.gov/ct2/show/NCT02166463?displayxml=true > NCT02166463.xml
curl https://clinicaltrials.gov/ct2/show/NCT02354586?displayxml=true > NCT02354586.xml
curl https://clinicaltrials.gov/ct2/show/NCT02285439?displayxml=true > NCT02285439.xml
curl https://clinicaltrials.gov/ct2/show/NCT02559778?displayxml=true > NCT02559778.xml
curl https://clinicaltrials.gov/ct2/show/NCT03065179?displayxml=true > NCT03065179.xml
curl https://clinicaltrials.gov/ct2/show/NCT01553071?displayxml=true > NCT01553071.xml
curl https://clinicaltrials.gov/ct2/show/NCT01042522?displayxml=true > NCT01042522.xml
curl https://clinicaltrials.gov/ct2/show/NCT02725268?displayxml=true > NCT02725268.xml
curl https://clinicaltrials.gov/ct2/show/NCT02655822?displayxml=true > NCT02655822.xml
curl https://clinicaltrials.gov/ct2/show/NCT02521493?displayxml=true > NCT02521493.xml
curl https://clinicaltrials.gov/ct2/show/NCT01614197?displayxml=true > NCT01614197.xml
curl https://clinicaltrials.gov/ct2/show/NCT02332668?displayxml=true > NCT02332668.xml
curl https://clinicaltrials.gov/ct2/show/NCT02576990?displayxml=true > NCT02576990.xml
curl https://clinicaltrials.gov/ct2/show/NCT02855125?displayxml=true > NCT02855125.xml
curl https://clinicaltrials.gov/ct2/show/NCT02450331?displayxml=true > NCT02450331.xml
curl https://clinicaltrials.gov/ct2/show/NCT02679144?displayxml=true > NCT02679144.xml
curl https://clinicaltrials.gov/ct2/show/NCT02135042?displayxml=true > NCT02135042.xml
curl https://clinicaltrials.gov/ct2/show/NCT02598661?displayxml=true > NCT02598661.xml
curl https://clinicaltrials.gov/ct2/show/NCT01803282?displayxml=true > NCT01803282.xml
curl https://clinicaltrials.gov/ct2/show/NCT02748135?displayxml=true > NCT02748135.xml
curl https://clinicaltrials.gov/ct2/show/NCT02013336?displayxml=true > NCT02013336.xml
curl https://clinicaltrials.gov/ct2/show/NCT02664961?displayxml=true > NCT02664961.xml
curl https://clinicaltrials.gov/ct2/show/NCT02303821?displayxml=true > NCT02303821.xml
curl https://clinicaltrials.gov/ct2/show/NCT02495415?displayxml=true > NCT02495415.xml
curl https://clinicaltrials.gov/ct2/show/NCT01659658?displayxml=true > NCT01659658.xml
curl https://clinicaltrials.gov/ct2/show/NCT01956669?displayxml=true > NCT01956669.xml
curl https://clinicaltrials.gov/ct2/show/NCT02339740?displayxml=true > NCT02339740.xml
curl https://clinicaltrials.gov/ct2/show/NCT00601003?displayxml=true > NCT00601003.xml
curl https://clinicaltrials.gov/ct2/show/NCT02178722?displayxml=true > NCT02178722.xml
curl https://clinicaltrials.gov/ct2/show/NCT02092324?displayxml=true > NCT02092324.xml
curl https://clinicaltrials.gov/ct2/show/NCT02568267?displayxml=true > NCT02568267.xml
curl https://clinicaltrials.gov/ct2/show/NCT01595061?displayxml=true > NCT01595061.xml
curl https://clinicaltrials.gov/ct2/show/NCT02728258?displayxml=true > NCT02728258.xml
curl https://clinicaltrials.gov/ct2/show/NCT02632708?displayxml=true > NCT02632708.xml
curl https://clinicaltrials.gov/ct2/show/NCT03024996?displayxml=true > NCT03024996.xml
curl https://clinicaltrials.gov/ct2/show/NCT02596503?displayxml=true > NCT02596503.xml
curl https://clinicaltrials.gov/ct2/show/NCT02853305?displayxml=true > NCT02853305.xml
curl https://clinicaltrials.gov/ct2/show/NCT02853604?displayxml=true > NCT02853604.xml
curl https://clinicaltrials.gov/ct2/show/NCT02631876?displayxml=true > NCT02631876.xml
curl https://clinicaltrials.gov/ct2/show/NCT02927769?displayxml=true > NCT02927769.xml
curl https://clinicaltrials.gov/ct2/show/NCT03029585?displayxml=true > NCT03029585.xml
curl https://clinicaltrials.gov/ct2/show/NCT00321685?displayxml=true > NCT00321685.xml
curl https://clinicaltrials.gov/ct2/show/NCT02851407?displayxml=true > NCT02851407.xml
curl https://clinicaltrials.gov/ct2/show/NCT02867592?displayxml=true > NCT02867592.xml
curl https://clinicaltrials.gov/ct2/show/NCT02684461?displayxml=true > NCT02684461.xml
curl https://clinicaltrials.gov/ct2/show/NCT02734537?displayxml=true > NCT02734537.xml
curl https://clinicaltrials.gov/ct2/show/NCT02398773?displayxml=true > NCT02398773.xml
curl https://clinicaltrials.gov/ct2/show/NCT03245151?displayxml=true > NCT03245151.xml
curl https://clinicaltrials.gov/ct2/show/NCT02706626?displayxml=true > NCT02706626.xml
curl https://clinicaltrials.gov/ct2/show/NCT02899195?displayxml=true > NCT02899195.xml
curl https://clinicaltrials.gov/ct2/show/NCT03155620?displayxml=true > NCT03155620.xml
curl https://clinicaltrials.gov/ct2/show/NCT02947347?displayxml=true > NCT02947347.xml
curl https://clinicaltrials.gov/ct2/show/NCT02989857?displayxml=true > NCT02989857.xml
curl https://clinicaltrials.gov/ct2/show/NCT03155997?displayxml=true > NCT03155997.xml
curl https://clinicaltrials.gov/ct2/show/NCT02715284?displayxml=true > NCT02715284.xml
curl https://clinicaltrials.gov/ct2/show/NCT02584478?displayxml=true > NCT02584478.xml
curl https://clinicaltrials.gov/ct2/show/NCT02729298?displayxml=true > NCT02729298.xml
curl https://clinicaltrials.gov/ct2/show/NCT03055013?displayxml=true > NCT03055013.xml
curl https://clinicaltrials.gov/ct2/show/NCT02703272?displayxml=true > NCT02703272.xml
curl https://clinicaltrials.gov/ct2/show/NCT03318497?displayxml=true > NCT03318497.xml
curl https://clinicaltrials.gov/ct2/show/NCT02043665?displayxml=true > NCT02043665.xml
curl https://clinicaltrials.gov/ct2/show/NCT02952534?displayxml=true > NCT02952534.xml
curl https://clinicaltrials.gov/ct2/show/NCT03065712?displayxml=true > NCT03065712.xml
curl https://clinicaltrials.gov/ct2/show/NCT03181126?displayxml=true > NCT03181126.xml
curl https://clinicaltrials.gov/ct2/show/NCT03151304?displayxml=true > NCT03151304.xml
curl https://clinicaltrials.gov/ct2/show/NCT03033511?displayxml=true > NCT03033511.xml
curl https://clinicaltrials.gov/ct2/show/NCT03077698?displayxml=true > NCT03077698.xml
curl https://clinicaltrials.gov/ct2/show/NCT02741570?displayxml=true > NCT02741570.xml
curl https://clinicaltrials.gov/ct2/show/NCT02828358?displayxml=true > NCT02828358.xml
curl https://clinicaltrials.gov/ct2/show/NCT03190915?displayxml=true > NCT03190915.xml
curl https://clinicaltrials.gov/ct2/show/NCT03303339?displayxml=true > NCT03303339.xml
curl https://clinicaltrials.gov/ct2/show/NCT03061812?displayxml=true > NCT03061812.xml
curl https://clinicaltrials.gov/ct2/show/NCT03268954?displayxml=true > NCT03268954.xml
curl https://clinicaltrials.gov/ct2/show/NCT02817113?displayxml=true > NCT02817113.xml
curl https://clinicaltrials.gov/ct2/show/NCT02595424?displayxml=true > NCT02595424.xml
curl https://clinicaltrials.gov/ct2/show/NCT03312114?displayxml=true > NCT03312114.xml
curl https://clinicaltrials.gov/ct2/show/NCT02793583?displayxml=true > NCT02793583.xml
curl https://clinicaltrials.gov/ct2/show/NCT03070886?displayxml=true > NCT03070886.xml
curl https://clinicaltrials.gov/ct2/show/NCT03091660?displayxml=true > NCT03091660.xml
curl https://clinicaltrials.gov/ct2/show/NCT03241550?displayxml=true > NCT03241550.xml
curl https://clinicaltrials.gov/ct2/show/NCT02567435?displayxml=true > NCT02567435.xml
curl https://clinicaltrials.gov/ct2/show/NCT03110562?displayxml=true > NCT03110562.xml
curl https://clinicaltrials.gov/ct2/show/NCT02913261?displayxml=true > NCT02913261.xml
curl https://clinicaltrials.gov/ct2/show/NCT03361748?displayxml=true > NCT03361748.xml
curl https://clinicaltrials.gov/ct2/show/NCT03117309?displayxml=true > NCT03117309.xml
curl https://clinicaltrials.gov/ct2/show/NCT03426865?displayxml=true > NCT03426865.xml
curl https://clinicaltrials.gov/ct2/show/NCT03137771?displayxml=true > NCT03137771.xml
curl https://clinicaltrials.gov/ct2/show/NCT03101566?displayxml=true > NCT03101566.xml
curl https://clinicaltrials.gov/ct2/show/NCT03164603?displayxml=true > NCT03164603.xml
curl https://clinicaltrials.gov/ct2/show/NCT03441360?displayxml=true > NCT03441360.xml
curl https://clinicaltrials.gov/ct2/show/NCT03138499?displayxml=true > NCT03138499.xml
curl https://clinicaltrials.gov/ct2/show/NCT03033576?displayxml=true > NCT03033576.xml
curl https://clinicaltrials.gov/ct2/show/NCT03343197?displayxml=true > NCT03343197.xml
curl https://clinicaltrials.gov/ct2/show/NCT02684058?displayxml=true > NCT02684058.xml
curl https://clinicaltrials.gov/ct2/show/NCT03095612?displayxml=true > NCT03095612.xml
curl https://clinicaltrials.gov/ct2/show/NCT02981628?displayxml=true > NCT02981628.xml
curl https://clinicaltrials.gov/ct2/show/NCT02203695?displayxml=true > NCT02203695.xml
curl https://clinicaltrials.gov/ct2/show/NCT03013998?displayxml=true > NCT03013998.xml
curl https://clinicaltrials.gov/ct2/show/NCT02724579?displayxml=true > NCT02724579.xml
curl https://clinicaltrials.gov/ct2/show/NCT03007147?displayxml=true > NCT03007147.xml
curl https://clinicaltrials.gov/ct2/show/NCT03365882?displayxml=true > NCT03365882.xml
curl https://clinicaltrials.gov/ct2/show/NCT02912559?displayxml=true > NCT02912559.xml
curl https://clinicaltrials.gov/ct2/show/NCT02717507?displayxml=true > NCT02717507.xml
curl https://clinicaltrials.gov/ct2/show/NCT02893930?displayxml=true > NCT02893930.xml
curl https://clinicaltrials.gov/ct2/show/NCT03298451?displayxml=true > NCT03298451.xml
curl https://clinicaltrials.gov/ct2/show/NCT03067181?displayxml=true > NCT03067181.xml
curl https://clinicaltrials.gov/ct2/show/NCT03141034?displayxml=true > NCT03141034.xml
curl https://clinicaltrials.gov/ct2/show/NCT03519997?displayxml=true > NCT03519997.xml
curl https://clinicaltrials.gov/ct2/show/NCT02924376?displayxml=true > NCT02924376.xml
curl https://clinicaltrials.gov/ct2/show/NCT03215511?displayxml=true > NCT03215511.xml
curl https://clinicaltrials.gov/ct2/show/NCT03289039?displayxml=true > NCT03289039.xml
curl https://clinicaltrials.gov/ct2/show/NCT02392429?displayxml=true > NCT02392429.xml
curl https://clinicaltrials.gov/ct2/show/NCT03142334?displayxml=true > NCT03142334.xml
curl https://clinicaltrials.gov/ct2/show/NCT03533582?displayxml=true > NCT03533582.xml
curl https://clinicaltrials.gov/ct2/show/NCT02892201?displayxml=true > NCT02892201.xml
curl https://clinicaltrials.gov/ct2/show/NCT03382561?displayxml=true > NCT03382561.xml
curl https://clinicaltrials.gov/ct2/show/NCT02498951?displayxml=true > NCT02498951.xml
curl https://clinicaltrials.gov/ct2/show/NCT03126916?displayxml=true > NCT03126916.xml
curl https://clinicaltrials.gov/ct2/show/NCT03336216?displayxml=true > NCT03336216.xml
curl https://clinicaltrials.gov/ct2/show/NCT02719574?displayxml=true > NCT02719574.xml
curl https://clinicaltrials.gov/ct2/show/NCT03306264?displayxml=true > NCT03306264.xml
curl https://clinicaltrials.gov/ct2/show/NCT02572453?displayxml=true > NCT02572453.xml
curl https://clinicaltrials.gov/ct2/show/NCT02549651?displayxml=true > NCT02549651.xml
#!/usr/bin/perl -w
#integrate_datasets.pl
my $bamreadct = shift @ARGV;
open NRC, "<$bamreadct" or die $!;
open OUT, ">$bamreadct\.cttable.txt" or die $!;
while (my $line = <NRC>) {
chomp($line);
my ($chrom,$pos,$ref,$depth,@reads) = split(/\t/,$line);
next unless ($depth > 10);
$chrom = 'chr'.$chrom if ($chrom !~ m/^chr/);
my $ro;
my %hash;
foreach my $rct (@reads) {
my ($base,$basect,@otherstats) = split(/:/,$rct);
if ($ref eq $base) {
$ro = $basect;
}else {
if ($base =~ m/\+|\-/) {
$base =~ s/\+/$ref/;
#$base =~ s/\-/$ref/;
}
$hash{$base} = $basect if ($basect);
}
}
my @basecalls;
foreach (keys %hash) {
push @basecalls, join(":",$_,$hash{$_});
}
print OUT join("\t",$chrom,$pos,$depth,$ref,$ro,join(";",@basecalls)),"\n";
}
close NRC;
#!/usr/bin/perl -w
#parse_gencode.pl
my $keep = shift @ARGV;
open KEEP, "<$keep" or die $!;
while (my $line = <KEEP>) {
chomp($line);
my ($sym) = split(/\t/,$line);
$keep{$sym} = 1;
}
open OUT, ">$keep\.bed" or die $!;
open GCODE, "</project/shared/bicf_workflow_ref/GRCh38/gencode.gtf" or die $!;
while (my $line = <GCODE>) {
chomp($line);
next if ($line =~ m/^#/);
my ($chrom,$source,$feature,$start,$end,$filter,$phase,$frame,$info) =
split(/\t/,$line);
next unless ($feature eq 'CDS');
$info =~ s/\"//g;
my %hash;
foreach $a (split(/;\s*/,$info)) {
my ($key,$val) = split(/ /,$a);
$hash{$key} = $val;
}
$hash{gene_id} =~ s/\.\d+//;
next unless ($keep{$hash{gene_name}});
print OUT join("\t",$chrom,$start,$end,join("|",$hash{gene_name},$hash{gene_id},$hash{exon_number})),"\n";
}
#!/usr/bin/perl -w
#parse_gencode.pl
my $keep = shift @ARGV;
open KEEP, "<$keep" or die $!;
while (my $line = <KEEP>) {
chomp($line);
my ($sym) = split(/\t/,$line);
$keep{$sym} = 1;
}
open OUT, ">$keep\.bed" or die $!;
open GCODE, "</project/shared/bicf_workflow_ref/GRCh38/gencode.gtf" or die $!;
while (my $line = <GCODE>) {
chomp($line);
next if ($line =~ m/^#/);
my ($chrom,$source,$feature,$start,$end,$filter,$phase,$frame,$info) =
split(/\t/,$line);
next unless ($feature eq 'gene');
$info =~ s/\"//g;
my %hash;
foreach $a (split(/;\s*/,$info)) {
my ($key,$val) = split(/ /,$a);
$hash{$key} = $val;
}
$hash{gene_id} =~ s/\.\d+//;
next unless ($keep{$hash{gene_name}});
print OUT join("\t",$chrom,$start,$end,join("|",$hash{gene_name},$hash{gene_id})),"\n";
}
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