20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,25 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+
+my $usage = "usage: $0 bams.list\n\n";
+
+my $bam_list_file = $ARGV[0] or die $usage;
+
+open (my $fh, $bam_list_file) or die $!;
+while (<$fh>) {
+    chomp;
+    my $bam_file = $_;
+
+    my $base_dir = dirname($bam_file);
+    
+    my $cmd = "cufflinks -o $base_dir/ $bam_file";
+
+    print "$cmd\n";
+}
+
+exit(0);
+
+
@@ -0,0 +1,28 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "usage: $0 cuff_gtf.list\n\n";
+
+my $trans_gtf_files = $ARGV[0] or die $usage;
+
+main: {
+
+    open (my $fh, $trans_gtf_files) or die $!;
+
+    while (<$fh>) {
+        chomp;
+        my $filename = $_;
+
+        my $cmd = "cufflinks_gtf_to_bed.pl $filename > $filename.bed";
+        
+        print "$cmd\n";
+    }
+    
+    close $fh;
+
+    exit(0);
+}
+
+
@@ -0,0 +1,28 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "usage: $0 gene_gff3.list\n\n";
+
+my $gene_gff3_files = $ARGV[0] or die $usage;
+
+main: {
+
+    open (my $fh, $gene_gff3_files) or die $!;
+
+    while (<$fh>) {
+        chomp;
+        my $filename = $_;
+
+        my $cmd = "gene_gff3_to_bed.pl $filename > $filename.bed";
+
+        print "$cmd\n";
+    }
+
+    close $fh;
+
+    exit(0);
+}
+
+
@@ -0,0 +1,45 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+use Cwd;
+
+my $usage = "usage: $0 trin_fa.list\n\n";
+
+my $trin_fa_files = $ARGV[0] or die $usage;
+
+my $workdir = cwd();
+
+
+open (my $fh, $trin_fa_files) or die "Error, cannot open file $trin_fa_files";
+while (<$fh>) {
+    chomp;
+    my $trin_fa_file = $_;
+    
+    my $outdir = dirname($trin_fa_file);
+
+    my $cmd = "gmap -g $outdir/gene.fa $trin_fa_file -f 3 > $trin_fa_file.gff3";
+    
+    
+    #&process_cmd($cmd);
+    print "$cmd\n";
+    
+}
+exit(0);
+
+
+####
+sub process_cmd {
+    my ($cmd) = @_;
+
+    print STDERR "CMD: $cmd\n";
+    my $ret = system($cmd);
+    if ($ret) {
+        die "Error, cmd: $cmd died with ret $ret";
+    }
+
+    return;
+}
+
+
@@ -0,0 +1,41 @@
+## partition the genes
+~/GITHUB/trinityrnaseq/util/misc/genome_gff3_to_gene_gff3_partitions.pl  genes.gff3 genes.fa 500
+find gene_contigs/ -regex ".*gene.fa" | tee fa_files.list
+
+## simulate reads:
+sim_reads.pl fa_files.list  | tee sim.cmds
+
+
+# Trinity
+~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/run_trinity_no_LR.pl fa_files.list  | tee trin.noFL.cmds
+
+~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/run_trinity_WITH_LR.pl ./fa_files.list  | tee trin.withFL.cmds
+
+# gmap the Trinity reconstructed transcripts to the gene sequence
+find gene_contigs/ -regex ".*Trinity.fasta" > trin_fa.list
+~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/gmap_to_ref.pl trin_fa.list  > gmap.cmds
+
+# cufflinks reconstruct
+find gene_contigs/ -regex ".*genome.sam.coordSorted.bam" | tee bams.list
+~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/bam_to_cuff.pl  bams.list  | tee cuff.cmds
+
+# convert gff3 files to bed
+find gene_contigs/ -regex ".*gene.gff3" | tee gene.gff3.list
+~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/gene_gff3_to_bed_cmds.pl  gene.gff3.list  > gene.gff3.list.cmds
+
+# convert cuff gtf to bed:
+~/GITHUB/trinityrnaseq/util/misc/iso_reco_analysis/cuff_gtf_to_bed.pl  cuff.list  |tee cuff.list.cmds
+
+
+
+########################################
+# pull together all results for viewing.
+
+find bin_0/ -regex '.*gene.gff3.bed' -exec cat {} \; | sort -k1,1 -k2,2n > all_genes.gff3.bed
+
+find bin_0 -regex ".*trinity_WITH_LR_outdir.Trinity.fasta.gff3.bed" -exec cat {} \; | sort -k1,1 -k2,2n > trin.WITH_LR.bed
+
+find bin_0 -regex ".*trinity_no_LR_outdir.Trinity.fasta.gff3.bed" -exec cat {} \; | sort -k1,1 -k2,2n > trin.no_LR.bed
+
+find bin_0 -regex ".*transcripts.gtf.bed" -exec cat {} \; | sort -k1,1 -k2,2n > cuff_trans.bed
+
@@ -0,0 +1,49 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+use Cwd;
+
+my $usage = "usage: $0 genome_fa_files.list\n\n";
+
+my $genome_fa_files = $ARGV[0] or die $usage;
+
+my $workdir = cwd();
+
+
+open (my $fh, $genome_fa_files) or die "Error, cannot open file $genome_fa_files";
+while (<$fh>) {
+    chomp;
+    my $genome_file = $_;
+    
+    my $outdir = dirname($genome_file);
+    
+    if ($outdir !~ /^\./) {
+        $outdir = "$workdir/$outdir";
+    }
+    
+
+    my $cmd = "$ENV{TRINITY_HOME}/Trinity --seqType fa --single $outdir/simul.reads.fa --CPU 1 --max_memory 1G --output $outdir/trinity_WITH_LR_outdir --full_cleanup --long_reads $outdir/simul.transcriptome.cdnas --trinity_complete";
+    
+    #&process_cmd($cmd);
+    print "$cmd\n";
+    
+}
+exit(0);
+
+
+####
+sub process_cmd {
+    my ($cmd) = @_;
+
+    print STDERR "CMD: $cmd\n";
+    my $ret = system($cmd);
+    if ($ret) {
+        die "Error, cmd: $cmd died with ret $ret";
+    }
+
+    return;
+}
+
+
@@ -0,0 +1,40 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+
+my $usage = "usage: $0 genome_fa_files.list\n\n";
+
+my $genome_fa_files = $ARGV[0] or die $usage;
+
+open (my $fh, $genome_fa_files) or die "Error, cannot open file $genome_fa_files";
+while (<$fh>) {
+    chomp;
+    my $genome_file = $_;
+    
+    my $outdir = dirname($genome_file);
+    
+    my $cmd = "$ENV{TRINITY_HOME}/Trinity --seqType fa --single $outdir/simul.reads.fa --CPU 1 --max_memory 1G --output $outdir/trinity_no_LR_outdir --full_cleanup --trinity_complete";
+    
+    #&process_cmd($cmd);
+    print "$cmd\n";
+    
+}
+exit(0);
+
+
+####
+sub process_cmd {
+    my ($cmd) = @_;
+
+    print STDERR "CMD: $cmd\n";
+    my $ret = system($cmd);
+    if ($ret) {
+        die "Error, cmd: $cmd died with ret $ret";
+    }
+
+    return;
+}
+
+
@@ -0,0 +1,43 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+
+my $usage = "usage: $0 genome_fa_files.list\n\n";
+
+my $genome_fa_files = $ARGV[0] or die $usage;
+
+open (my $fh, $genome_fa_files) or die "Error, cannot open file $genome_fa_files";
+while (<$fh>) {
+    chomp;
+    my $genome_file = $_;
+    
+    my $gff3_file = $genome_file;
+    $gff3_file =~ s/\.fa$/\.gff3/;
+
+    my $outdir = dirname($gff3_file);
+
+    my $cmd = "$ENV{TRINITY_HOME}/util/misc/simulate_reads_sam_and_fa.pl --gff3 $gff3_file --genome $genome_file --frag_length 300 --read_length 76 --SS_lib_type F --out_prefix $outdir/simul";
+    
+    #&process_cmd($cmd);
+    print "$cmd\n";
+    
+}
+exit(0);
+
+
+####
+sub process_cmd {
+    my ($cmd) = @_;
+
+    print STDERR "CMD: $cmd\n";
+    my $ret = system($cmd);
+    if ($ret) {
+        die "Error, cmd: $cmd died with ret $ret";
+    }
+
+    return;
+}
+
+
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+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "usage: $0 trans_gff3.list\n\n";
+
+my $trans_gff3_files = $ARGV[0] or die $usage;
+
+main: {
+
+    open (my $fh, $trans_gff3_files) or die $!;
+
+    while (<$fh>) {
+        chomp;
+        my $filename = $_;
+
+        my $cmd = "transcript_gff3_to_bed.pl $filename > $filename.bed";
+        
+        print "$cmd\n";
+    }
+
+    close $fh;
+
+    exit(0);
+}
+
+