tool to retrieve and generate stats from logfile

misc-scripts/chimp/get_stats.pl

+use strict;
+use warnings;
+
+use StatMsg;
+
+my $tr_split_count = 0;
+my $tr_translates_count = 0;
+my $tr_partial_translates_count = 0;
+my $tr_entire_translates_count = 0;
+my $tr_no_sequence_left_count = 0;
+my $tr_no_cds_left_count = 0;
+my $tr_doesnt_translate_count = 0;
+my $tr_partial_doesnt_translate_count = 0;
+my $tr_entire_doesnt_translate_count = 0;
+
+my $ex_delete_count = 0;
+my $ex_short_delete_count  = 0;
+my $ex_medium_delete_count = 0;
+my $ex_long_delete_count   = 0;
+my $ex_entire_delete_count = 0;
+my $ex_cds_delete_count    = 0;
+my $ex_utr_delete_count    = 0;
+my $ex_frameshift_delete_count = 0;
+my $ex_long_frameshift_delete_count = 0;
+my $ex_medium_frameshift_delete_count = 0;
+my $ex_short_frameshift_delete_count = 0;
+
+my $ex_insert_count        = 0;
+my $ex_short_insert_count  = 0;
+my $ex_medium_insert_count = 0;
+my $ex_long_insert_count   = 0;
+my $ex_cds_insert_count    = 0;
+my $ex_utr_insert_count    = 0;
+my $ex_frameshift_insert_count = 0;
+my $ex_long_frameshift_insert_count = 0;
+my $ex_medium_frameshift_insert_count = 0;
+my $ex_short_frameshift_insert_count = 0;
+
+my $ex_split_count    = 0;
+my $ex_confused_count = 0;
+
+while(my $code = <>) {
+  chomp($code);
+
+  if($code & StatMsg::TRANSCRIPT) {
+    if($code & StatMsg::TRANSLATES) {
+      $tr_translates_count++;
+
+      if($code & StatMsg::PARTIAL) {
+        $tr_partial_translates_count++;
+      }
+      if($code & StatMsg::ENTIRE) {
+        $tr_entire_translates_count++;
+      }
+    }
+
+    if($code & StatMsg::DOESNT_TRANSLATE) {
+      $tr_doesnt_translate_count++;
+
+      if($code & StatMsg::PARTIAL) {
+        $tr_partial_doesnt_translate_count++;
+      }
+      if($code & StatMsg::ENTIRE) {
+        $tr_entire_doesnt_translate_count++;
+      }
+    }
+
+
+    if($code & StatMsg::NO_SEQUENCE_LEFT) {
+      $tr_no_sequence_left_count++;
+    }
+
+    if($code & StatMsg::NO_CDS_LEFT) {
+      $tr_no_cds_left_count++;
+    }
+
+    if($code & StatMsg::SPLIT) {
+      $tr_split_count++;
+    }
+  }
+
+  elsif($code & StatMsg::EXON) {
+    if($code & StatMsg::DELETE) {
+      $ex_delete_count++;
+
+      if($code & StatMsg::LONG) {
+        $ex_long_delete_count++;
+      }
+      elsif($code & StatMsg::MEDIUM) {
+        $ex_medium_delete_count++;
+      }
+      elsif($code & StatMsg::SHORT) {
+        $ex_short_delete_count++;
+      }
+
+      if($code & StatMsg::ENTIRE) {
+        $ex_entire_delete_count++;
+      }
+
+      if($code & StatMsg::CDS) {
+        $ex_cds_delete_count++;
+      }
+
+      if($code & StatMsg::UTR) {
+        $ex_utr_delete_count++;
+      }
+
+      if($code & StatMsg::FRAMESHIFT) {
+        $ex_frameshift_delete_count++;
+
+        if($code & StatMsg::SHORT) {
+          $ex_short_frameshift_delete_count++;
+        }
+        elsif($code & StatMsg::MEDIUM) {
+          $ex_medium_frameshift_delete_count++;
+        }
+        elsif($code & StatMsg::LONG) {
+          $ex_long_frameshift_delete_count++;
+        }
+      }
+    }
+    elsif($code & StatMsg::INSERT) {
+      $ex_insert_count++;
+
+      if($code & StatMsg::LONG) {
+        $ex_long_insert_count++;
+      }
+      elsif($code & StatMsg::MEDIUM) {
+        $ex_medium_insert_count++;
+      }
+      elsif($code & StatMsg::SHORT) {
+        $ex_short_insert_count++;
+      }
+
+      if($code & StatMsg::CDS) {
+        $ex_cds_insert_count++;
+      }
+
+      if($code & StatMsg::UTR) {
+        $ex_utr_insert_count++;
+      }
+
+      if($code & StatMsg::FRAMESHIFT) {
+        $ex_frameshift_insert_count++;
+
+        if($code & StatMsg::SHORT) {
+          $ex_short_frameshift_insert_count++;
+        }
+        elsif($code & StatMsg::MEDIUM) {
+          $ex_medium_frameshift_insert_count++;
+        }
+        elsif($code & StatMsg::LONG) {
+          $ex_long_frameshift_insert_count++;
+        }
+      }
+    }
+
+    if($code & StatMsg::CONFUSED) {
+      $ex_confused_count++;
+    }
+
+    if($code & StatMsg::SPLIT) {
+      $ex_split_count++;
+    }
+
+  }
+
+}
+
+print "Transcript Summary:\n";
+print "  Split Events = $tr_split_count\n";
+print "  Translates (Partial/Entire) = $tr_translates_count\n";
+print "    Partial = $tr_partial_translates_count\n";
+print "    Entire = $tr_entire_translates_count\n";
+print "  Doesn't Translate = $tr_doesnt_translate_count\n";
+print "    Partial = $tr_partial_doesnt_translate_count\n";
+print "    Entire = $tr_entire_doesnt_translate_count\n";
+print "  No Sequence Left = $tr_no_sequence_left_count\n";
+print "  No CDS Left = $tr_no_cds_left_count\n";
+
+print "\nExon Summary:\n";
+print "  Split Events = $ex_split_count\n";
+print "  Inserts = $ex_insert_count\n";
+print "    Long = $ex_long_insert_count\n";
+print "    Medium = $ex_medium_insert_count\n";
+print "    Short = $ex_short_insert_count\n";
+print "    CDS = $ex_cds_insert_count\n";
+print "      Frameshifting = $ex_frameshift_insert_count\n";
+print "        Long = $ex_long_frameshift_insert_count\n";
+print "        Medium = $ex_medium_frameshift_insert_count\n";
+print "        Short = $ex_short_frameshift_insert_count\n";
+print "    UTR = $ex_utr_insert_count\n";
+print "  Deletes = $ex_delete_count\n";
+print "    Entire = $ex_entire_delete_count\n";
+print "    Long = $ex_long_delete_count\n";
+print "    Medium = $ex_medium_delete_count\n";
+print "    Short = $ex_short_delete_count\n";
+print "    CDS = $ex_cds_delete_count\n";
+print "      Frameshifting = $ex_frameshift_delete_count\n";
+print "        Long = $ex_long_frameshift_delete_count\n";
+print "        Medium = $ex_medium_frameshift_delete_count\n";
+print "        Short = $ex_short_frameshift_delete_count\n";
+print "    UTR = $ex_utr_delete_count\n";
+print "  Confused Events = $ex_confused_count\n";