For BEERS see http://cbil.upenn.edu/BEERS/

beers_help

$ perl reads_simulator.pl # Help

usage: reads_simulator.pl <num_reads> <name> [options]

<name> string is used in the names of the output files.
Use only alphanumeric, underscores and dashes in this string.

This program outputs a fasta file of reads and a .cig file and .bed file representing
the truth of where these reads map.
   - bed file is in one-based coords and contains both endpoints of each span.
   - cig file has a cigar string representation of the mapping coordinates, and a more human
     readable representation of the coordinates.  All coords are one-based.
Also output are: a file of indels, a file of substitutions, a file of splice forms, and a file of junctions 
and gaps crossed by the simulated reads.

   options:
      -readlength n   : Set readlength to n>0 bases (default n = 100).
      -numgenes n     : Choose n>=1 genes at random from a master pool of gene models (default n = 30000).
                        This only works with the four config files that have no stem (see below for more info).
      -strandspecific : Generate strand specific data
      -error x        : Set the error rate that any given base is sequenced wrong to 0<=x<=1 (default x = 0.005).
      -subfreq x      : Set substitution rate to 0<=x<1 (default x = 0.001).
      -indelfreq x    : Set indel rate to 0<=x<1 (default x = 0.0005).
      -nointron       : Set this to have no signal coming from introns.
      -tlen n         : Set the length of the low quality tail to n bases (default n = 10).
      -tpercent x     : Set the percent of tails that are low quality to 0<=x<=1
                        (default x = 0).
      -tqual x        : Set quality of the low quality tail to 0<=x<=1 (default x = 0.8).
      -nalt n         : Set the number of novel splice forms per gene to n>1 (default n = 2).
      -palt x         : Set the percentage of signal coming from novel splice
                        forms to 0<=x<=1 (default x = 0.2).
      -sn             : Add sequence number to the first column of the bed file.
      -configstem x   : The stem x will be added to the four default filenames for the four
                        required files.  Use this if you have made your own config files (see
                        below about config files and custom config files).
                        E.g. "simulator_config_geneinfo" becomes "simulator_config_geneinfo_x".
      -cntstart n     : Start the read counter at n (default n = 1).
      -outdir x       : x is a path to a directory to write to.  Default is the current directory.
      -mastercfgdir x : x is a path to a directory where the master config files are.  Default is the
                        current directory.
      -customcfgdir x : If you are using -configstem option, then x is a path to a directory where the
                        custom config files are.  Default is the directory specified by -outdir, which.
                        itself defaults to the current directory.
      -usesubs x      : x is a file of substitutions in the format output by this program in case you want
                        to resuse them for another run with the same gene models.
      -useindels x    : x is a file of indels in the format output by this program in case you want
                        to resuse them for another run with the same gene models.
      -usealts x      : x is a file of transcripts in the format output by this program in case you want
                        to resuse them for another run with the same gene models.  This must be used in
                        conjunction with -configstem for the same four files used the first time (those
                        will be the files ending in 'temp' if you used the master pool the first time).

This program depends on four (master config) files:
  1) simulator_config_geneinfo
  2) simulator_config_geneseq
  3) simulator_config_intronseq
  4) simulator_config_featurequantifications

With these files the program chooses -numgenes of them at random.
If you create custom config files with a suffix and use the -configstem mode
it then uses all genes in the file.
To create custom config files for a subset of genes in the master config, use the script:
   - make_config_files_for_subset_of_gene_ids.pl
Run it with no parameters for the usage
To use the custom config files with this program put them in the same directory as the script, or
in the directory specified by -outdir (not -mastercfgdir which specifies the master config files)
and use the option -configstem

See http://www.cbil.upenn.edu/BEERS for more information.

$ ls -lh
total 1.4G
-rw-r--r-- 1 brb brb  44M Sep 16  2010 simulator_config_featurequantifications_refseq
-rw-r--r-- 1 brb brb 7.7M Sep 15  2010 simulator_config_geneinfo_refseq
-rw-r--r-- 1 brb brb 106M Sep 15  2010 simulator_config_geneseq_refseq
-rw-r--r-- 1 brb brb 1.3G Sep 15  2010 simulator_config_intronseq_refseq

$ more simulator_config_featurequantifications_refseq 
basereads_total= 3896500899
--------------------------------------------------------------------
GENE.20704	-
    Type	Location          	Count	Ave_Cnt	Ave_Nrm	Length
    gene	chr1_gl000191_random:36275-50281	11873	5.3797	1.3806	2207
  exon 1	chr1_gl000191_random:50009-50281	2139	7.83516	2.0108	273
intron 1	chr1_gl000191_random:48652-50008	866	0.6381	0.1637	1357
  exon 2	chr1_gl000191_random:48545-48651	796	7.43925	1.9092	107
intron 2	chr1_gl000191_random:44911-48544	6809	1.8736	0.4808	3634
  exon 3	chr1_gl000191_random:44809-44910	439	4.30392	1.1045	102
intron 3	chr1_gl000191_random:41846-44808	3290	1.1103	0.2849	2963
  exon 4	chr1_gl000191_random:41683-41845	1519	9.31901	2.3916	163
intron 4	chr1_gl000191_random:41460-41682	80	0.3587	0.092	223
  exon 5	chr1_gl000191_random:41406-41459	503	9.31481	2.3905	54
intron 5	chr1_gl000191_random:37783-41405	18832	5.1979	1.3339	3623
  exon 6	chr1_gl000191_random:36275-37782	6477	4.29509	1.1022	1508
--------------------------------------------------------------------
GENE.20822	-
    Type	Location          	Count	Ave_Cnt	Ave_Nrm	Length
    gene	chr1_gl000191_random:36275-50281	11097	4.6803	1.2011	2371
  exon 1	chr1_gl000191_random:50009-50281	2139	7.83516	2.0108	273
intron 1	chr1_gl000191_random:48652-50008	866	0.6381	0.1637	1357
  exon 2	chr1_gl000191_random:48487-48651	952	5.76969	1.4807	165
intron 2	chr1_gl000191_random:48108-48486	28	0.0738	0.0189	379
  exon 3	chr1_gl000191_random:47745-48107	574	1.58126	0.4058	363
intron 3	chr1_gl000191_random:44887-47744	6100	2.1343	0.5477	2858
  exon 4	chr1_gl000191_random:44809-44886	390	5	1.2832	78
intron 4	chr1_gl000191_random:41846-44808	3290	1.1103	0.2849	2963
  exon 5	chr1_gl000191_random:41683-41845	1519	9.31901	2.3916	163
intron 5	chr1_gl000191_random:41460-41682	80	0.3587	0.092	223
  exon 6	chr1_gl000191_random:41406-41459	503	9.31481	2.3905	54
intron 6	chr1_gl000191_random:37550-41405	20289	5.2616	1.3503	3856
  exon 7	chr1_gl000191_random:36275-37549	5020	3.93725	1.0104	1275
--------------------------------------------------------------------
...

$ head simulator_config_geneinfo_refseq 
chr1	-	14362	29370	11	14362,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320	14829,15038,15947,16765,17055,17368,17742,18061,18366,24891,29370	GENE.14211
chr1	-	34611	36081	3	34611,35276,35720	35174,35481,36081	GENE.16185
chr1	+	69090	70008	1	69090	70008	GENE.4391
chr1	+	323891	328580	4	323891,324287,324438,327035	324060,324345,326938,328580	GENE.1388
chr1	+	323891	328580	3	323891,324287,324438	324060,324345,328580	GENE.27751
chr1	+	367658	368595	1	367658	368595	GENE.31890
chr1	-	566188	566265	1	566188	566265	GENE.5863
chr1	-	621097	622034	1	621097	622034	GENE.27342
chr1	-	661139	665731	3	661139,665277,665562	665184,665335,665731	GENE.14244
chr1	-	700244	714068	7	700244,701708,703927,704876,708355,709550,713663	700627,701767,703993,705092,708487,709660,714068	GENE.30215
$ grep GENE.20704 simulator_config_geneinfo_refseq
chr1_gl000191_random	-	36274	50281	6	36274,41405,41682,44808,48544,50008	37782,41459,41845,44910,48651,50281	GENE.20704

$ head -6 simulator_config_geneseq_refseq
>GENE.14211:chr1:14362-29370_-
CCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTGCTGCTGCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGGCCAGCCACCGGAGGGGTCAACCACTTCCCTGGGAGCTCCCTGGACTGAAGGAGACGCGCTGCTGCTGCTGTCGTCCTGCCTGGCGCCTTGGCCTACAGGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCTGGGGGTGGTGGTGGGGGCGGTGGGGGTGGTGTTAGTACCCCATCTTGTAGGTCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTGGCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGGGCTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGCAGGGCCCGCTCGTCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCAGGCCAGGGTCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCCCTGGAGCAGGGTACTTGGCACTGGAGAACACCTTGATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGCCTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGAAGATGTCTCCAGAGACCTTCTGCAGGTACTGCAGGGCATCCGCCATCTGCTGGACGGCCTCCTCTCGCCGCAGGTCTGGCTGGATGAAGGGCACGGCATAGGTCTGACCTGCCAGGGAGTGCTGCATCCTCACAGGAGTCATGGTGCCTGCGAGCCGCCCTCCCGGAAGCTCCCGCCGCCGCTTCCGCTCTGCCGGA
>GENE.16185:chr1:34611-36081_-
AAAGGCTTAAACACAATGGAAGTTTATTTCTCACTAAGGGAACATCCAAATCCATGATACTTTAAGTCAGGGACCCAGGTTCCTCCCATCTATGGTTCTGCCATCACTAATCTGGGTCTTCCACAATTGCCGTGCTCCTTGGAGGTGGGAAGAGCAGGCGGAGGACACGTGGGAGGTTTTAGGGACAAGCCTGGAGGCAGCATGCGTCACTCCCATGCAGAGTCCATTGGCCAATGCTGGCTCCGATGGCCACATCTCACTGCAGGGGCAGCTGGGAAATACAGTCTGGCTGTCTACCCAGGAGGAAGAGCAGCCAGTTTCTGCTGCTGATGATCAGGAGGTGGAGAAAATGTTCAGTCAGGCAGGGAGTGGGAATAGACAAGACCACAAGCAGCTTGGTGCCTCTGAAAGGGAGAGGGGTGGAGGGGAGACTAGAGAGGTGGGTAGGAATACTGGATTCCACTGACCACGTGCTGGATGTCACGCTTAGCCCTCCTGCTCTGTGCCGGGTTAGGCACCTGGTGTTTTACGTACATAATCTCAATTCTGTGAGGGCATCCGACAAGAATTTGGTGGGGAAAATATTACCATCTTTCCCTTTTGTGATTGGAGAAAAATGAGGCTTTGAAGGGTTTAAGAACTTGCCCAAGGTCGGCCAGGTGCAGTGGCTCATGTCTATAATCCCAACACTTTGGGAGGCTGAGGTGGGAGGATCGCTTGAGGCCAGGAGTTCAAGACCAGCCTGAGCAACATAGTGAGACTTTGTCTCTATAGTCAGCAGCATCGGGGGTCAGGAAAGACTTCACGAAGCCATAAATGCATCCTTCTCGGGGCAGCACCTGGCTCTCCCAGGTGAGAGAGGACTCCATTTTCACAGGCAGGCGTGGGAGCTTCAGCACCCATCTCTGGGCCCAGAATGACCCACTGGAGACCTTACAGCTCTCCTGTCACCCCCAATTCCTGCCCCCTCTGCAGCCTTGGAGGAGAATGGAGCTGAAGGGCCTGCCCTCTGTAGGGTGAGAAAGGGAGGCTAAAGCCTGGTGCCCACTGCCCTGGCTGCTCCGCATTGCAGGAGCTGCGCCCTTCCTTTCCTGGCACAGGGTCCACAGCCCCGAAACCCCGTTGTGTG
>GENE.4391:chr1:69090-70008_+
ATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTCACAGCCCCCAAGATGATTACTGACTTTTTCAGCCAGCGCAAAGTCATCTCTTTCAAGGGCTGCCTTGTTCAGATATTTCTCCTTCACTTCTTTGGTGGGAGTGAGATGGTGATCCTCATAGCCATGGGCTTTGACAGATATATAGCAATATGCAAGCCCCTACACTACACTACAATTATGTGTGGCAACGCATGTGTCGGCATTATGGCTGTCACATGGGGAATTGGCTTTCTCCATTCGGTGAGCCAGTTGGCGTTTGCCGTGCACTTACTCTTCTGTGGTCCCAATGAGGTCGATAGTTTTTATTGTGACCTTCCTAGGGTAATCAAACTTGCCTGTACAGATACCTACAGGCTAGATATTATGGTCATTGCTAACAGTGGTGTGCTCACTGTGTGTTCTTTTGTTCTTCTAATCATCTCATACACTATCATCCTAATGACCATCCAGCATCGCCCTTTAGATAAGTCGTCCAAAGCTCTGTCCACTTTGACTGCTCACATTACAGTAGTTCTTTTGTTCTTTGGACCATGTGTCTTTATTTATGCCTGGCCATTCCCCATCAAGTCATTAGATAAATTCCTTGCTGTATTTTATTCTGTGATCACCCCTCTCTTGAACCCAATTATATACACACTGAGGAACAAAGACATGAAGACGGCAATAAGACAGCTGAGAAAATGGGATGCACATTCTAGTGTAAAGTTTTAG
$ grep GENE.20704 simulator_config_geneseq_refseq
>GENE.20704:chr1_gl000191_random:36274-50281_-
$ wc -l simulator_config_geneseq_refseq
72934 simulator_config_geneseq_refseq

$ head -6 simulator_config_intronseq_refseq
>chr1:43870222-43871953
GTATTGCATCATCTCTCCAAGTTTGTACCCTCAGACCAAATTTCTATTAGTCCTCTGACCAAGTCCTTATCCTGTCTCTGCTGTTTGTCCCCAAAGTCCCGAGCTCTGCTGGCTTCTTGAACCTGTTTTCTAGTCATCCTCATGAGTCTCTCTCTCCTTGAGAAGAACCAGTTCCTCTGGACTTAAAGGGCTTTCCTATAGACTTCGGGTCAGTTGGTGTTGATTGGACACCTGCCTTTTTCACTGCTCCTGTAAATCTCTTTGATTCTGACCACTGGATGTCTGTTTTCTCCATTCCCCTCTTCTCCTTTAGTTCTGTTGGATGGTTTGCTGATGCGCTGGCTCTGGCTAGTACCCTCAGGAGATGGTCTTTTGGAATAGTTTTGTGATTTTGAAAGACAGCACATAACCCAGAAATGTAATTGGTTTCAAGGATAGAGGAGGGTCATTTTTTGTTGTTGTCTTTTTTTGAGACGGAGTTTCGCTCTTTTTGCCCAGGCTGGAGTGCAATGGCACAATCTTGGCTCACTGCAACCTCCGCCTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCAAGTAACGGGGATGATAGGCACTCACCACCAGGCCCAGCTTATTTATTTATTTATTTATTTTTAGTAGAGACGGGGTTTTGCCATGTTGGCCAGGCTGGTCTTGAACTCCCGACCTCAGGTGATCTGCCAGCCTCGGCCTCCCAAAGTGCTAGGATTACAGGCGTGAGCCACCGTGCCCAGTGTGGGTCATTTTTTTTTTGAGGGCCATGTGAACTGTTGGTTATAATGCTGACCACACAGATAATTACAGGGCTTATCCAGCACTCAAGGAGGCTATCACAAGACACTCCTTTTGGAGAATGGCCAAGTCTGTTACTGGAATATCTGTTTATGACTTAGATAAGCATTGGCCCAGTTTCCCCTCATCTGCTTTTAACTACCCTTAACTCATTGGTAAAGGCTTTCCCTGAAACTGTCCGTGATGGCTGCATTGTCACCTTAGCTATCAAACTGGATTTGAGAGATAAGATATTGGGAACATGATCTAAGGGTCTGAAACATACAGCAACAAAATTGGTGCATACCTGGATCCCAGGGCAGGGATTGCCAGCCCTCTGCCCTAGTTTAAAGTGCTTTCCTAGTATAGCCGTTAGGACTATCAGTTGTGGGCTGCATCCCCAGATGGGGGCCAGGTTTTGCAGGCACTGATAGCCAAGGCAGGGAGAGCATGGATGTTAGGTAATCACTCAAAACTTGGTTCAGGTTGGCAAACACTTAATGAAGCCTGAGCTATACCAGGCCTGAGCAGGTCCTGAAGACACAGATGAATCAGACCTTGTCTTTCTCCTGATGTGAAGAGTTGAGATTTTAGTGGGGGAGATAAATATTAAAGGGAGGTAATTGTAGTTGAATGTGATAAGGGCACCGATAAGATGACTCAGGTGCTATGGGAGCACCAAGAGGGAGCACCCAACCAAGCATGGGGCCACAATAGAGAAGTCTTTCAGACAAAGCAGCATTTGTTTTTCATGTTTTTGAGACAGAGTCTTGCTCTGTTGCCCGGGCTAGAGTGCAGTGGTGCAACCTTGGCTCACTGCACCCTCCACCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTTTCAAGTAGCTGGGATTACAGGTGCCCACTACCACACCCGGCTAATTTTTGTTTTTTTTGTTTTTTTTGGTAG
>chr1:153603588-153604509
CTGAATGAACAAAAGCATGGGAGAAAGAAGAATGTGGAGCATGTCAGTAGTTTCATTCAACTGGCATGAAGGATGTAGAAAACTAGGCTGCTAAGGCTAACCAGGGCCCCAAAGTAAAGAAGCCTCAGGATACGGTAGAAAGTGCACCGGTTTTGAGGTTTTATTGGACTGGGTTCAAATTCCAGCCCTGCTACTTTCTAGCTGTGGGACTTTGGGCATATTTATTTAACCACCGATTACCAATTTGTTTCTTCTCTAGAATGGAAATAATGAAACATACCTCACATTATTTGTATTAGAATTAAATTAGACAGTGCTTGTAAAGCTCCTAGTGTAGTGCTTGCTTTATTATAGGCACTGAACATACGGTAACTGGTGTCATTATTATTCATTCTGCCAGGTGAAAGAGCTTATGCTGTAGGCAACAGAAGCCCTCAAGACCTTTGAGGAGGCCTAGAAGAGTCCCATAATTCAATGCAGTTCCTCTCGCTCATCTTTGCCTCCTGCTCCTCAACCACCCCCTTGCCTCTGACTCAGTGCTGTACCCTTCCCTATACACCTCCCTCTTCCTCTCCTCCCACCACAGGCCCAGAAGGATGTGGATGCTGTGGACAAGGTGATGAAGGAGCTAGACGAGAATGGAGACGGGGAGGTGGACTTCCAGGAGTATGTGGTGCTTGTGGCTGCTCTCACAGTGGCCTGTAACAATTTCTTCTGGGAGAACAGTTGAGCAGACAGCCACATTGGGCAGCGCCCTTCCTCTCCACCCTCCCAGACCTGCCTCTTCCCCCTGCTTCCACCTCACCCCACTTATCCCTCTCCATAACCCCACCCTTGCCCACCCCACCCCCACCCCCACCAAGGGCGCAAGAGTAGCGGTCCAAGCCTGCAACTCATCTTTCATTAAAGGCTTCTCTCTCAC
>chr1:38166194-38167425
GTAAGTGGACACTGAGGTTGGAGGCTGGGGGTTATCACAAGACAAGCAAATACAAATGCATAAAATACACTGTTGTACACCAGAGCTCACAGTTTAGTAGAGATGATCCTACTTTACATGGCAATGACAAAAGAGATAATTGACTGGTGTGCAAAGTGTGTAGAACACAGAAGAGGAAGCTAGCAAGCCTCCCCTACCCCACTAGGACATAGACAGGCCTTTCAAGGTGAGTGAGAGTCTACTAGCTAGAGAAGAAAGGGAAGAGGAACAGTATTCAGGATAGATGGGGGAGGCGGAAAACTGAAGATGAGGAAACCAGTTAGAAGCCTATGAATTCTTGAACTGACATGCTGACACTATAGAATGAAGGGATGGTTTTTAGATAGGTTTTAGAAAGAAGTGGCATGGTTGGTGGAGAAAAGGAGGAATCAGAGACAACTGCATGGTTTCTAGCTAAGGCAAATGCTATCCAGTGAGGTGTGGGACCCAGGTGGCAGAGGGTGCTGGACTGGGGGTGGTGGAGCACATGCCAATTGCATGACATGTTGACCATTCATTACTTTTCCAGGACATCTAGGCTAGACAGAAATTTCAGCCTGGAGCTCAGGGAGAAGAGGGAGATTTGAGAGATACACTGCCTCCCAGATCTTTAGGTGTTTGTCCCAGTGTGGGAGTGGAGATGGTTGTGCAGGGAGAGCAGGAAGGGAGGGAGTCAGGGTGGACACTAGAGGGAGGGTAGAGAGAGGAGCTCCTAAGGCAGACTGCCAAGGAAGTTAGAGAAGCAGGAAAGACAGATCCATCACGGAGGACAAGGGAGGAGAGAATATATGGAAGATAAGGAGTGATTCTTGCCAGGGACCTCCCAGGCCCCAGGAAGGGAGCACTGCAGGGTTTGCCTTTGATTGGGCACCTGGGACGCCCTGAGTGACCTTCACAGCAGCCCTTTATGTAAAGTAGTGGGGTACAAGCCAGGCTGCAATCAGTTCAAAAGAGATTTACCTTTAATCTTGGTCAAAATCCTCTATTTTGAAAACCCAGCCAGTGGAAGTCCTTATTCAATTAGTTATGTTCTGAACTTTTTAAGTCATTGAATTCTGAGATACACCTTATTATATTTAGTATTAACTATCCAAAGCTTGTTCTTAATGCTTTAAAAAAAAAAAAAAAACCCTCCTTACCTTCCTCTTTGCTGGGTTTTTTGTAACCTTAGTCTCATTTGATTGTGACTGCAG
$ wc -l simulator_config_intronseq_refseq
416376 simulator_config_intronseq_refseq