Mercurial > repos > iuc > extract_genomic_dna

changeset 2:702970e4a134 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
author iuc
date Wed, 09 Mar 2016 05:07:21 -0500
parents 9af3f57e50b9
children b71579ad576c
files extract_genomic_dna.py extract_genomic_dna.xml extract_genomic_dna_utils.py test-data/1.bed test-data/cufflinks_out1.gtf test-data/droPer1.bed test-data/extract_genomic_dna_out1.fasta test-data/extract_genomic_dna_out2.fasta test-data/extract_genomic_dna_out3.gff test-data/extract_genomic_dna_out3.interval test-data/extract_genomic_dna_out4.gff test-data/extract_genomic_dna_out5.fasta test-data/extract_genomic_dna_out6.fasta test-data/extract_genomic_dna_out7.fasta test-data/gff_filter_by_attribute_out1.gff test-data/mm9.fasta test-data/mm9_input1.gff test-data/tophat_in1.fasta
diffstat 18 files changed, 193 insertions(+), 348 deletions(-) [+]
line wrap: on
line diff
--- a/extract_genomic_dna.py	Wed Jan 20 09:49:37 2016 -0500
+++ b/extract_genomic_dna.py	Wed Mar 09 05:07:21 2016 -0500
@@ -17,6 +17,8 @@
 parser.add_argument('--reference_genome_source', dest='reference_genome_source', help="Source of reference genome file")
 parser.add_argument('--reference_genome', dest='reference_genome', help="Reference genome file")
 parser.add_argument('--output_format', dest='output_format', help="Output format")
+parser.add_argument('--fasta_header_type', dest='fasta_header_type', default=None, help="Fasta header format")
+parser.add_argument('--fasta_header_delimiter', dest='fasta_header_delimiter', default=None, help="Fasta header field delimiter")
 parser.add_argument('--output', dest='output', help="Output dataset")
 args = parser.parse_args()
 
@@ -158,12 +160,21 @@
         c = 0
         if input_is_gff:
             start, end = egdu.convert_bed_coords_to_gff([start, end])
-        fields = [args.genome, str(chrom), str(start), str(end), strand]
-        meta_data = "_".join(fields)
-        if name.strip():
-            out.write(">%s %s\n" % (meta_data, name))
+        if args.fasta_header_type == "bedtools_getfasta_default":
+            out.write(">%s\n" % egdu.get_bedtools_getfasta_default_header(str(chrom),
+                                                                          str(start),
+                                                                          str(end),
+                                                                          strand,
+                                                                          includes_strand_col))
         else:
-            out.write(">%s\n" % meta_data)
+            # args.fasta_header_type == "char_delimited":
+            fields = [args.genome, str(chrom), str(start), str(end), strand]
+            field_delimiter = egdu.get_fasta_header_delimiter(args.fasta_header_delimiter)
+            meta_data = field_delimiter.join(fields)
+            if name.strip():
+                out.write(">%s %s\n" % (meta_data, name))
+            else:
+                out.write(">%s\n" % meta_data)
         while c < l:
             b = min(c + 50, l)
             out.write("%s\n" % str(sequence[c:b]))
@@ -181,7 +192,7 @@
                                    ".",
                                    egdu.gff_attributes_to_str(feature.attributes, "GTF")])
         else:
-            # Where is fields being set here?
+            # Here fields was set up around line 73.
             meta_data = "\t".join(fields)
         if input_is_gff:
             format_str = "%s seq \"%s\";\n"
--- a/extract_genomic_dna.xml	Wed Jan 20 09:49:37 2016 -0500
+++ b/extract_genomic_dna.xml	Wed Mar 09 05:07:21 2016 -0500
@@ -1,8 +1,10 @@
-<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.1">
+<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.2">
     <description>using coordinates from assembled/unassembled genomes</description>
     <requirements>
+        <requirement type="package" version="35x1">faToTwoBit</requirement>
         <requirement type="package" version="0.7.1">bx-python</requirement>
-        <requirement type="package" version="35x1">faToTwoBit</requirement>
+        <!-- conda dependencies -->
+        <requirement type="package" version="324">ucsc-fatotwobit</requirement>
     </requirements>
     <command>
         <![CDATA[
@@ -26,7 +28,13 @@
             #else:
                 --reference_genome $reference_genome_cond.reference_genome
             #end if
-            --output_format $output_format
+            --output_format $output_format_cond.output_format
+            #if str($output_format_cond.output_format) == "fasta":
+                --fasta_header_type $output_format_cond.fasta_header_type_cond.fasta_header_type
+                #if str($output_format_cond.fasta_header_type_cond.fasta_header_type) == "char_delimited":
+                    --fasta_header_delimiter $output_format_cond.fasta_header_type_cond.fasta_header_delimiter
+                #end if
+            #end if
             --output $output
         ]]>
     </command>
@@ -60,71 +68,74 @@
                 </param>
             </when>
         </conditional>
-        <param name="output_format" type="select" label="Select output format">
-            <option value="fasta" selected="True">fasta</option>
-            <option value="interval">interval</option>
-        </param>
+        <conditional name="output_format_cond">
+            <param name="output_format" type="select" label="Select output format">
+                <option value="fasta" selected="True">fasta</option>
+                <option value="interval">interval</option>
+            </param>
+            <when value="fasta">
+                <conditional name="fasta_header_type_cond">
+                    <param name="fasta_header_type" type="select" label="Select fasta header format">
+                        <option value="bedtools_getfasta_default" selected="True">bedtools getfasta default</option>
+                        <option value="char_delimited">character delimited field values</option>
+                    </param>
+                    <when value="bedtools_getfasta_default"/>
+                    <when value="char_delimited">
+                        <param name="fasta_header_delimiter" type="select" label="Select fasta header field delimiter">
+                            <option value="underscore" selected="True">underscore (_)</option>
+                            <option value="semicolon">semicolon (;)</option>
+                            <option value="comma">comma (,)</option>
+                            <option value="tilde">tilde (~)</option>
+                            <option value="vertical_bar">vertical bar (|)</option>
+                        </param>
+                    </when>
+                </conditional>
+            </when>
+            <when value="interval"/>
+        </conditional>
     </inputs>
     <outputs>
         <data format_source="input" name="output" metadata_source="input">
             <change_format>
-                <when input="output_format" value="fasta" format="fasta" />
+                <when input="output_format_cond.output_format" value="fasta" format="fasta" />
             </change_format>
         </data>
     </outputs>
     <tests>
         <test>
-            <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
-            <param name="interpret_features" value="yes"/>
-            <param name="index_source" value="cached"/>
-            <param name="out_format" value="fasta"/>
-            <output name="out_file1" file="extract_genomic_dna_out1.fasta" compare="contains" />
-        </test>
-        <test>
-            <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />
-            <param name="interpret_features" value="yes"/>
-            <param name="index_source" value="cached"/>
-            <param name="out_format" value="fasta"/>
-            <output name="out_file1" file="extract_genomic_dna_out2.fasta" compare="contains" />
+            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
+            <param name="interpret_features" value="no"/>
+            <param name="reference_genome_source" value="history"/>
+            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="output_format" value="fasta"/>
+            <param name="fasta_header_type" value="char_delimited"/>
+            <param name="fasta_header_delimiter" value="tilde"/>
+            <output name="output" file="extract_genomic_dna_out1.fasta" compare="contains" />
         </test>
         <test>
-            <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
+            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="yes"/>
-            <param name="index_source" value="cached"/>
-            <param name="out_format" value="interval"/>
-            <output name="out_file1" file="extract_genomic_dna_out3.interval" compare="contains" />
-        </test>
-        <!-- Test GFF file support. -->
-        <test>
-            <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
-            <param name="interpret_features" value="no"/>
-            <param name="index_source" value="cached"/>
-            <param name="out_format" value="interval"/>
-            <output name="out_file1" file="extract_genomic_dna_out4.gff" compare="contains" />
+            <param name="reference_genome_source" value="history"/>
+            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="output_format" value="fasta"/>
+            <param name="fasta_header_type" value="bedtools_getfasta_default"/>
+            <output name="output" file="extract_genomic_dna_out2.fasta" compare="contains" />
         </test>
         <test>
-            <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
+            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="no"/>
-            <param name="out_format" value="fasta"/>
-            <param name="index_source" value="cached"/>
-            <output name="out_file1" file="extract_genomic_dna_out5.fasta" compare="contains" />
-        </test>
-        <!-- Test custom sequences support and GFF feature interpretation. -->
-        <test>
-            <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
-            <param name="interpret_features" value="no"/>
-            <param name="index_source" value="history"/>
-            <param name="ref_file" value="tophat_in1.fasta"/>
-            <param name="out_format" value="fasta"/>
-            <output name="out_file1" file="extract_genomic_dna_out6.fasta" compare="contains" />
+            <param name="reference_genome_source" value="history"/>
+            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="output_format" value="interval"/>
+            <output name="output" file="extract_genomic_dna_out3.gff" compare="contains" />
         </test>
         <test>
-            <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
+            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="yes"/>
-            <param name="index_source" value="history"/>
-            <param name="ref_file" value="tophat_in1.fasta"/>
-            <param name="out_format" value="fasta"/>
-            <output name="out_file1" file="extract_genomic_dna_out7.fasta" compare="contains" />
+            <param name="reference_genome_source" value="history"/>
+            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="output_format" value="interval"/>
+            <output name="output" file="extract_genomic_dna_out4.gff" compare="contains" />
         </test>
     </tests>
     <help>
@@ -145,16 +156,33 @@
  - Chromosome, start or end coordinates that are invalid for the specified build.
  - Any lines whose data columns are not separated by a **TAB** character ( other white-space characters are invalid ).
 
-.. class:: infomark
-
- **Extract genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes** previously were achieved by two separate tools. 
-
 -----
 
 **What it does**
 
 This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA or interval format.
 
+If the output format is FASTA, the header format can be specified.  Selecting the **bedtools getfasta default**
+option produces a FASTA header formatted like the default header produced the the bedtools getfasta tool, and
+the "force strandedness" option is assumed.  If the input data includes a strand column and the strand is '+'
+or '-', it is included in the header.  If the input data includes a strand column and the value is anything but
+'+' or '-', a '.' is included in the header.  If the input data does not include a strand column, a '.' is included
+in the header.
+
+An example FASTA header produced by selecting this option is:
+
+    &gt;chr7:127475281-127475310(+)
+
+Selecing the **character delimited field values** option allows selection of a character delimiter that is used
+when generating the FASTA header with fields genome, chrom, start, end, strand (name) delimited by the
+selected character.  For example, selecting an underscore will produce a FASTA header like this:
+
+    &gt;mm9_53_550_+ test_chromosome
+
+while selecting a vertical bar will produce a FASTA header like this:
+
+    &gt;mm9|53|550|+ test_chromosome
+
 If strand is not defined, the default value is "+".
 
 -----
@@ -167,7 +195,7 @@
     chr7  127485994  127486166  NM_000230  0  +
     chr7  127486011  127486166  D49487     0  +
 
-Extracting sequences with **FASTA** output data type returns::
+Extracting sequences with **FASTA** output data type, **character delimited field values** as header format and **header field delimiter** set to the underscore character returns::
 
     &gt;hg17_chr7_127475281_127475310_+ NM_000230
     GTAGGAATCGCAGCGCCAGCGGTTGCAAG
--- a/extract_genomic_dna_utils.py	Wed Jan 20 09:49:37 2016 -0500
+++ b/extract_genomic_dna_utils.py	Wed Mar 09 05:07:21 2016 -0500
@@ -292,6 +292,39 @@
         stop_err('Error running faToTwoBit. ' + str(e))
 
 
+def get_bedtools_getfasta_default_header(chrom, start, end, strand, includes_strand_col):
+    """
+    Return a fasta header that is the default produced by the bedtools
+    getfasta tool, assuming "force strandedness".  This will produce a
+    header with this format: <chrom>:<start>-<end>(strand).  If the input
+    data includes a strand column and the strand is '+' or '-', then use it.
+    If the input data includes a strand column and the value of strand is
+    anything but '+' or '-', set strand to '.' in the header.  If the input
+    data does not include a strand column, set strand to '.' in the header.
+    """
+    if includes_strand_col and strand in ['+', '-']:
+        strand_val = strand
+    else:
+        strand_val = '.'
+    return '%s:%s-%s(%s)' % (chrom, start, end, strand_val)
+
+
+def get_fasta_header_delimiter(delimiter):
+    # Return a specified fasta header delimiter.
+    if delimiter == 'underscore':
+        return '_'
+    if delimiter == 'semicolon':
+        return ';'
+    if delimiter == 'comma':
+        return ','
+    if delimiter == 'tilde':
+        return '~'
+    if delimiter == 'vertical_bar':
+        return '|'
+    # Set the default to underscore.
+    return '_'
+
+
 def get_lines(feature):
     # Get feature's line(s).
     if isinstance(feature, GFFFeature):
--- a/test-data/1.bed	Wed Jan 20 09:49:37 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-
-chr1	147984545	147984630	CCDS990.1_cds_0_0_chr1_147984546_f	0	+
-chr1	148078400	148078582	CCDS993.1_cds_0_0_chr1_148078401_r	0	-
-chr1	148185136	148185276	CCDS996.1_cds_0_0_chr1_148185137_f	0	+
-chr10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-
-chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-
-chr11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+
-chr11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-
-chr11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	0	+
-chr12	38440094	38440321	CCDS8736.1_cds_0_0_chr12_38440095_r	0	-
-chr13	112381694	112381953	CCDS9526.1_cds_0_0_chr13_112381695_f	0	+
-chr14	98710240	98712285	CCDS9949.1_cds_0_0_chr14_98710241_r	0	-
-chr15	41486872	41487060	CCDS10096.1_cds_0_0_chr15_41486873_r	0	-
-chr15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+
-chr15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-
-chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+
-chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+
-chr16	179963	180135	CCDS10401.1_cds_0_0_chr16_179964_r	0	-
-chr16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+
-chr16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-
-chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-
-chr18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+
-chr18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-
-chr18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+
-chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+
-chr19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-
-chr19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+
-chr19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-
-chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+
-chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-
-chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+
-chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-
-chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-
-chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+
-chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-
-chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+
-chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+
-chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-
-chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+
-chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-
-chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+
-chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-
-chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+
-chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_r	0	-
-chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+
-chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-
-chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+
-chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-
-chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-
-chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+
-chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-
-chr6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+
-chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+
-chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-
-chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+
-chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-
-chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-
-chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+
-chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-
-chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+
-chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-
-chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+
-chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-
-chrX	152691446	152691471	CCDS14735.1_cds_0_0_chrX_152691447_f	0	+
-chrX	152694029	152694263	CCDS14736.1_cds_0_0_chrX_152694030_r	0	-
--- a/test-data/cufflinks_out1.gtf	Wed Jan 20 09:49:37 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-test_chromosome	Cufflinks	transcript	53	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
-test_chromosome	Cufflinks	exon	53	250	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
-test_chromosome	Cufflinks	exon	351	400	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
-test_chromosome	Cufflinks	exon	501	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
--- a/test-data/droPer1.bed	Wed Jan 20 09:49:37 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-super_1	139823	139913	AK028861	0	-	139823	139913	0	1	90,	0,
-super_1	156750	156844	BC126698	0	-	156750	156844	0	1	94,	0,
--- a/test-data/extract_genomic_dna_out1.fasta	Wed Jan 20 09:49:37 2016 -0500
+++ b/test-data/extract_genomic_dna_out1.fasta	Wed Mar 09 05:07:21 2016 -0500
@@ -1,88 +1,20 @@
->hg17_chr1_147962192_147962580_-
-ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG
-GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT
-GATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGT
-CCCTGTTCGTGAGGTCTGTCCAGTGACCCATCGTCCAGCCCTATACCGGG
-ACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATT
-CGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGC
-CTCAGCCCTGGGCCCCGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTG
-GGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA
->hg17_chr1_147984545_147984630_+
-ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTT
-TGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
->hg17_chr1_148078400_148078582_-
-GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAA
-GAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGA
-GCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACG
-GCTTCCAGTACCTCACCAACGGCATCATGTGA
->hg17_chr1_148185136_148185276_+
-ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGC
-CCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATC
-CGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA
->hg17_chr10_55251623_55253124_-
-TCTTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCT
-CAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACT
-ATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAGAGCAACAA
-ACTGAAGTCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAA
-GTGCCCATAATCCCCTTTATAAGGAAAACATAAGTCAAGTATCAACAAAT
-TCAGACATTTCACAGAGAACAGATTTTGTAGACCCATTTTCACCCAAAAT
-ACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGC
-TGTGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGTTCCA
-AATAGACCAGAGATCATAGATCTGCAGCAGTGGCAAGGCACCAGGCAGAA
-AGCTGAAAATGAAAACACTGGAATCTGTACAAACAAAAGAGGTAGCAGCA
-ATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATA
-AGGCAAGGTGAAACACTGATGATAGAAGGAACAGAACAGTTGAAATCTCT
-CTCTTCAGACTCTTCATTTTGCTTTCCCAGGCCTCACTTCTCATTCTCCA
-CTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTC
-ATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTTCAAGGCCTTG
-TGTTTTACATTCTTCACTCTCTAGGAGAGAGACACCTATTTGTATGTTAC
-CTATTGAAACCGAAAGAAATATTTTTGAAAATTTTGCCCATCCACCAAAC
-ATCTCTCCTTCTGCCTGtccccttccccctcctcctcctatttctcctcc
-ttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctc
-ctttttctcttttttgtcctcctccctctcctccttctatccctcttcct
-cttcctcctcctACATTTTTTCCACTTTCCGTTTCAACGTCTGGTCCCCC
-AACAccacctcttctacctccatttccaactcctcttcctccaccacctc
-cttctattccttgccctccacctccttcAGCTTCATTTCTGTCCACAGAG
-TGTGTCTGTATAACAGGTGTTAAATGCACGACCAACTTGATGCCTGCCGA
-GAAAATTAAGTCCTCTATGACACAGCTATCAACAACGACAGTGTGTAAAA
-CAGACCCTCAGAGAGAACCAAAAGGCATCCTCAGACACGTTAAAAACTTA
-GCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGAAAAAAA
-CTATCTACGCACAAATGTTTCAGAACTTCAAACTATGTGCCCTTCAGAAG
-TAACAAATATGGAAATCACATCTGAACAAAACAAGGGGAGTTTGAACAAT
-ATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTA
-A
->hg17_chr11_116124407_116124501_-
-ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGG
-CAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATATGTAA
->hg17_chr11_116206508_116206563_+
-ATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTC
-TGCCC
->hg17_chr11_116211733_116212337_-
-CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGC
-TGCGCGAACAGCTCGGCCCTGTGACCCAGGAGTTCTGGGATAACCTGGAA
-AAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGT
-GAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGG
-AGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCAGAGCTC
-CAAGAGGGCGCGCGCCAGAAGCTGCACGAGCTGCAAGAGAAGCTGAGCCC
-ACTGGGCGAGGAGATGCGCGACCGCGCGCGCGCCCATGTGGACGCGCTGC
-GCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCG
-CGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCA
-CGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGCCCG
-CGCTCGAGGACCTCCGCCAAGGCCTGCTGCCCGTGCTGGAGAGCTTCAAG
-GTCAGCTTCCTGAGCGCTCTCGAGGAGTACACTAAGAAGCTCAACACCCA
-GTGA
->hg17_chr11_1812377_1812407_+
-ATGCTCCACCTGCATGGCTGGCAAACCATG
->hg17_chr12_38440094_38440321_-
-GAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCATC
-TATGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGGAAATTGAATC
-ACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAG
-GGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCT
-GACAATGATGCTTCTGATGTGGAATAA
->hg17_chr13_112381694_112381953_+
-ATGAACTCACCAGAGGCGAGGCTCTGCGTTGCTCAATGCAGAGACTCTTA
-CCCAGGGTGTCAGCCTCTGAAAGATACACGTGCCTGGGCCTCTTCCCTGA
-AGATGGACCCGGCAGGTCTGGAGGGAGGCCCCCGTGATGAATCCCGTGAT
-GAGCCGCCGATCCGAGCTCAGGCTGCGTCATGGGACCAGCCACAAGGTTG
-CCTGACCTATAAAGGTCGCAGGAGTGCCTCAGGGACACAGAAGCAGTTAC
-AGCTGCCAG
+>mm9~test_chromosome~53~550~+
+TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC
+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG
+CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC
+GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGT
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAC
+TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGT
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTT
+TTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
+>mm9~test_chromosome~53~250~+
+TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC
+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG
+CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC
+GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC
+>mm9~test_chromosome~351~400~+
+ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT
+>mm9~test_chromosome~501~550~+
+TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
--- a/test-data/extract_genomic_dna_out2.fasta	Wed Jan 20 09:49:37 2016 -0500
+++ b/test-data/extract_genomic_dna_out2.fasta	Wed Mar 09 05:07:21 2016 -0500
@@ -1,6 +1,17 @@
->droPer1_super_1_139823_139913_- AK028861
-CGTCGGCTTCTGCTTCTGCTGATGATGGTCGTTCTTCTTCCTTTACTTCT
-TCCTATTTTTCTTCCTTCCCTTACACTATATCTTCCTTTA
->droPer1_super_1_156750_156844_- BC126698
-CCGGGCTGCGGCAAGGGATTCACCTGCTCCAAACAGCTCAAGGTGCACTC
-CCGCACGCACACGGGCGAGAAGCCCTATCACTGCGACATCTGCT
+>test_chromosome:53-550(+)
+TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC
+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG
+CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC
+GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGT
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAC
+TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGT
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTT
+TTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGCTA
+CTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTA
+CGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG
+ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGT
+ATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTA
+TTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTT
+CTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_genomic_dna_out3.gff	Wed Mar 09 05:07:21 2016 -0500
@@ -0,0 +1,4 @@
+test_chromosome	Cufflinks	transcript	53	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; seq "TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC";
+test_chromosome	Cufflinks	exon	53	250	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; seq "TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC";
+test_chromosome	Cufflinks	exon	351	400	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; seq "ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT";
+test_chromosome	Cufflinks	exon	501	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; seq "TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC";
--- a/test-data/extract_genomic_dna_out3.interval	Wed Jan 20 09:49:37 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-	ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTGGACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGTGATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGTCCCTGTTCGTGAGGTCTGTCCAGTGACCCATCGTCCAGCCCTATACCGGGACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATTCGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGCCTCAGCCCTGGGCCCCGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTGGGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA
-chr1	147984545	147984630	CCDS990.1_cds_0_0_chr1_147984546_f	0	+	ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
-chr1	148078400	148078582	CCDS993.1_cds_0_0_chr1_148078401_r	0	-	GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA
-chr1	148185136	148185276	CCDS996.1_cds_0_0_chr1_148185137_f	0	+	ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGCCCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATCCGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA
-chr10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-	TCTTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCTCAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACTATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAGAGCAACAAACTGAAGTCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAAGTGCCCATAATCCCCTTTATAAGGAAAACATAAGTCAAGTATCAACAAATTCAGACATTTCACAGAGAACAGATTTTGTAGACCCATTTTCACCCAAAATACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGCTGTGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGTTCCAAATAGACCAGAGATCATAGATCTGCAGCAGTGGCAAGGCACCAGGCAGAAAGCTGAAAATGAAAACACTGGAATCTGTACAAACAAAAGAGGTAGCAGCAATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATAAGGCAAGGTGAAACACTGATGATAGAAGGAACAGAACAGTTGAAATCTCTCTCTTCAGACTCTTCATTTTGCTTTCCCAGGCCTCACTTCTCATTCTCCACTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTCATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTTCAAGGCCTTGTGTTTTACATTCTTCACTCTCTAGGAGAGAGACACCTATTTGTATGTTACCTATTGAAACCGAAAGAAATATTTTTGAAAATTTTGCCCATCCACCAAACATCTCTCCTTCTGCCTGtccccttccccctcctcctcctatttctcctccttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctcctttttctcttttttgtcctcctccctctcctccttctatccctcttcctcttcctcctcctACATTTTTTCCACTTTCCGTTTCAACGTCTGGTCCCCCAACAccacctcttctacctccatttccaactcctcttcctccaccacctccttctattccttgccctccacctccttcAGCTTCATTTCTGTCCACAGAGTGTGTCTGTATAACAGGTGTTAAATGCACGACCAACTTGATGCCTGCCGAGAAAATTAAGTCCTCTATGACACAGCTATCAACAACGACAGTGTGTAAAACAGACCCTCAGAGAGAACCAAAAGGCATCCTCAGACACGTTAAAAACTTAGCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGAAAAAAACTATCTACGCACAAATGTTTCAGAACTTCAAACTATGTGCCCTTCAGAAGTAACAAATATGGAAATCACATCTGAACAAAACAAGGGGAGTTTGAACAATATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTAA
-chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-	ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATATGTAA
-chr11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+	ATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTCTGCCC
-chr11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-	CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTGTGACCCAGGAGTTCTGGGATAACCTGGAAAAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGTGAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGGAGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCAGAGCTCCAAGAGGGCGCGCGCCAGAAGCTGCACGAGCTGCAAGAGAAGCTGAGCCCACTGGGCGAGGAGATGCGCGACCGCGCGCGCGCCCATGTGGACGCGCTGCGCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCACGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGCCCGCGCTCGAGGACCTCCGCCAAGGCCTGCTGCCCGTGCTGGAGAGCTTCAAGGTCAGCTTCCTGAGCGCTCTCGAGGAGTACACTAAGAAGCTCAACACCCAGTGA
-chr11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	0	+	ATGCTCCACCTGCATGGCTGGCAAACCATG
-chr12	38440094	38440321	CCDS8736.1_cds_0_0_chr12_38440095_r	0	-	GAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCATCTATGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGGAAATTGAATCACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAGGGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCTGACAATGATGCTTCTGATGTGGAATAA
--- a/test-data/extract_genomic_dna_out4.gff	Wed Jan 20 09:49:37 2016 -0500
+++ b/test-data/extract_genomic_dna_out4.gff	Wed Mar 09 05:07:21 2016 -0500
@@ -1,10 +1,1 @@
-chr10	Cufflinks	transcript	62044837	62045189	1000	.	.	gene_id "CUFF.23531"; transcript_id "CUFF.23531.1"; FPKM "19.5178121606"; frac "1.000000"; conf_lo "9.264456"; conf_hi "29.771168"; cov "1.108611"; seq "AATTACAAGATCGACACACCAAGATAGGCAGATCCATGGTTGGTTTTACTTTGTAAATCTAAAAGTATGTTGGAAAACGATGCAATGAATTCTTATCCTTTTTCAAAATGAAGAATTTGTGATGGTTAGTGGACAGTTCAGAAGCCTCTCTGCAAGAAAGGGGGCGCTGAGAAGTGGTAAAAAAAGGAAGGAAGCACTCGGGCTTTGTCAGCAGGGTGGACCCTGGGGTCCACAGTGGGAACAGTCCCTTCTGGCCTCTACTCACTGACCAAACGCTTTACTAAAACTCCGCTTCTGGCCTCTGTTGCCACCTCCTGGTCGCTGTCCTCGGAAGTTTCTACTTCCTCCTCGCT";
-chr10	Cufflinks	transcript	75372919	75373002	1000	.	.	gene_id "CUFF.24985"; transcript_id "CUFF.24985.1"; FPKM "124.4970510798"; frac "1.000000"; conf_lo "71.411330"; conf_hi "177.582772"; cov "7.071429"; seq "GCGTCTCGCAGCTTCTGCCCGTCGATCTCCATGTCGAGCCGGATGGGCACCAGCACCTCAGGCTGTGACGCATTCTCATGGATC";
-chr10	Cufflinks	transcript	80362428	80363292	1000	-	.	gene_id "CUFF.26065"; transcript_id "CUFF.26065.1"; FPKM "43.6170921216"; frac "1.000000"; conf_lo "32.260169"; conf_hi "54.974016"; cov "2.477449"; seq "ATGACGGACAAGTGTTTCCGGAAGTGCATCGGGAAGCCCGGGGGCTCCTTGGATAACTCGGAGCAGGTGAGACATCTCGGGAACCCGGGGTGGTGAGGGGCGCGGGGTCAGGAGCGTCTAGGAGGTTGAGAGATGTGCGCGTGCGCGGCCTCTAGCCTTAGCTACTGAGGAAGTTGTGCGCGTGCGCGGGGTGAGGACCCGGCTTCTGTGCCTAGATCGGTGCAGCCTTCATGGGTGATCCTCGGGTCGTGTGACCGTCAGTCAGGGATCCCCCTCCACGCTTTGCAGAAATGCATCGCCATGTGCATGGACCGCTACATGGACGCCTGGAATACCGTGTCCCGCGCCTACAACTCTCGACTGCAGCGGGAACGAGCCAACATGTGACCGGGACCTGTGCCTCGGGACACCGTGCTTATGGTCTGAACTGTTTTCCCTGCCAGTTAGGGTGTCTCCTCCTAGCCGCCCTGAAGTCTGGCAGCATGGAGGGCTTGGGGATCGAGGCCTCTCCCCTGGGTTGCTGCGTCCAGCTCAATCTCAGAAGAGAGTGAGGACCCGACAGAGCACAGGGATCTGGCTGGCCCCACTGACCTGTGACCTCAGGAGAGCAGGCCAATAAATCGCTGCTGGGGCAGTAAAGCAGGCGTGTCACCTCACTGCTTCAGGTCCCTTCCCCTGAGTAGGCCCAGACCTCCCAGGGTATCTTTCCCCTTGGGGTCAGTGGGCTGCTGGCTCTCAGGGAATTCGGAGCATGATCTCAGGTGTTTGGTCATCCCGGGGAGACCAGCCGAGGTTAAGAAGCAAGGCTTCATGTagccttcacctatcatgcatgaggcccagggtgctgaccttaactctgaat";
-chr11	Cufflinks	transcript	7904565	7904642	1000	.	.	gene_id "CUFF.33508"; transcript_id "CUFF.33508.1"; FPKM "61.6484988869"; frac "1.000000"; conf_lo "22.882428"; conf_hi "100.414569"; cov "3.501633"; seq "CATCTTCTATTTGAGCCTCCATCCAGGCACCTCTGAAACAAAGGTGCACTCACTGCATGTCCACTTGTCACAGGAGCC";
-chr11	Cufflinks	exon	78140156	78140259	1000	.	.	gene_id "CUFF.43148"; transcript_id "CUFF.43148.1"; exon_number "1"; FPKM "54.8483511750"; frac "1.000000"; conf_lo "23.181641"; conf_hi "86.515061"; cov "3.115385"; seq "CTGCTTGCTAATTTTCTCTCTTGGGATCAGGGGGACGTGAACTCCAGCCCTGACTCGTGCTCCTTATGCTCTGAGTACATAGCAAATAAATGAGAGCAAAACAC";
-chr11	Cufflinks	exon	105616462	105616737	1000	.	.	gene_id "CUFF.48385"; transcript_id "CUFF.48385.1"; exon_number "1"; FPKM "18.9452034252"; frac "1.000000"; conf_lo "7.520816"; conf_hi "30.369591"; cov "1.076087"; seq "TAGGTGTAATAGTGGAAAACAATAGTTTTTAAACTTCAGAGTCCAGGGCTGTAACTCAGTAGTAACAGTGTTCTCTAAGTATGTTATTCTTCCTCTACATGCTGAAATTTTTCATATTTGGAGCATTCACTGTTCCATGTATCAGTAAATTATATTGTGAGCTGTCATCATATCTAAGCACCATATTGAATATTTTTCATGATTAAAATTTGTTGAAACAACAATTCTATGACCGAAAAAAGCAAGGCTTTGTAAATAACATGTTTGTTACTAGTA";
-chr12	Cufflinks	exon	30701762	30702509	1000	.	.	gene_id "CUFF.53897"; transcript_id "CUFF.53897.1"; exon_number "1"; FPKM "48.9333329111"; frac "1.000000"; conf_lo "37.780391"; conf_hi "60.086275"; cov "2.779412"; seq "TGTGGAGTGTACTTATATGATCCCTATGCTGATAGGATTACCTTCCTAGACATAGCTAGACGCAAAGCCACATGTGTAAGGCTGCTGAGCAAAGACAGCATCCCAGCATGGGTGTGTTCACGGTGGATTCACCACGTTGCATATGTAAAGTGGTCCCCTTGGCTTACCCTTCACTTTGCTCATGAGATTCAGAAGCTGGTGGTCCAGCAGGGGTGAGCATTTGTGAAATAGTAAGCTGAACTTAGTGGTGAGATTTCAGAACAGACTTCTGTGAAGTAAGAGATGTAACCATGCATCTAAAATCAGATGGCCGTGTAACTGCTCGGGCATAGAAATGGTGGGAGAACCTGTCCTGGGTACCTGGCATTTCACATGAGCCCAGGGATATGTCTTGTGCCAAGGCACACAAGTGTCCATGGACTTGGACAGGTGCCAAGGGTTTTTGTCTCTGTTCCTATGTGGGAGGCTGGCTGTGATTTACATTAATTTCTGTATTTCAAACGAAGATGTCTGCAGATCTCCATTTTGATGTTACAGCCTCATTGCCCAGGCAGTGGGCAGTGCCCAGACACCCTTTCTGACTAGCCACTGCATTGGGCTTCTGTGATTCAAAGTAGTGTATATATTTATTTACTTCTCTGACTGTGGCCAACAGCCAAATGCCATTTTATGTTCCTTGTATTCAGTCCATTACCAAAGAGGTGTTTGCACTTTGTAATGATACCTTTCAGTTCAAATAAAAGGACCA";
-chr13	Cufflinks	exon	49159496	49159569	1000	.	.	gene_id "CUFF.67788"; transcript_id "CUFF.67788.1"; exon_number "1"; FPKM "44.9657653777"; frac "1.000000"; conf_lo "10.974842"; conf_hi "78.956689"; cov "2.554054"; seq "ttttcttttggattacttgatttttttttatttgatcttatttatgatgattttgagtacatttttgaacagtt";
-chr13	Cufflinks	transcript	100200304	100200330	1000	.	.	gene_id "CUFF.73108"; transcript_id "CUFF.73108.1"; FPKM "123.2395051093"; frac "1.000000"; conf_lo "30.079196"; conf_hi "216.399814"; cov "7.000000"; seq "TCTCATATGAATAGCCACCCTCTTCTG";
-chr14	Cufflinks	transcript	31949103	31949152	1000	.	.	gene_id "CUFF.77316"; transcript_id "CUFF.77316.1"; FPKM "85.5634278330"; frac "1.000000"; conf_lo "28.521143"; conf_hi "142.605713"; cov "4.860000"; seq "GGATGCTATCCGCGATGTGCATGTAAAGGGCCTCATGTACCAGTGGATCG";
+test_chromosome	galaxy_extract_genomic_dna	interval	52	550	1000	+	.	frac "1.000000" ; cov "145.770185" ; conf_lo "8543307.525072" ; FPKM "10679134.4063403048" ; transcript_id "CUFF.1.1" ; gene_id "CUFF.1" ; conf_hi "12814961.287608" seq "TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGCTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC";
--- a/test-data/extract_genomic_dna_out5.fasta	Wed Jan 20 09:49:37 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
->mm9_chr10_62044837_62045189_+
-AATTACAAGATCGACACACCAAGATAGGCAGATCCATGGTTGGTTTTACT
-TTGTAAATCTAAAAGTATGTTGGAAAACGATGCAATGAATTCTTATCCTT
-TTTCAAAATGAAGAATTTGTGATGGTTAGTGGACAGTTCAGAAGCCTCTC
-TGCAAGAAAGGGGGCGCTGAGAAGTGGTAAAAAAAGGAAGGAAGCACTCG
-GGCTTTGTCAGCAGGGTGGACCCTGGGGTCCACAGTGGGAACAGTCCCTT
-CTGGCCTCTACTCACTGACCAAACGCTTTACTAAAACTCCGCTTCTGGCC
-TCTGTTGCCACCTCCTGGTCGCTGTCCTCGGAAGTTTCTACTTCCTCCTC
-GCT
->mm9_chr10_75372919_75373002_+
-GCGTCTCGCAGCTTCTGCCCGTCGATCTCCATGTCGAGCCGGATGGGCAC
-CAGCACCTCAGGCTGTGACGCATTCTCATGGATC
->mm9_chr10_80362428_80363292_-
-ATGACGGACAAGTGTTTCCGGAAGTGCATCGGGAAGCCCGGGGGCTCCTT
-GGATAACTCGGAGCAGGTGAGACATCTCGGGAACCCGGGGTGGTGAGGGG
-CGCGGGGTCAGGAGCGTCTAGGAGGTTGAGAGATGTGCGCGTGCGCGGCC
-TCTAGCCTTAGCTACTGAGGAAGTTGTGCGCGTGCGCGGGGTGAGGACCC
-GGCTTCTGTGCCTAGATCGGTGCAGCCTTCATGGGTGATCCTCGGGTCGT
-GTGACCGTCAGTCAGGGATCCCCCTCCACGCTTTGCAGAAATGCATCGCC
-ATGTGCATGGACCGCTACATGGACGCCTGGAATACCGTGTCCCGCGCCTA
-CAACTCTCGACTGCAGCGGGAACGAGCCAACATGTGACCGGGACCTGTGC
-CTCGGGACACCGTGCTTATGGTCTGAACTGTTTTCCCTGCCAGTTAGGGT
-GTCTCCTCCTAGCCGCCCTGAAGTCTGGCAGCATGGAGGGCTTGGGGATC
-GAGGCCTCTCCCCTGGGTTGCTGCGTCCAGCTCAATCTCAGAAGAGAGTG
-AGGACCCGACAGAGCACAGGGATCTGGCTGGCCCCACTGACCTGTGACCT
-CAGGAGAGCAGGCCAATAAATCGCTGCTGGGGCAGTAAAGCAGGCGTGTC
-ACCTCACTGCTTCAGGTCCCTTCCCCTGAGTAGGCCCAGACCTCCCAGGG
-TATCTTTCCCCTTGGGGTCAGTGGGCTGCTGGCTCTCAGGGAATTCGGAG
-CATGATCTCAGGTGTTTGGTCATCCCGGGGAGACCAGCCGAGGTTAAGAA
-GCAAGGCTTCATGTagccttcacctatcatgcatgaggcccagggtgctg
-accttaactctgaat
--- a/test-data/extract_genomic_dna_out6.fasta	Wed Jan 20 09:49:37 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
->mm9_test_chromosome_53_550_+
-TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC
-TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG
-CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC
-GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGT
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAC
-TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGT
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTT
-TTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
->mm9_test_chromosome_53_250_+
-TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC
-TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG
-CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC
-GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC
->mm9_test_chromosome_351_400_+
-ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT
->mm9_test_chromosome_501_550_+
-TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
--- a/test-data/extract_genomic_dna_out7.fasta	Wed Jan 20 09:49:37 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
->mm9_test_chromosome_53_550_+
-TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC
-TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG
-CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC
-GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGT
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAC
-TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGT
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTT
-TTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGCTA
-CTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTA
-CGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG
-ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGT
-ATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTA
-TTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTT
-CTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
--- a/test-data/gff_filter_by_attribute_out1.gff	Wed Jan 20 09:49:37 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-chr10	Cufflinks	transcript	62044837	62045189	1000	.	.	gene_id "CUFF.23531"; transcript_id "CUFF.23531.1"; FPKM "19.5178121606"; frac "1.000000"; conf_lo "9.264456"; conf_hi "29.771168"; cov "1.108611";
-chr10	Cufflinks	transcript	75372919	75373002	1000	.	.	gene_id "CUFF.24985"; transcript_id "CUFF.24985.1"; FPKM "124.4970510798"; frac "1.000000"; conf_lo "71.411330"; conf_hi "177.582772"; cov "7.071429";
-chr10	Cufflinks	transcript	80362428	80363292	1000	-	.	gene_id "CUFF.26065"; transcript_id "CUFF.26065.1"; FPKM "43.6170921216"; frac "1.000000"; conf_lo "32.260169"; conf_hi "54.974016"; cov "2.477449";
-chr11	Cufflinks	transcript	7904565	7904642	1000	.	.	gene_id "CUFF.33508"; transcript_id "CUFF.33508.1"; FPKM "61.6484988869"; frac "1.000000"; conf_lo "22.882428"; conf_hi "100.414569"; cov "3.501633";
-chr11	Cufflinks	exon	78140156	78140259	1000	.	.	gene_id "CUFF.43148"; transcript_id "CUFF.43148.1"; exon_number "1"; FPKM "54.8483511750"; frac "1.000000"; conf_lo "23.181641"; conf_hi "86.515061"; cov "3.115385";
-chr11	Cufflinks	exon	105616462	105616737	1000	.	.	gene_id "CUFF.48385"; transcript_id "CUFF.48385.1"; exon_number "1"; FPKM "18.9452034252"; frac "1.000000"; conf_lo "7.520816"; conf_hi "30.369591"; cov "1.076087";
-chr12	Cufflinks	exon	30701762	30702509	1000	.	.	gene_id "CUFF.53897"; transcript_id "CUFF.53897.1"; exon_number "1"; FPKM "48.9333329111"; frac "1.000000"; conf_lo "37.780391"; conf_hi "60.086275"; cov "2.779412";
-chr13	Cufflinks	exon	49159496	49159569	1000	.	.	gene_id "CUFF.67788"; transcript_id "CUFF.67788.1"; exon_number "1"; FPKM "44.9657653777"; frac "1.000000"; conf_lo "10.974842"; conf_hi "78.956689"; cov "2.554054";
-chr13	Cufflinks	transcript	100200304	100200330	1000	.	.	gene_id "CUFF.73108"; transcript_id "CUFF.73108.1"; FPKM "123.2395051093"; frac "1.000000"; conf_lo "30.079196"; conf_hi "216.399814"; cov "7.000000";
-chr14	Cufflinks	transcript	31949103	31949152	1000	.	.	gene_id "CUFF.77316"; transcript_id "CUFF.77316.1"; FPKM "85.5634278330"; frac "1.000000"; conf_lo "28.521143"; conf_hi "142.605713"; cov "4.860000";
-chr14	Cufflinks	exon	67604227	67604668	1000	.	.	gene_id "CUFF.81446"; transcript_id "CUFF.81446.1"; exon_number "1"; FPKM "123.6776546104"; frac "1.000000"; conf_lo "100.611653"; conf_hi "146.743656"; cov "7.024887";
-chr14	Cufflinks	exon	75165582	75165744	1000	.	.	gene_id "CUFF.82088"; transcript_id "CUFF.82088.1"; exon_number "1"; FPKM "20.4139057543"; frac "1.000000"; conf_lo "4.982443"; conf_hi "35.845368"; cov "1.159509";
-chr16	Cufflinks	transcript	57154027	57154067	1000	.	.	gene_id "CUFF.103364"; transcript_id "CUFF.103364.1"; FPKM "162.3154457537"; frac "1.000000"; conf_lo "75.554191"; conf_hi "249.076701"; cov "9.219512";
-chr16	Cufflinks	exon	74862302	74862560	1000	.	.	gene_id "CUFF.105450"; transcript_id "CUFF.105450.1"; exon_number "1"; FPKM "11.0120241741"; frac "1.000000"; conf_lo "2.020744"; conf_hi "20.003304"; cov "0.625483";
-chr16	Cufflinks	transcript	98168779	98168914	1000	.	.	gene_id "CUFF.107834"; transcript_id "CUFF.107834.1"; FPKM "24.4666664555"; frac "1.000000"; conf_lo "5.971605"; conf_hi "42.961728"; cov "1.389706";
-chr17	Cufflinks	exon	8483212	8483268	1000	.	.	gene_id "CUFF.108498"; transcript_id "CUFF.108498.1"; exon_number "1"; FPKM "50.0370923000"; frac "1.000000"; conf_lo "9.181978"; conf_hi "90.892207"; cov "2.842105";
-chr17	Cufflinks	exon	30355791	30355913	1000	.	.	gene_id "CUFF.111759"; transcript_id "CUFF.111759.1"; exon_number "1"; FPKM "19.3232673516"; frac "1.000000"; conf_lo "2.040012"; conf_hi "36.606523"; cov "1.097561";
-chr18	Cufflinks	transcript	39571718	39571880	1000	.	.	gene_id "CUFF.123569"; transcript_id "CUFF.123569.1"; FPKM "20.4139057543"; frac "1.000000"; conf_lo "4.982443"; conf_hi "35.845368"; cov "1.159509";
-chr19	Cufflinks	exon	17633088	17633203	1000	.	.	gene_id "CUFF.131333"; transcript_id "CUFF.131333.1"; exon_number "1"; FPKM "20.4893265884"; frac "1.000000"; conf_lo "2.163116"; conf_hi "38.815537"; cov "1.163793";
-chr19	Cufflinks	transcript	41997624	41997859	1000	.	.	gene_id "CUFF.133569"; transcript_id "CUFF.133569.1"; FPKM "28.1988698132"; frac "1.000000"; conf_lo "13.125940"; conf_hi "43.271800"; cov "1.601695";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9.fasta	Wed Mar 09 05:07:21 2016 -0500
@@ -0,0 +1,14 @@
+>test_chromosome
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC
+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC
+AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT
+ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC
+GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
+ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT
+GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
+TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_input1.gff	Wed Mar 09 05:07:21 2016 -0500
@@ -0,0 +1,4 @@
+test_chromosome	Cufflinks	transcript	53	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
+test_chromosome	Cufflinks	exon	53	250	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
+test_chromosome	Cufflinks	exon	351	400	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
+test_chromosome	Cufflinks	exon	501	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
--- a/test-data/tophat_in1.fasta	Wed Jan 20 09:49:37 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
->test_chromosome
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC
-ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC
-AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT
-ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC
-GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
-ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT
-GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
-TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA