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changeset 4:0cf496c45054 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
author iuc
date Fri, 01 Nov 2019 12:54:23 -0400
parents 29769f789b8f
children f312cff50fda
files cuff_macros.xml gffread.xml test-data/Homo_sapiens.GRCh37_19.71.gff3 test-data/ecoli-k12.processed.gff3
diffstat 4 files changed, 217 insertions(+), 241 deletions(-) [+]
line wrap: on
line diff
--- a/cuff_macros.xml	Tue Oct 01 12:19:52 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,85 +0,0 @@
-<macros>
-  <token name="@VERSION@">2.2.1</token>
-
-  <xml name="requirements">
-    <requirements>
-      <requirement type="package" version="2.2.1">cufflinks</requirement>
-      <yield />
-    </requirements>
-  </xml>
-
-  <xml name="condition_inputs">
-    <!-- DEFAULT : use BAM/SAM files -->
-    <conditional name="in_type">
-        <param name="set_in_type" type="select" label="Input data type"
-            help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">
-            <option value="BAM">SAM/BAM</option>
-            <option value="CXB">Cuffquant (CXB)</option>
-            <option value="CONDITION_LIST">List of single replicate conditions</option>
-            <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>
-        </param>
-        <when value="BAM">
-            <repeat name="conditions" title="Condition" min="2">
-                <param name="name" label="Condition name" type="text"/>
-                <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>
-            </repeat>
-        </when>
-        <when value="CXB">
-            <repeat name="conditions" title="Condition" min="2">
-                <param name="name" label="Condition name" type="text"/>
-                <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
-            </repeat>
-        </when>
-        <when value="CONDITION_LIST">
-            <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
-        </when>
-        <when value="CONDITION_REPLICATE_LIST">
-            <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
-        </when>
-    </conditional>
-  </xml>
-  <token name="@CONDITION_SAMPLES@">
-            #if $in_type.set_in_type in ['BAM', 'CXB']
-                #for $condition in $in_type.conditions:
-                    #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] )
-                    '$samples'
-                #end for
-            #elif $in_type.set_in_type == 'CONDITION_LIST'
-                #for $sample in $in_type.conditions:
-                    '$sample'
-                #end for
-            #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
-                #for $condition_list in $in_type.conditions:
-                    #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] )
-                    '$samples'
-                #end for
-            #end if
-  </token>
-  <token name="@CONDITION_LABELS@">
-            #import re
-            #if $in_type.set_in_type in ['BAM', 'CXB']
-                #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\''
-            #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST']
-                #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\''
-            #end if
-            --labels $labels
-  </token>
-  <xml name="cufflinks_gtf_inputs">
-    <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
-    <repeat name="additional_inputs" title="Additional GTF Inputs (type Dataset Collection Lists)">
-      <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" />
-    </repeat>
-  </xml>
-  <token name="@CUFFLINKS_GTF_INPUTS@">
-            ## Inputs.
-            #for $input_file in $inputs:
-                '${input_file}'
-            #end for
-            #for $additional_input in $additional_inputs:
-                #for $input_file in $additional_input.additional_inputs:
-                    '${input_file}'
-                #end for
-            #end for
-  </token>
-  <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
-</macros>
--- a/gffread.xml	Tue Oct 01 12:19:52 2019 -0400
+++ b/gffread.xml	Fri Nov 01 12:54:23 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="gffread" name="gffread" version="@VERSION@.2">
+<tool id="gffread" name="gffread" version="@VERSION@.1">
     <description>Filters and/or converts GFF3/GTF2 records</description>
     <macros>
-        <import>cuff_macros.xml</import>
+        <token name="@VERSION@">0.11.4</token>
         <xml name="fasta_output_select">
             <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs">
                 <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w exons.fa)</option>
@@ -47,7 +47,9 @@
             </param>
         </xml>
     </macros>
-    <expand macro="requirements" />
+    <requirements>
+        <requirement type="package" version="@VERSION@">gffread</requirement>
+    </requirements>
     <command detect_errors="aggressive">
 <![CDATA[
     #if $reference_genome.source == 'history':
@@ -124,7 +126,9 @@
             <option value="-C">coding only: discard mRNAs that have no CDS feature (-C)</option>
             <option value="-G">only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) (-G)</option>
             <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>
-            <option value="--no-pseudo">filter out records matching the 'pseudo' keyword (--no-pseudo)</option>
+            <!-- The no-pseudo option is broken in 0.11.4 of gffread.
+                 See https://github.com/gpertea/gffread/issues/43 -->
+            <!-- <option value="\-\-no-pseudo">filter out records matching the 'pseudo' keyword (\-\-no-pseudo)</option> -->
         </param>
         <conditional name="region">
             <param name="region_filter" type="select" label="Filter by genome region">
@@ -272,10 +276,13 @@
             <param name="full_gff_attribute_preservation" value="-F"/>
             <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" />
         </test>
-
+        
+<!-- The no-pseudo option is broken in 0.11.4 of gffread.
+     See https://github.com/gpertea/gffread/issues/43 -->
+<!-- 
         <test>
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
-            <param name="filtering" value="--no-pseudo"/>
+            <param name="filtering" value="/-/-no-pseudo"/> # Fix dashes when uncommenting
             <param name="gff_fmt" value="gtf"/>
             <output name="output_gtf">
                 <assert_contents>
@@ -283,6 +290,7 @@
                 </assert_contents>
             </output>
         </test>
+-->
 
         <test>
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
@@ -335,25 +343,25 @@
             <param name="gff_fmt" value="gtf"/>
             <output name="output_gtf">
                 <assert_contents>
-                    <not_has_text text="ENST00000587541" />
+                    <has_text text="ENST00000587541" />
                     <has_text text="ENST00000382683" />
                 </assert_contents>
             </output>
             <output name="output_exons">
                 <assert_contents>
-                    <has_text text="ENST00000346144 gene=MADCAM1 CDS=47-932" />
+                    <has_text text="ENST00000346144 CDS=47-934" />
                     <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" />
                 </assert_contents>
             </output>
             <output name="output_cds">
                 <assert_contents>
-                    <has_text text="ENST00000346144 gene=MADCAM1" />
+                    <has_text text="ENST00000346144" />
                     <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" />
                 </assert_contents>
             </output>
             <output name="output_pep">
                 <assert_contents>
-                    <has_text text="ENST00000346144 gene=MADCAM1" />
+                    <has_text text="ENST00000346144" />
                     <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" />
                 </assert_contents>
             </output>
@@ -364,89 +372,140 @@
 <![CDATA[
 **gffread   Filters and/or converts GFF3/GTF2 records**
 
-The gffread command is distributed with the cufflinks_ package.
-
-.. _cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
-
-Usage: ::
+The gffread command is documented with the stringtie_ package.
 
- gffread "input_gff" [-g "genomic_seqs_fasta" | "dir"][-s "seq_info.fsize"]
-   [-o "outfile.gff"] [-t "tname"] [-r [["strand"]"chr":]"start".."end" [-R]]
-   [-CTVNJMKQAFGUBHZWTOLE] [-w "exons.fa"] [-x "cds.fa"] [-y "tr_cds.fa"]
-   [-i "maxintron"]
+.. _stringtie: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
 
-Options: ::
+
+gffread v0.11.4. Usage: ::
 
-  -g  full path to a multi-fasta file with the genomic sequences
-      for all input mappings, OR a directory with single-fasta files
-      (one per genomic sequence, with file names matching sequence names)
-  -s  <seq_info.fsize> is a tab-delimited file providing this info
-      for each of the mapped sequences:
-      <seq-name> <seq-length> <seq-description>
-      (useful for -A option with mRNA/EST/protein mappings)
-  -i  discard transcripts having an intron larger than <maxintron>
-  -r  only show transcripts overlapping coordinate range <start>..<end>
-      (on chromosome/contig <chr>, strand <strand> if provided)
-  -R  for -r option, discard all transcripts that are not fully
-      contained within the given range
-  -U  discard single-exon transcripts
-  -C  coding only: discard mRNAs that have no CDS feature
-  -F  full GFF attribute preservation (all attributes are shown)
-  -G  only parse additional exon attributes from the first exon
-      and move them to the mRNA level (useful for GTF input)
-  -A  use the description field from <seq_info.fsize> and add it
-      as the value for a 'descr' attribute to the GFF record
+    gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] 
+     [-o <outfile>] [-t <trackname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]
+     [-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]
+     [-i <maxintron>] [--bed] [--table <attrlist>] [--sort-by <refseq_list.txt>]
+     
+     Filter, convert or cluster GFF/GTF/BED records, extract the sequence of
+     transcripts (exon or CDS) and more.
+     By default (i.e. without -O) only transcripts are processed, discarding any
+     other non-transcript features. Default output is a simplified GFF3 with only
+     the basic attributes.
+     
+     <input_gff> is a GFF file, use '-' for stdin
+ 
+    Options:
 
-  -O  process also non-transcript GFF records (by default non-transcript
-      records are ignored)
-  -V  discard any mRNAs with CDS having in-frame stop codons
-  -H  for -V option, check and adjust the starting CDS phase
-      if the original phase leads to a translation with an
-      in-frame stop codon
-  -B  for -V option, single-exon transcripts are also checked on the
-      opposite strand
-  -N  discard multi-exon mRNAs that have any intron with a non-canonical
-      splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
-  -J  discard any mRNAs that either lack initial START codon
-      or the terminal STOP codon, or have an in-frame stop codon
-      (only print mRNAs with a fulll, valid CDS)
-  --no-pseudo: filter out records matching the 'pseudo' keyword
-
-  -M/--merge : cluster the input transcripts into loci, collapsing matching
-       transcripts (those with the same exact introns and fully contained)
-  -d <dupinfo> : for -M option, write collapsing info to file <dupinfo>
-  --cluster-only: same as --merge but without collapsing matching transcripts
-  -K  for -M option: also collapse shorter, fully contained transcripts
-      with fewer introns than the container
-  -Q  for -M option, remove the containment restriction:
-      (multi-exon transcripts will be collapsed if just their introns match,
-      while single-exon transcripts can partially overlap (80%))
-
-  --force-exons: make sure that the lowest level GFF features are printed as
-      "exon" features
-  -E  expose (warn about) duplicate transcript IDs and other potential
-      problems with the given GFF/GTF records
-  -D  decode url encoded characters within attributes
-  -Z  merge close exons into a single exon (for intron size<4)
-  -w  write a fasta file with spliced exons for each GFF transcript
-  -x  write a fasta file with spliced CDS for each GFF transcript
-  -W  for -w and -x options, also write for each fasta record the exon
-      coordinates projected onto the spliced sequence
-  -y  write a protein fasta file with the translation of CDS for each record
-  -L  Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
-  -m  <chr_replace> is a reference (genomic) sequence replacement table with
-      this format:
-      <original_ref_ID> <new_ref_ID>
-      For example from UCSC naming to Ensembl naming:
-      chr1	1
-      chr2	2
-      GFF records on reference sequences that are not found among the
-      <original_ref_ID> entries in this file will be filtered out
-  -o  the "filtered" GFF records will be written to <outfile.gff>
-      (use -o- for printing to stdout)
-  -t  use <trackname> in the second column of each GFF output line
-  -T  -o option will output GTF format instead of GFF3
-
+     -i   discard transcripts having an intron larger than <maxintron>
+     -l   discard transcripts shorter than <minlen> bases
+     -r   only show transcripts overlapping coordinate range <start>..<end>
+          (on chromosome/contig <chr>, strand <strand> if provided)
+     -R   for -r option, discard all transcripts that are not fully 
+          contained within the given range
+     -U   discard single-exon transcripts
+     -C   coding only: discard mRNAs that have no CDS features
+     --nc non-coding only: discard mRNAs that have CDS features
+     --ignore-locus : discard locus features and attributes found in the input
+     -A   use the description field from <seq_info.fsize> and add it
+          as the value for a 'descr' attribute to the GFF record
+     -s   <seq_info.fsize> is a tab-delimited file providing this info
+          for each of the mapped sequences:
+          <seq-name> <seq-length> <seq-description>
+          (useful for -A option with mRNA/EST/protein mappings)
+      
+     Sorting: (by default, chromosomes are kept in the order they were found)
+     --sort-alpha : chromosomes (reference sequences) are sorted alphabetically
+     --sort-by : sort the reference sequences by the order in which their
+          names are given in the <refseq.lst> file
+              
+    Misc options: 
+     -F   preserve all GFF attributes (for non-exon features)
+     --keep-exon-attrs : for -F option, do not attempt to reduce redundant
+          exon/CDS attributes
+     -G   do not keep exon attributes, move them to the transcript feature
+          (for GFF3 output)
+     --keep-genes : in transcript-only mode (default), also preserve gene records
+     --keep-comments: for GFF3 input/output, try to preserve comments
+     -O   process other non-transcript GFF records (by default non-transcript
+          records are ignored)
+     -V   discard any mRNAs with CDS having in-frame stop codons (requires -g)
+     -H   for -V option, check and adjust the starting CDS phase
+          if the original phase leads to a translation with an 
+          in-frame stop codon
+     -B   for -V option, single-exon transcripts are also checked on the
+          opposite strand (requires -g)
+     -P   add transcript level GFF attributes about the coding status of each
+          transcript, including partialness or in-frame stop codons (requires -g)
+     --add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
+          that have CDS features
+     --adj-stop stop codon adjustment: enables -P and performs automatic
+          adjustment of the CDS stop coordinate if premature or downstream
+     -N   discard multi-exon mRNAs that have any intron with a non-canonical
+          splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
+     -J   discard any mRNAs that either lack initial START codon
+          or the terminal STOP codon, or have an in-frame stop codon
+          (i.e. only print mRNAs with a complete CDS)
+     --no-pseudo: filter out records matching the 'pseudo' keyword
+     --in-bed: input should be parsed as BED format (automatic if the input
+               filename ends with .bed*)
+     --in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
+               features (see --tlf option below); automatic if the input
+               filename ends with .tlf)
+               
+    Clustering:
+     -M/--merge : cluster the input transcripts into loci, discarding
+          "duplicated" transcripts (those with the same exact introns
+          and fully contained or equal boundaries)
+     -d <dupinfo> : for -M option, write duplication info to file <dupinfo>
+     --cluster-only: same as -M/--merge but without discarding any of the
+          "duplicate" transcripts, only create "locus" features
+     -K   for -M option: also discard as redundant the shorter, fully contained
+           transcripts (intron chains matching a part of the container)
+     -Q   for -M option, no longer require boundary containment when assessing
+          redundancy (can be combined with -K); only introns have to match for
+          multi-exon transcripts, and >=80% overlap for single-exon transcripts
+     -Y   for -M option, enforce -Q but also discard overlapping single-exon 
+          transcripts, even on the opposite strand (can be combined with -K)
+          
+    Output options:
+     --force-exons: make sure that the lowest level GFF features are considered
+           "exon" features
+     --gene2exon: for single-line genes not parenting any transcripts, add an
+           exon feature spanning the entire gene (treat it as a transcript)
+     --t-adopt:  try to find a parent gene overlapping/containing a transcript
+           that does not have any explicit gene Parent
+     -D    decode url encoded characters within attributes
+     -Z    merge very close exons into a single exon (when intron size<4)
+     -g   full path to a multi-fasta file with the genomic sequences
+          for all input mappings, OR a directory with single-fasta files
+          (one per genomic sequence, with file names matching sequence names)
+     -w    write a fasta file with spliced exons for each GFF transcript
+     -x    write a fasta file with spliced CDS for each GFF transcript
+     -y    write a protein fasta file with the translation of CDS for each record
+     -W    for -w and -x options, write in the FASTA defline the exon
+           coordinates projected onto the spliced sequence;
+           for -y option, write transcript attributes in the FASTA defline
+     -S    for -y option, use '*' instead of '.' as stop codon translation
+     -L    Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
+     -m    <chr_replace> is a name mapping table for converting reference 
+           sequence names, having this 2-column format:
+           <original_ref_ID> <new_ref_ID>
+           WARNING: all GFF records on reference sequences whose original IDs
+           are not found in the 1st column of this table will be discarded!
+     -t    use <trackname> in the 2nd column of each GFF/GTF output line
+     -o    write the records into <outfile> instead of stdout
+     -T    main output will be GTF instead of GFF3
+     --bed output records in BED format instead of default GFF3
+     --tlf output "transcript line format" which is like GFF
+           but exons, CDS features and related data are stored as GFF 
+           attributes in the transcript feature line, like this:
+             exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords> 
+           <exons> is a comma-delimited list of exon_start-exon_end coordinates;
+           <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>
+     --table output a simple tab delimited format instead of GFF, with columns
+           having the values of GFF attributes given in <attrlist>; special
+           pseudo-attributes (prefixed by @) are recognized:
+           @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen
+     -v,-E expose (warn about) duplicate transcript IDs and other potential
+           problems with the given GFF/GTF records
 ]]>
     </help>
     <citations>
--- a/test-data/Homo_sapiens.GRCh37_19.71.gff3	Tue Oct 01 12:19:52 2019 -0400
+++ b/test-data/Homo_sapiens.GRCh37_19.71.gff3	Fri Nov 01 12:54:23 2019 -0400
@@ -1,4 +1,5 @@
-# gffread test-data/Homo_sapiens.GRCh37_19.71.gtf -o test-data/Homo_sapiens.GRCh37_19.71.gff3
+# gffread /tmp/tmpq6d_yfqc/files/9/2/2/dataset_922cd54b-d77c-48fb-abf7-6fc8d8fdb97c.dat -o output.gff3
+# gffread v0.11.4
 ##gff-version 3
 19	snRNA	transcript	223158	223261	.	-	.	ID=ENST00000410397;geneID=ENSG00000222329;gene_name=U6
 19	snRNA	exon	223158	223261	.	-	.	Parent=ENST00000410397
@@ -9,55 +10,55 @@
 19	processed_pseudogene	exon	239145	239247	.	-	.	Parent=ENST00000588755
 19	processed_pseudogene	transcript	279495	280170	.	+	.	ID=ENST00000589981;geneID=ENSG00000267447;gene_name=VN2R11P
 19	processed_pseudogene	exon	279495	280170	.	+	.	Parent=ENST00000589981
-19	protein_coding	mRNA	281043	291386	.	-	.	ID=ENST00000269812;geneID=ENSG00000141934;gene_name=PPAP2C
+19	protein_coding	transcript	281043	291386	.	-	.	ID=ENST00000269812;geneID=ENSG00000141934;gene_name=PPAP2C
 19	protein_coding	exon	281043	281537	.	-	.	Parent=ENST00000269812
 19	protein_coding	exon	282134	282310	.	-	.	Parent=ENST00000269812
 19	protein_coding	exon	282752	282809	.	-	.	Parent=ENST00000269812
 19	protein_coding	exon	287474	287751	.	-	.	Parent=ENST00000269812
 19	protein_coding	exon	288020	288171	.	-	.	Parent=ENST00000269812
 19	protein_coding	exon	291285	291386	.	-	.	Parent=ENST00000269812
-19	protein_coding	CDS	281391	281537	.	-	0	Parent=ENST00000269812
+19	protein_coding	CDS	281388	281537	.	-	0	Parent=ENST00000269812
 19	protein_coding	CDS	282134	282310	.	-	0	Parent=ENST00000269812
 19	protein_coding	CDS	282752	282809	.	-	1	Parent=ENST00000269812
 19	protein_coding	CDS	287474	287751	.	-	0	Parent=ENST00000269812
 19	protein_coding	CDS	288020	288171	.	-	2	Parent=ENST00000269812
 19	protein_coding	CDS	291285	291336	.	-	0	Parent=ENST00000269812
-19	protein_coding	mRNA	281345	291393	.	-	.	ID=ENST00000434325;geneID=ENSG00000141934;gene_name=PPAP2C
+19	protein_coding	transcript	281345	291393	.	-	.	ID=ENST00000434325;geneID=ENSG00000141934;gene_name=PPAP2C
 19	protein_coding	exon	281345	281537	.	-	.	Parent=ENST00000434325
 19	protein_coding	exon	282134	282310	.	-	.	Parent=ENST00000434325
 19	protein_coding	exon	282752	282809	.	-	.	Parent=ENST00000434325
 19	protein_coding	exon	287474	287751	.	-	.	Parent=ENST00000434325
 19	protein_coding	exon	288020	288171	.	-	.	Parent=ENST00000434325
 19	protein_coding	exon	291326	291393	.	-	.	Parent=ENST00000434325
-19	protein_coding	CDS	281391	281537	.	-	0	Parent=ENST00000434325
+19	protein_coding	CDS	281388	281537	.	-	0	Parent=ENST00000434325
 19	protein_coding	CDS	282134	282310	.	-	0	Parent=ENST00000434325
 19	protein_coding	CDS	282752	282809	.	-	1	Parent=ENST00000434325
 19	protein_coding	CDS	287474	287751	.	-	0	Parent=ENST00000434325
 19	protein_coding	CDS	288020	288055	.	-	0	Parent=ENST00000434325
-19	protein_coding	mRNA	281388	291200	.	-	.	ID=ENST00000327790;geneID=ENSG00000141934;gene_name=PPAP2C
+19	protein_coding	transcript	281388	291200	.	-	.	ID=ENST00000327790;geneID=ENSG00000141934;gene_name=PPAP2C
 19	protein_coding	exon	281388	281537	.	-	.	Parent=ENST00000327790
 19	protein_coding	exon	282134	282310	.	-	.	Parent=ENST00000327790
 19	protein_coding	exon	282752	282809	.	-	.	Parent=ENST00000327790
 19	protein_coding	exon	287474	287751	.	-	.	Parent=ENST00000327790
 19	protein_coding	exon	288020	288171	.	-	.	Parent=ENST00000327790
 19	protein_coding	exon	290952	291200	.	-	.	Parent=ENST00000327790
-19	protein_coding	CDS	281391	281537	.	-	0	Parent=ENST00000327790
+19	protein_coding	CDS	281388	281537	.	-	0	Parent=ENST00000327790
 19	protein_coding	CDS	282134	282310	.	-	0	Parent=ENST00000327790
 19	protein_coding	CDS	282752	282809	.	-	1	Parent=ENST00000327790
 19	protein_coding	CDS	287474	287751	.	-	0	Parent=ENST00000327790
 19	protein_coding	CDS	288020	288171	.	-	2	Parent=ENST00000327790
 19	protein_coding	CDS	290952	291066	.	-	0	Parent=ENST00000327790
-19	protein_coding	mRNA	281991	287636	.	-	.	ID=ENST00000586998;geneID=ENSG00000141934;gene_name=PPAP2C
+19	protein_coding	transcript	281991	287636	.	-	.	ID=ENST00000586998;geneID=ENSG00000141934;gene_name=PPAP2C
 19	protein_coding	exon	281991	282310	.	-	.	Parent=ENST00000586998
 19	protein_coding	exon	282752	282809	.	-	.	Parent=ENST00000586998
 19	protein_coding	exon	287474	287636	.	-	.	Parent=ENST00000586998
-19	protein_coding	CDS	282125	282310	.	-	0	Parent=ENST00000586998
+19	protein_coding	CDS	282122	282310	.	-	0	Parent=ENST00000586998
 19	protein_coding	CDS	282752	282809	.	-	1	Parent=ENST00000586998
 19	protein_coding	CDS	287474	287636	.	-	2	Parent=ENST00000586998
 19	retained_intron	transcript	287161	288530	.	-	.	ID=ENST00000589672;geneID=ENSG00000141934;gene_name=PPAP2C
 19	retained_intron	exon	287161	287751	.	-	.	Parent=ENST00000589672
 19	retained_intron	exon	288020	288530	.	-	.	Parent=ENST00000589672
-19	protein_coding	mRNA	287474	291382	.	-	.	ID=ENST00000591572;geneID=ENSG00000141934;gene_name=PPAP2C
+19	protein_coding	transcript	287474	291382	.	-	.	ID=ENST00000591572;geneID=ENSG00000141934;gene_name=PPAP2C
 19	protein_coding	exon	287474	287751	.	-	.	Parent=ENST00000591572
 19	protein_coding	exon	288020	288189	.	-	.	Parent=ENST00000591572
 19	protein_coding	exon	291285	291382	.	-	.	Parent=ENST00000591572
@@ -67,7 +68,7 @@
 19	antisense	transcript	305573	306467	.	+	.	ID=ENST00000591533;geneID=ENSG00000267124;gene_name=CTD-3113P16.5
 19	antisense	exon	305573	305703	.	+	.	Parent=ENST00000591533
 19	antisense	exon	306057	306467	.	+	.	Parent=ENST00000591533
-19	protein_coding	mRNA	305575	344793	.	-	.	ID=ENST00000264819;geneID=ENSG00000105556;gene_name=MIER2
+19	protein_coding	transcript	305575	344793	.	-	.	ID=ENST00000264819;geneID=ENSG00000105556;gene_name=MIER2
 19	protein_coding	exon	305575	306711	.	-	.	Parent=ENST00000264819
 19	protein_coding	exon	307119	307536	.	-	.	Parent=ENST00000264819
 19	protein_coding	exon	308577	308665	.	-	.	Parent=ENST00000264819
@@ -82,7 +83,7 @@
 19	protein_coding	exon	334400	334542	.	-	.	Parent=ENST00000264819
 19	protein_coding	exon	336083	336173	.	-	.	Parent=ENST00000264819
 19	protein_coding	exon	344774	344793	.	-	.	Parent=ENST00000264819
-19	protein_coding	CDS	306693	306711	.	-	1	Parent=ENST00000264819
+19	protein_coding	CDS	306690	306711	.	-	1	Parent=ENST00000264819
 19	protein_coding	CDS	307119	307536	.	-	2	Parent=ENST00000264819
 19	protein_coding	CDS	308577	308665	.	-	1	Parent=ENST00000264819
 19	protein_coding	CDS	308801	308925	.	-	0	Parent=ENST00000264819
@@ -113,7 +114,7 @@
 19	retained_intron	transcript	334115	344798	.	-	.	ID=ENST00000587966;geneID=ENSG00000105556;gene_name=MIER2
 19	retained_intron	exon	334115	334542	.	-	.	Parent=ENST00000587966
 19	retained_intron	exon	344774	344798	.	-	.	Parent=ENST00000587966
-19	protein_coding	mRNA	361750	376013	.	-	.	ID=ENST00000342640;geneID=ENSG00000105549;gene_name=THEG
+19	protein_coding	transcript	361750	376013	.	-	.	ID=ENST00000342640;geneID=ENSG00000105549;gene_name=THEG
 19	protein_coding	exon	361750	362426	.	-	.	Parent=ENST00000342640
 19	protein_coding	exon	367065	367224	.	-	.	Parent=ENST00000342640
 19	protein_coding	exon	371205	371322	.	-	.	Parent=ENST00000342640
@@ -122,7 +123,7 @@
 19	protein_coding	exon	373940	374011	.	-	.	Parent=ENST00000342640
 19	protein_coding	exon	374299	374421	.	-	.	Parent=ENST00000342640
 19	protein_coding	exon	375663	376013	.	-	.	Parent=ENST00000342640
-19	protein_coding	CDS	362203	362426	.	-	2	Parent=ENST00000342640
+19	protein_coding	CDS	362200	362426	.	-	2	Parent=ENST00000342640
 19	protein_coding	CDS	367065	367224	.	-	0	Parent=ENST00000342640
 19	protein_coding	CDS	371205	371322	.	-	1	Parent=ENST00000342640
 19	protein_coding	CDS	372631	372700	.	-	2	Parent=ENST00000342640
@@ -134,7 +135,7 @@
 19	retained_intron	exon	362058	362426	.	-	.	Parent=ENST00000530711
 19	retained_intron	exon	367065	367224	.	-	.	Parent=ENST00000530711
 19	retained_intron	exon	374299	374620	.	-	.	Parent=ENST00000530711
-19	protein_coding	mRNA	362200	375970	.	-	.	ID=ENST00000346878;geneID=ENSG00000105549;gene_name=THEG
+19	protein_coding	transcript	362200	375970	.	-	.	ID=ENST00000346878;geneID=ENSG00000105549;gene_name=THEG
 19	protein_coding	exon	362200	362426	.	-	.	Parent=ENST00000346878
 19	protein_coding	exon	367065	367224	.	-	.	Parent=ENST00000346878
 19	protein_coding	exon	371205	371322	.	-	.	Parent=ENST00000346878
@@ -142,7 +143,7 @@
 19	protein_coding	exon	373470	373531	.	-	.	Parent=ENST00000346878
 19	protein_coding	exon	374299	374421	.	-	.	Parent=ENST00000346878
 19	protein_coding	exon	375663	375970	.	-	.	Parent=ENST00000346878
-19	protein_coding	CDS	362203	362426	.	-	2	Parent=ENST00000346878
+19	protein_coding	CDS	362200	362426	.	-	2	Parent=ENST00000346878
 19	protein_coding	CDS	367065	367224	.	-	0	Parent=ENST00000346878
 19	protein_coding	CDS	371205	371322	.	-	1	Parent=ENST00000346878
 19	protein_coding	CDS	372631	372700	.	-	2	Parent=ENST00000346878
@@ -158,10 +159,10 @@
 19	processed_transcript	transcript	397589	398941	.	+	.	ID=ENST00000591757;geneID=ENSG00000267443;gene_name=AC010641.1
 19	processed_transcript	exon	397589	397633	.	+	.	Parent=ENST00000591757
 19	processed_transcript	exon	398690	398941	.	+	.	Parent=ENST00000591757
-19	protein_coding	mRNA	405445	409139	.	-	.	ID=ENST00000332235;geneID=ENSG00000183186;gene_name=C2CD4C
+19	protein_coding	transcript	405445	409139	.	-	.	ID=ENST00000332235;geneID=ENSG00000183186;gene_name=C2CD4C
 19	protein_coding	exon	405445	408401	.	-	.	Parent=ENST00000332235
 19	protein_coding	exon	409006	409139	.	-	.	Parent=ENST00000332235
-19	protein_coding	CDS	407099	408361	.	-	0	Parent=ENST00000332235
+19	protein_coding	CDS	407096	408361	.	-	0	Parent=ENST00000332235
 19	retained_intron	transcript	416583	419879	.	-	.	ID=ENST00000587423;geneID=ENSG00000129946;gene_name=SHC2
 19	retained_intron	exon	416583	417322	.	-	.	Parent=ENST00000587423
 19	retained_intron	exon	418923	419879	.	-	.	Parent=ENST00000587423
@@ -169,7 +170,7 @@
 19	retained_intron	exon	416583	417322	.	-	.	Parent=ENST00000588376
 19	retained_intron	exon	418923	419056	.	-	.	Parent=ENST00000588376
 19	retained_intron	exon	422146	422828	.	-	.	Parent=ENST00000588376
-19	protein_coding	mRNA	416593	460996	.	-	.	ID=ENST00000264554;geneID=ENSG00000129946;gene_name=SHC2
+19	protein_coding	transcript	416593	460996	.	-	.	ID=ENST00000264554;geneID=ENSG00000129946;gene_name=SHC2
 19	protein_coding	exon	416593	417322	.	-	.	Parent=ENST00000264554
 19	protein_coding	exon	418923	419056	.	-	.	Parent=ENST00000264554
 19	protein_coding	exon	422146	422456	.	-	.	Parent=ENST00000264554
@@ -183,7 +184,7 @@
 19	protein_coding	exon	438970	439030	.	-	.	Parent=ENST00000264554
 19	protein_coding	exon	440862	440932	.	-	.	Parent=ENST00000264554
 19	protein_coding	exon	460529	460996	.	-	.	Parent=ENST00000264554
-19	protein_coding	CDS	418931	419056	.	-	0	Parent=ENST00000264554
+19	protein_coding	CDS	418928	419056	.	-	0	Parent=ENST00000264554
 19	protein_coding	CDS	422146	422456	.	-	2	Parent=ENST00000264554
 19	protein_coding	CDS	425097	425231	.	-	2	Parent=ENST00000264554
 19	protein_coding	CDS	430684	430747	.	-	0	Parent=ENST00000264554
@@ -207,14 +208,14 @@
 19	retained_intron	exon	438718	438837	.	-	.	Parent=ENST00000589922
 19	retained_intron	exon	438970	439030	.	-	.	Parent=ENST00000589922
 19	retained_intron	exon	440862	441384	.	-	.	Parent=ENST00000589922
-19	nonsense_mediated_decay	mRNA	417200	436258	.	-	.	ID=ENST00000590170;geneID=ENSG00000129946;gene_name=SHC2
+19	nonsense_mediated_decay	transcript	417200	436258	.	-	.	ID=ENST00000590170;geneID=ENSG00000129946;gene_name=SHC2
 19	nonsense_mediated_decay	exon	417200	417322	.	-	.	Parent=ENST00000590170
 19	nonsense_mediated_decay	exon	418923	419056	.	-	.	Parent=ENST00000590170
 19	nonsense_mediated_decay	exon	422146	422379	.	-	.	Parent=ENST00000590170
 19	nonsense_mediated_decay	exon	430684	430747	.	-	.	Parent=ENST00000590170
 19	nonsense_mediated_decay	exon	434709	434865	.	-	.	Parent=ENST00000590170
 19	nonsense_mediated_decay	exon	436165	436258	.	-	.	Parent=ENST00000590170
-19	nonsense_mediated_decay	CDS	434765	434865	.	-	2	Parent=ENST00000590170
+19	nonsense_mediated_decay	CDS	434762	434865	.	-	2	Parent=ENST00000590170
 19	nonsense_mediated_decay	CDS	436165	436258	.	-	0	Parent=ENST00000590170
 19	processed_transcript	transcript	417200	436258	.	-	.	ID=ENST00000591948;geneID=ENSG00000129946;gene_name=SHC2
 19	processed_transcript	exon	417200	417322	.	-	.	Parent=ENST00000591948
@@ -223,7 +224,7 @@
 19	processed_transcript	exon	430684	430747	.	-	.	Parent=ENST00000591948
 19	processed_transcript	exon	434709	434865	.	-	.	Parent=ENST00000591948
 19	processed_transcript	exon	436165	436258	.	-	.	Parent=ENST00000591948
-19	nonsense_mediated_decay	mRNA	434702	460571	.	-	.	ID=ENST00000590222;geneID=ENSG00000129946;gene_name=SHC2
+19	nonsense_mediated_decay	transcript	434702	460571	.	-	.	ID=ENST00000590222;geneID=ENSG00000129946;gene_name=SHC2
 19	nonsense_mediated_decay	exon	434702	434865	.	-	.	Parent=ENST00000590222
 19	nonsense_mediated_decay	exon	436165	436291	.	-	.	Parent=ENST00000590222
 19	nonsense_mediated_decay	exon	436380	436431	.	-	.	Parent=ENST00000590222
@@ -233,7 +234,7 @@
 19	nonsense_mediated_decay	exon	439233	439491	.	-	.	Parent=ENST00000590222
 19	nonsense_mediated_decay	exon	440862	440932	.	-	.	Parent=ENST00000590222
 19	nonsense_mediated_decay	exon	460529	460571	.	-	.	Parent=ENST00000590222
-19	nonsense_mediated_decay	CDS	439401	439491	.	-	1	Parent=ENST00000590222
+19	nonsense_mediated_decay	CDS	439398	439491	.	-	1	Parent=ENST00000590222
 19	nonsense_mediated_decay	CDS	440862	440932	.	-	0	Parent=ENST00000590222
 19	nonsense_mediated_decay	CDS	460529	460571	.	-	1	Parent=ENST00000590222
 19	retained_intron	transcript	435771	436534	.	-	.	ID=ENST00000591388;geneID=ENSG00000129946;gene_name=SHC2
@@ -249,20 +250,20 @@
 19	processed_transcript	exon	438970	439031	.	-	.	Parent=ENST00000590113
 19	rRNA	transcript	453134	453245	.	+	.	ID=ENST00000516730;geneID=ENSG00000252539;gene_name=RNA5SP462
 19	rRNA	exon	453134	453245	.	+	.	Parent=ENST00000516730
-19	protein_coding	mRNA	463346	474983	.	-	.	ID=ENST00000315489;geneID=ENSG00000181781;gene_name=ODF3L2
+19	protein_coding	transcript	463346	474983	.	-	.	ID=ENST00000315489;geneID=ENSG00000181781;gene_name=ODF3L2
 19	protein_coding	exon	463346	464364	.	-	.	Parent=ENST00000315489
 19	protein_coding	exon	467649	467762	.	-	.	Parent=ENST00000315489
 19	protein_coding	exon	472394	472501	.	-	.	Parent=ENST00000315489
 19	protein_coding	exon	474621	474983	.	-	.	Parent=ENST00000315489
-19	protein_coding	CDS	463847	464364	.	-	2	Parent=ENST00000315489
+19	protein_coding	CDS	463844	464364	.	-	2	Parent=ENST00000315489
 19	protein_coding	CDS	467649	467762	.	-	2	Parent=ENST00000315489
 19	protein_coding	CDS	472394	472501	.	-	2	Parent=ENST00000315489
 19	protein_coding	CDS	474621	474747	.	-	0	Parent=ENST00000315489
-19	protein_coding	mRNA	463467	474880	.	-	.	ID=ENST00000382696;geneID=ENSG00000181781;gene_name=ODF3L2
+19	protein_coding	transcript	463467	474880	.	-	.	ID=ENST00000382696;geneID=ENSG00000181781;gene_name=ODF3L2
 19	protein_coding	exon	463467	464364	.	-	.	Parent=ENST00000382696
 19	protein_coding	exon	467649	467762	.	-	.	Parent=ENST00000382696
 19	protein_coding	exon	474621	474880	.	-	.	Parent=ENST00000382696
-19	protein_coding	CDS	463847	464364	.	-	2	Parent=ENST00000382696
+19	protein_coding	CDS	463844	464364	.	-	2	Parent=ENST00000382696
 19	protein_coding	CDS	467649	467762	.	-	2	Parent=ENST00000382696
 19	protein_coding	CDS	474621	474747	.	-	0	Parent=ENST00000382696
 19	retained_intron	transcript	464146	472631	.	-	.	ID=ENST00000591681;geneID=ENSG00000181781;gene_name=ODF3L2
@@ -277,7 +278,7 @@
 19	antisense	exon	490046	490353	.	-	.	Parent=ENST00000592413
 19	antisense	exon	501541	501624	.	-	.	Parent=ENST00000592413
 19	antisense	exon	507376	507813	.	-	.	Parent=ENST00000592413
-19	protein_coding	mRNA	496454	505207	.	+	.	ID=ENST00000346144;geneID=ENSG00000099866;gene_name=MADCAM1
+19	protein_coding	transcript	496454	505207	.	+	.	ID=ENST00000346144;geneID=ENSG00000099866;gene_name=MADCAM1
 19	protein_coding	exon	496454	496551	.	+	.	Parent=ENST00000346144
 19	protein_coding	exon	497833	498117	.	+	.	Parent=ENST00000346144
 19	protein_coding	exon	498496	498825	.	+	.	Parent=ENST00000346144
@@ -285,8 +286,8 @@
 19	protein_coding	CDS	496500	496551	.	+	0	Parent=ENST00000346144
 19	protein_coding	CDS	497833	498117	.	+	2	Parent=ENST00000346144
 19	protein_coding	CDS	498496	498825	.	+	2	Parent=ENST00000346144
-19	protein_coding	CDS	504745	504963	.	+	2	Parent=ENST00000346144
-19	protein_coding	mRNA	496454	505347	.	+	.	ID=ENST00000215637;geneID=ENSG00000099866;gene_name=MADCAM1
+19	protein_coding	CDS	504745	504965	.	+	2	Parent=ENST00000346144
+19	protein_coding	transcript	496454	505347	.	+	.	ID=ENST00000215637;geneID=ENSG00000099866;gene_name=MADCAM1
 19	protein_coding	exon	496454	496551	.	+	.	Parent=ENST00000215637
 19	protein_coding	exon	497833	498117	.	+	.	Parent=ENST00000215637
 19	protein_coding	exon	498496	498825	.	+	.	Parent=ENST00000215637
@@ -296,18 +297,18 @@
 19	protein_coding	CDS	497833	498117	.	+	2	Parent=ENST00000215637
 19	protein_coding	CDS	498496	498825	.	+	2	Parent=ENST00000215637
 19	protein_coding	CDS	501669	501929	.	+	2	Parent=ENST00000215637
-19	protein_coding	CDS	504745	504963	.	+	2	Parent=ENST00000215637
-19	protein_coding	mRNA	496500	504965	.	+	.	ID=ENST00000382683;geneID=ENSG00000099866;gene_name=MADCAM1
+19	protein_coding	CDS	504745	504965	.	+	2	Parent=ENST00000215637
+19	protein_coding	transcript	496500	504965	.	+	.	ID=ENST00000382683;geneID=ENSG00000099866;gene_name=MADCAM1
 19	protein_coding	exon	496500	496551	.	+	.	Parent=ENST00000382683
 19	protein_coding	exon	498496	498825	.	+	.	Parent=ENST00000382683
 19	protein_coding	exon	504745	504965	.	+	.	Parent=ENST00000382683
 19	protein_coding	CDS	496500	496551	.	+	0	Parent=ENST00000382683
 19	protein_coding	CDS	498496	498825	.	+	2	Parent=ENST00000382683
-19	protein_coding	CDS	504745	504963	.	+	2	Parent=ENST00000382683
-19	protein_coding	mRNA	507299	519654	.	+	.	ID=ENST00000359315;geneID=ENSG00000141933;gene_name=TPGS1
+19	protein_coding	CDS	504745	504965	.	+	2	Parent=ENST00000382683
+19	protein_coding	transcript	507299	519654	.	+	.	ID=ENST00000359315;geneID=ENSG00000141933;gene_name=TPGS1
 19	protein_coding	exon	507299	507844	.	+	.	Parent=ENST00000359315
 19	protein_coding	exon	518889	519654	.	+	.	Parent=ENST00000359315
 19	protein_coding	CDS	507507	507844	.	+	0	Parent=ENST00000359315
-19	protein_coding	CDS	518889	519421	.	+	1	Parent=ENST00000359315
+19	protein_coding	CDS	518889	519423	.	+	1	Parent=ENST00000359315
 19	retained_intron	transcript	507500	510372	.	+	.	ID=ENST00000588278;geneID=ENSG00000141933;gene_name=TPGS1
 19	retained_intron	exon	507500	510372	.	+	.	Parent=ENST00000588278
--- a/test-data/ecoli-k12.processed.gff3	Tue Oct 01 12:19:52 2019 -0400
+++ b/test-data/ecoli-k12.processed.gff3	Fri Nov 01 12:54:23 2019 -0400
@@ -1,32 +1,33 @@
-# gffread /home/hxr/arbeit/galaxy/database/files/000/dataset_791.dat -F -D -E -o output.gff3
+# gffread /tmp/tmpq6d_yfqc/files/2/7/7/dataset_277f6e18-b25a-4b59-b712-49b5c202a183.dat -F -o output.gff3
+# gffread v0.11.4
 ##gff-version 3
-NC_000913.3	RefSeq	gene	190	255	.	+	.	ID=gene-b0001;geneID=gene-b0001;gene_name=thrL;Dbxref=ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0001;locus_tag=b0001;protein_id=NP_414542.1
-NC_000913.3	RefSeq	CDS	190	255	.	+	0	Parent=gene-b0001;Dbxref=UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;gbkey=CDS;locus_tag=b0001;orig_transcript_id=gnl|b0001|mrna.b0001;product=thr operon leader peptide;transl_table=11
-NC_000913.3	RefSeq	gene	337	2799	.	+	.	ID=gene-b0002;geneID=gene-b0002;gene_name=thrA;Dbxref=ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,thrA1,thrA2,thrD;locus_tag=b0002;protein_id=NP_414543.1
-NC_000913.3	RefSeq	CDS	337	2799	.	+	0	Parent=gene-b0002;Dbxref=UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;gbkey=CDS;locus_tag=b0002;orig_transcript_id=gnl|b0002|mrna.b0002;product=fused aspartate kinase/homoserine dehydrogenase 1;transl_table=11
-NC_000913.3	RefSeq	gene	2801	3733	.	+	.	ID=gene-b0003;geneID=gene-b0003;gene_name=thrB;Dbxref=ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0003;locus_tag=b0003;protein_id=NP_414544.1
-NC_000913.3	RefSeq	CDS	2801	3733	.	+	0	Parent=gene-b0003;Dbxref=UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;gbkey=CDS;locus_tag=b0003;orig_transcript_id=gnl|b0003|mrna.b0003;product=homoserine kinase;transl_table=11
-NC_000913.3	RefSeq	gene	3734	5020	.	+	.	ID=gene-b0004;geneID=gene-b0004;gene_name=thrC;Dbxref=ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0004;locus_tag=b0004;protein_id=NP_414545.1
-NC_000913.3	RefSeq	CDS	3734	5020	.	+	0	Parent=gene-b0004;Dbxref=UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;gbkey=CDS;locus_tag=b0004;orig_transcript_id=gnl|b0004|mrna.b0004;product=threonine synthase;transl_table=11
-NC_000913.3	RefSeq	gene	5234	5530	.	+	.	ID=gene-b0005;geneID=gene-b0005;gene_name=yaaX;Dbxref=ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0005;locus_tag=b0005;protein_id=NP_414546.1
-NC_000913.3	RefSeq	CDS	5234	5530	.	+	0	Parent=gene-b0005;Dbxref=UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;locus_tag=b0005;orig_transcript_id=gnl|b0005|mrna.b0005;product=DUF2502 domain-containing protein YaaX;transl_table=11
-NC_000913.3	RefSeq	gene	5683	6459	.	-	.	ID=gene-b0006;geneID=gene-b0006;gene_name=yaaA;Dbxref=ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0006;locus_tag=b0006;protein_id=NP_414547.1
-NC_000913.3	RefSeq	CDS	5683	6459	.	-	0	Parent=gene-b0006;Dbxref=UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;locus_tag=b0006;orig_transcript_id=gnl|b0006|mrna.b0006;product=peroxide stress resistance protein YaaA;transl_table=11
-NC_000913.3	RefSeq	gene	6529	7959	.	-	.	ID=gene-b0007;geneID=gene-b0007;gene_name=yaaJ;Dbxref=ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=yaaJ;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0007;locus_tag=b0007;protein_id=NP_414548.1
-NC_000913.3	RefSeq	CDS	6529	7959	.	-	0	Parent=gene-b0007;Dbxref=UniProtKB/Swiss-Prot:P30143,Genbank:NP_414548.1,ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=NP_414548.1;gbkey=CDS;locus_tag=b0007;orig_transcript_id=gnl|b0007|mrna.b0007;product=putative transporter YaaJ;transl_table=11
-NC_000913.3	RefSeq	gene	8238	9191	.	+	.	ID=gene-b0008;geneID=gene-b0008;gene_name=talB;Dbxref=ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=talB;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0008,yaaK;locus_tag=b0008;protein_id=NP_414549.1
-NC_000913.3	RefSeq	CDS	8238	9191	.	+	0	Parent=gene-b0008;Dbxref=UniProtKB/Swiss-Prot:P0A870,Genbank:NP_414549.1,ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=NP_414549.1;gbkey=CDS;locus_tag=b0008;orig_transcript_id=gnl|b0008|mrna.b0008;product=transaldolase B;transl_table=11
-NC_000913.3	RefSeq	gene	9306	9893	.	+	.	ID=gene-b0009;geneID=gene-b0009;gene_name=mog;Dbxref=ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=mog;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=bisD,chlG,ECK0009,mogA,yaaG;locus_tag=b0009;protein_id=NP_414550.1
-NC_000913.3	RefSeq	CDS	9306	9893	.	+	0	Parent=gene-b0009;Dbxref=UniProtKB/Swiss-Prot:P0AF03,Genbank:NP_414550.1,ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=NP_414550.1;gbkey=CDS;locus_tag=b0009;orig_transcript_id=gnl|b0009|mrna.b0009;product=molybdopterin adenylyltransferase;transl_table=11
-NC_000913.3	RefSeq	gene	9928	10494	.	-	.	ID=gene-b0010;geneID=gene-b0010;gene_name=satP;Dbxref=ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=satP;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0010,yaaH;locus_tag=b0010;protein_id=NP_414551.1
-NC_000913.3	RefSeq	CDS	9928	10494	.	-	0	Parent=gene-b0010;Dbxref=UniProtKB/Swiss-Prot:P0AC98,Genbank:NP_414551.1,ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=NP_414551.1;gbkey=CDS;locus_tag=b0010;orig_transcript_id=gnl|b0010|mrna.b0010;product=acetate/succinate:H(+) symporter;transl_table=11
-NC_000913.3	RefSeq	gene	10643	11356	.	-	.	ID=gene-b0011;geneID=gene-b0011;gene_name=yaaW;Dbxref=ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=yaaW;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0011;locus_tag=b0011;protein_id=NP_414552.1
-NC_000913.3	RefSeq	CDS	10643	11356	.	-	0	Parent=gene-b0011;Dbxref=UniProtKB/Swiss-Prot:P75617,Genbank:NP_414552.1,ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=NP_414552.1;gbkey=CDS;locus_tag=b0011;orig_transcript_id=gnl|b0011|mrna.b0011;product=putative enzyme-specific chaperone YaaW;transl_table=11
-NC_000913.3	RefSeq	gene	10830	11315	.	+	.	ID=gene-b0012;geneID=gene-b0012;gene_name=mbiA;Dbxref=ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=mbiA;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0012,htgA,htpY;locus_tag=b0012;protein_id=YP_009518733.1
-NC_000913.3	RefSeq	CDS	10830	11315	.	+	0	Parent=gene-b0012;Dbxref=UniProtKB/Swiss-Prot:P28697,Genbank:YP_009518733.1,ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=YP_009518733.1;gbkey=CDS;locus_tag=b0012;orig_transcript_id=gnl|b0012|mrna.CDS13;product=uncharacterized protein MbiA;transl_table=11
-NC_000913.3	RefSeq	gene	11382	11786	.	-	.	ID=gene-b0013;geneID=gene-b0013;gene_name=yaaI;Dbxref=ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=yaaI;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0013;locus_tag=b0013;protein_id=NP_414554.1
-NC_000913.3	RefSeq	CDS	11382	11786	.	-	0	Parent=gene-b0013;Dbxref=UniProtKB/Swiss-Prot:P28696,Genbank:NP_414554.1,ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=NP_414554.1;gbkey=CDS;locus_tag=b0013;orig_transcript_id=gnl|b0013|mrna.b0013;product=DUF2541 domain-containing protein YaaI;transl_table=11
-NC_000913.3	RefSeq	gene	12163	14079	.	+	.	ID=gene-b0014;geneID=gene-b0014;gene_name=dnaK;Dbxref=ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=dnaK;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0014,groPAB,groPC,groPF,grpC,grpF,seg;locus_tag=b0014;protein_id=NP_414555.1
-NC_000913.3	RefSeq	CDS	12163	14079	.	+	0	Parent=gene-b0014;Dbxref=UniProtKB/Swiss-Prot:P0A6Y8,Genbank:NP_414555.1,ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=NP_414555.1;gbkey=CDS;locus_tag=b0014;orig_transcript_id=gnl|b0014|mrna.b0014;product=chaperone protein DnaK;transl_table=11
-NC_000913.3	RefSeq	gene	14168	15298	.	+	.	ID=gene-b0015;geneID=gene-b0015;gene_name=dnaJ;Dbxref=ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=dnaJ;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0015,groP,grpC;locus_tag=b0015;protein_id=NP_414556.1
-NC_000913.3	RefSeq	CDS	14168	15298	.	+	0	Parent=gene-b0015;Dbxref=UniProtKB/Swiss-Prot:P08622,Genbank:NP_414556.1,ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=NP_414556.1;gbkey=CDS;locus_tag=b0015;orig_transcript_id=gnl|b0015|mrna.b0015;product=chaperone protein DnaJ;transl_table=11
+NC_000913.3	RefSeq	gene	190	255	.	+	.	ID=gene-b0001;geneID=gene-b0001;gene_name=thrL;Dbxref=ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene=thrL;gene_biotype=protein_coding;gene_synonym=ECK0001;locus_tag=b0001
+NC_000913.3	RefSeq	CDS	190	255	.	+	0	Parent=gene-b0001;Dbxref=UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;gbkey=CDS;gene=thrL;locus_tag=b0001;orig_transcript_id=gnl|b0001|mrna.b0001;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11
+NC_000913.3	RefSeq	gene	337	2799	.	+	.	ID=gene-b0002;geneID=gene-b0002;gene_name=thrA;Dbxref=ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene=thrA;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,thrA1,thrA2,thrD;locus_tag=b0002
+NC_000913.3	RefSeq	CDS	337	2799	.	+	0	Parent=gene-b0002;Dbxref=UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;gbkey=CDS;gene=thrA;locus_tag=b0002;orig_transcript_id=gnl|b0002|mrna.b0002;product=fused aspartate kinase/homoserine dehydrogenase 1;protein_id=NP_414543.1;transl_table=11
+NC_000913.3	RefSeq	gene	2801	3733	.	+	.	ID=gene-b0003;geneID=gene-b0003;gene_name=thrB;Dbxref=ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene=thrB;gene_biotype=protein_coding;gene_synonym=ECK0003;locus_tag=b0003
+NC_000913.3	RefSeq	CDS	2801	3733	.	+	0	Parent=gene-b0003;Dbxref=UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;gbkey=CDS;gene=thrB;locus_tag=b0003;orig_transcript_id=gnl|b0003|mrna.b0003;product=homoserine kinase;protein_id=NP_414544.1;transl_table=11
+NC_000913.3	RefSeq	gene	3734	5020	.	+	.	ID=gene-b0004;geneID=gene-b0004;gene_name=thrC;Dbxref=ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene=thrC;gene_biotype=protein_coding;gene_synonym=ECK0004;locus_tag=b0004
+NC_000913.3	RefSeq	CDS	3734	5020	.	+	0	Parent=gene-b0004;Dbxref=UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;gbkey=CDS;gene=thrC;locus_tag=b0004;orig_transcript_id=gnl|b0004|mrna.b0004;product=threonine synthase;protein_id=NP_414545.1;transl_table=11
+NC_000913.3	RefSeq	gene	5234	5530	.	+	.	ID=gene-b0005;geneID=gene-b0005;gene_name=yaaX;Dbxref=ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene=yaaX;gene_biotype=protein_coding;gene_synonym=ECK0005;locus_tag=b0005
+NC_000913.3	RefSeq	CDS	5234	5530	.	+	0	Parent=gene-b0005;Dbxref=UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;gene=yaaX;locus_tag=b0005;orig_transcript_id=gnl|b0005|mrna.b0005;product=DUF2502 domain-containing protein YaaX;protein_id=NP_414546.1;transl_table=11
+NC_000913.3	RefSeq	gene	5683	6459	.	-	.	ID=gene-b0006;geneID=gene-b0006;gene_name=yaaA;Dbxref=ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene=yaaA;gene_biotype=protein_coding;gene_synonym=ECK0006;locus_tag=b0006
+NC_000913.3	RefSeq	CDS	5683	6459	.	-	0	Parent=gene-b0006;Dbxref=UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;gene=yaaA;locus_tag=b0006;orig_transcript_id=gnl|b0006|mrna.b0006;product=peroxide stress resistance protein YaaA;protein_id=NP_414547.1;transl_table=11
+NC_000913.3	RefSeq	gene	6529	7959	.	-	.	ID=gene-b0007;geneID=gene-b0007;gene_name=yaaJ;Dbxref=ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=yaaJ;gbkey=Gene;gene=yaaJ;gene_biotype=protein_coding;gene_synonym=ECK0007;locus_tag=b0007
+NC_000913.3	RefSeq	CDS	6529	7959	.	-	0	Parent=gene-b0007;Dbxref=UniProtKB/Swiss-Prot:P30143,Genbank:NP_414548.1,ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=NP_414548.1;gbkey=CDS;gene=yaaJ;locus_tag=b0007;orig_transcript_id=gnl|b0007|mrna.b0007;product=putative transporter YaaJ;protein_id=NP_414548.1;transl_table=11
+NC_000913.3	RefSeq	gene	8238	9191	.	+	.	ID=gene-b0008;geneID=gene-b0008;gene_name=talB;Dbxref=ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=talB;gbkey=Gene;gene=talB;gene_biotype=protein_coding;gene_synonym=ECK0008,yaaK;locus_tag=b0008
+NC_000913.3	RefSeq	CDS	8238	9191	.	+	0	Parent=gene-b0008;Dbxref=UniProtKB/Swiss-Prot:P0A870,Genbank:NP_414549.1,ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=NP_414549.1;gbkey=CDS;gene=talB;locus_tag=b0008;orig_transcript_id=gnl|b0008|mrna.b0008;product=transaldolase B;protein_id=NP_414549.1;transl_table=11
+NC_000913.3	RefSeq	gene	9306	9893	.	+	.	ID=gene-b0009;geneID=gene-b0009;gene_name=mog;Dbxref=ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=mog;gbkey=Gene;gene=mog;gene_biotype=protein_coding;gene_synonym=bisD,chlG,ECK0009,mogA,yaaG;locus_tag=b0009
+NC_000913.3	RefSeq	CDS	9306	9893	.	+	0	Parent=gene-b0009;Dbxref=UniProtKB/Swiss-Prot:P0AF03,Genbank:NP_414550.1,ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=NP_414550.1;gbkey=CDS;gene=mog;locus_tag=b0009;orig_transcript_id=gnl|b0009|mrna.b0009;product=molybdopterin adenylyltransferase;protein_id=NP_414550.1;transl_table=11
+NC_000913.3	RefSeq	gene	9928	10494	.	-	.	ID=gene-b0010;geneID=gene-b0010;gene_name=satP;Dbxref=ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=satP;gbkey=Gene;gene=satP;gene_biotype=protein_coding;gene_synonym=ECK0010,yaaH;locus_tag=b0010
+NC_000913.3	RefSeq	CDS	9928	10494	.	-	0	Parent=gene-b0010;Dbxref=UniProtKB/Swiss-Prot:P0AC98,Genbank:NP_414551.1,ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=NP_414551.1;gbkey=CDS;gene=satP;locus_tag=b0010;orig_transcript_id=gnl|b0010|mrna.b0010;product=acetate/succinate:H(+) symporter;protein_id=NP_414551.1;transl_table=11
+NC_000913.3	RefSeq	gene	10643	11356	.	-	.	ID=gene-b0011;geneID=gene-b0011;gene_name=yaaW;Dbxref=ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=yaaW;gbkey=Gene;gene=yaaW;gene_biotype=protein_coding;gene_synonym=ECK0011;locus_tag=b0011
+NC_000913.3	RefSeq	CDS	10643	11356	.	-	0	Parent=gene-b0011;Dbxref=UniProtKB/Swiss-Prot:P75617,Genbank:NP_414552.1,ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=NP_414552.1;gbkey=CDS;gene=yaaW;locus_tag=b0011;orig_transcript_id=gnl|b0011|mrna.b0011;product=putative enzyme-specific chaperone YaaW;protein_id=NP_414552.1;transl_table=11
+NC_000913.3	RefSeq	gene	10830	11315	.	+	.	ID=gene-b0012;geneID=gene-b0012;gene_name=mbiA;Dbxref=ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=mbiA;gbkey=Gene;gene=mbiA;gene_biotype=protein_coding;gene_synonym=ECK0012,htgA,htpY;locus_tag=b0012
+NC_000913.3	RefSeq	CDS	10830	11315	.	+	0	Parent=gene-b0012;Dbxref=UniProtKB/Swiss-Prot:P28697,Genbank:YP_009518733.1,ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=YP_009518733.1;gbkey=CDS;gene=mbiA;locus_tag=b0012;orig_transcript_id=gnl|b0012|mrna.CDS13;product=uncharacterized protein MbiA;protein_id=YP_009518733.1;transl_table=11
+NC_000913.3	RefSeq	gene	11382	11786	.	-	.	ID=gene-b0013;geneID=gene-b0013;gene_name=yaaI;Dbxref=ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=yaaI;gbkey=Gene;gene=yaaI;gene_biotype=protein_coding;gene_synonym=ECK0013;locus_tag=b0013
+NC_000913.3	RefSeq	CDS	11382	11786	.	-	0	Parent=gene-b0013;Dbxref=UniProtKB/Swiss-Prot:P28696,Genbank:NP_414554.1,ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=NP_414554.1;gbkey=CDS;gene=yaaI;locus_tag=b0013;orig_transcript_id=gnl|b0013|mrna.b0013;product=DUF2541 domain-containing protein YaaI;protein_id=NP_414554.1;transl_table=11
+NC_000913.3	RefSeq	gene	12163	14079	.	+	.	ID=gene-b0014;geneID=gene-b0014;gene_name=dnaK;Dbxref=ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=dnaK;gbkey=Gene;gene=dnaK;gene_biotype=protein_coding;gene_synonym=ECK0014,groPAB,groPC,groPF,grpC,grpF,seg;locus_tag=b0014
+NC_000913.3	RefSeq	CDS	12163	14079	.	+	0	Parent=gene-b0014;Dbxref=UniProtKB/Swiss-Prot:P0A6Y8,Genbank:NP_414555.1,ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=NP_414555.1;gbkey=CDS;gene=dnaK;locus_tag=b0014;orig_transcript_id=gnl|b0014|mrna.b0014;product=chaperone protein DnaK;protein_id=NP_414555.1;transl_table=11
+NC_000913.3	RefSeq	gene	14168	15298	.	+	.	ID=gene-b0015;geneID=gene-b0015;gene_name=dnaJ;Dbxref=ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=dnaJ;gbkey=Gene;gene=dnaJ;gene_biotype=protein_coding;gene_synonym=ECK0015,groP,grpC;locus_tag=b0015
+NC_000913.3	RefSeq	CDS	14168	15298	.	+	0	Parent=gene-b0015;Dbxref=UniProtKB/Swiss-Prot:P08622,Genbank:NP_414556.1,ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=NP_414556.1;gbkey=CDS;gene=dnaJ;locus_tag=b0015;orig_transcript_id=gnl|b0015|mrna.b0015;product=chaperone protein DnaJ;protein_id=NP_414556.1;transl_table=11