| Next changeset 1:c6cf723c2ed4 (2014-06-10) |
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Commit message:
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository |
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added:
fml_gff_converter_programs/README fml_gff_converter_programs/galaxy/bed_to_gff3.xml fml_gff_converter_programs/galaxy/gff3_to_bed.xml fml_gff_converter_programs/galaxy/gff3_to_gtf.xml fml_gff_converter_programs/galaxy/gtf_to_gff3.xml fml_gff_converter_programs/scripts/bed_to_gff3_converter.py fml_gff_converter_programs/scripts/gff3_to_bed_converter.py fml_gff_converter_programs/scripts/gff3_to_gtf_converter.pl fml_gff_converter_programs/scripts/gtf_to_gff3_converter.py fml_gff_converter_programs/t/AceView_gff3_to_gtf.gtf fml_gff_converter_programs/t/AceView_ncbi_37.gff3 fml_gff_converter_programs/t/AceView_ncbi_37.gtf fml_gff_converter_programs/t/Aly_JGI.bed fml_gff_converter_programs/t/Aly_JGI.gff3 fml_gff_converter_programs/t/ENSEMBL_mm9.gff3 fml_gff_converter_programs/t/ENSEMBL_mm9.gtf fml_gff_converter_programs/t/ENSEMBL_mm9_gff3_to_gtf.gtf fml_gff_converter_programs/t/JGI_genes.gff3 fml_gff_converter_programs/t/JGI_genes.gtf fml_gff_converter_programs/t/MB7_3R.bed fml_gff_converter_programs/t/MB7_3R.gff3 fml_gff_converter_programs/t/UCSC_transcripts.gff3 fml_gff_converter_programs/t/UCSC_transcripts.gtf fml_gff_converter_programs/t/ccds_genes.bed fml_gff_converter_programs/t/ccds_genes.gff3 fml_gff_converter_programs/t/hs_2009.bed fml_gff_converter_programs/t/hs_2009.gff3 |
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| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/README Tue Jun 07 17:26:20 2011 -0400 |
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| @@ -0,0 +1,60 @@ +A collection of tools for converting genome annotation between GTF (Gene Transfer Format), BED (Browser Extensible Data) and GFF (Generic Feature Format) + +INTRODUCTION + +Several genome annotation centers provide their data in GTF, BED, GFF3 etc. I have few programs +they mainly deals with converting between GTF, BED and GFF3 formats. They are extensively tested +with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. Please follow the +instructions below to clone these tools into your galaxy instance. + +CONTENTS + +galaxy: Contains tool configuration files in *.xml format. + + Tool configuration files. Please add right path to locate the scripts. + + gtf_to_gff3.xml + + gff3_to_gtf.xml + + bed_to_gff3.xml + + gff3_to_bed.xml + +t: Test data set. (move to your galaxy root folder/test-data/) + + You may need to move the test files into your test-data directory so galaxy can find them. + If you want to run the functional tests eg as: + + sh run_functional_tests.sh -id fml_gtf2gff3 + +scripts: Python based and Perl based scripts. + + gtf_to_gff3_converter.py: This tool converts data from GTF format to valid GFF3 format. + + gff3_to_gtf_converter.pl: This tool converts data from GFF3 format to GTF format. + + bed_to_gff3_converter.py: This tool converts data from a 12 column UCSC wiggle BED format to GFF3 format. + + gff3_to_bed_converter.py: This tool converts gene transcript annotation from GFF3 format to UCSC wiggle 12 column BED format. + +REQUIREMENTS + + Python, Perl and if you are interested to use gff3_to_gtf_converter.pl please install Bio::Perl module. + +COMMENTS/QUESTIONS + +I can be reached at vipin.ts@tuebingen.mpg.de + +LICENSE + +Copyright (C) 2010 Friedrich Miescher Laboratory of the Max Planck Society + +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; either version 3 of the License, or +(at your option) any later version. + +COURTESY + +To the Galaxy Team. |
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| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/galaxy/bed_to_gff3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/galaxy/bed_to_gff3.xml Tue Jun 07 17:26:20 2011 -0400 |
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| @@ -0,0 +1,84 @@ +<tool id="fml_bed2gff" name="BED_to_GFF3" version="1.0.0"> + <description>converter</description> + <command interpreter="python">bed_to_gff3_converter.py $inf_bed > $gff_format + </command> + <inputs> + <param format="bed" name="inf_bed" type="data" label="Convert this query" help="Please look at About format section."/> + </inputs> + <outputs> + <data format="gff3" name="gff_format" /> + </outputs> + <tests> + <test> + <param name="inf_bed" value="ccds_genes.bed" /> + <output name="gff_format" file="ccds_genes.gff3" /> + </test> + <test> + <param name="inf_bed" value="hs_2009.bed" /> + <output name="gff_format" file="hs_2009.gff3" /> + </test> + </tests> + <help> + +**What it does** + +This tool converts data from a 12 column UCSC wiggle BED format to GFF3 format. + +-------- + +**Example** + +- The following data in UCSC Wiggle BED format:: + + chr1 11873 14409 uc001aaa.3 0 + 11873 11873 0 3 354,109,1189, 0,739,1347, + +- Will be converted to GFF3 format:: + + ##gff-version 3 + chr1 bed2gff gene 11874 14409 0 + . ID=Gene:uc001aaa.3;Name=Gene:uc001aaa.3 + chr1 bed2gff transcript 11874 14409 0 + . ID=uc001aaa.3;Name=uc001aaa.3;Parent=Gene:uc001aaa.3 + chr1 bed2gff exon 11874 12227 0 + . Parent=uc001aaa.3 + chr1 bed2gff exon 12613 12721 0 + . Parent=uc001aaa.3 + chr1 bed2gff exon 13221 14409 0 + . Parent=uc001aaa.3 + +-------- + +**About formats** + +**BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones: + +The first three BED fields (required) are:: + + 1. chrom - The name of the chromosome (e.g. chr1, chrY_random). + 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) + 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval). + +The additional BED fields (optional) are:: + + 4. name - The name of the BED line. + 5. score - A score between 0 and 1000. + 6. strand - Defines the strand - either '+' or '-'. + 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. + 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser. + 9. reserved - This should always be set to zero. + 10. blockCount - The number of blocks (exons) in the BED line. + 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount. + 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount. + +**GFF3 format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields: + + 1. seqid - Must be a chromosome or scaffold or contig. + 2. source - The program that generated this feature. + 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". + 4. start - The starting position of the feature in the sequence. The first base is numbered 1. + 5. stop - The ending position of the feature (inclusive). + 6. score - A score between 0 and 1000. If there is no score value, enter ".". + 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). + 8. phase - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'. + 9. attributes - All lines with the same group are linked together into a single item. + +-------- + +This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010 Vipin T. Sreedharan (vipin.ts@tuebingen.mpg.de) + </help> +</tool> |
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| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/galaxy/gff3_to_bed.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/galaxy/gff3_to_bed.xml Tue Jun 07 17:26:20 2011 -0400 |
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| @@ -0,0 +1,84 @@ +<tool id="fml_gff2bed" name="GFF3_to_BED" version="1.0.0"> + <description>converter</description> + <command interpreter="python">gff3_to_bed_converter.py $inf_gff > $bed_format + </command> + <inputs> + <param format="gff3" name="inf_gff" type="data" label="Genome annotation file in GFF3 format" help="Please look at About format section."/> + </inputs> + <outputs> + <data format="bed" name="bed_format"/> + </outputs> + <tests> + <test> + <param name="inf_gff" value="Aly_JGI.gff3" /> + <output name="bed_format" file="Aly_JGI.bed" /> + </test> + <test> + <param name="inf_gff" value="MB7_3R.gff3" /> + <output name="bed_format" file="MB7_3R.bed" /> + </test> + </tests> + <help> + +**What it does** + +This tool converts gene transcript annotation from GFF3 format to UCSC wiggle 12 column BED format. + +-------- + +**Example** + +- The following data in GFF3 format:: + + ##gff-version 3 + chr1 protein_coding gene 11874 14409 0 + . ID=Gene:uc001aaa.3;Name=Gene:uc001aaa.3 + chr1 protein_coding transcript 11874 14409 0 + . ID=uc001aaa.3;Name=uc001aaa.3;Parent=Gene:uc001aaa.3 + chr1 protein_coding exon 11874 12227 0 + . Parent=uc001aaa.3 + chr1 protein_coding exon 12613 12721 0 + . Parent=uc001aaa.3 + chr1 protein_coding exon 13221 14409 0 + . Parent=uc001aaa.3 + +- Will be converted to UCSC Wiggle BED format:: + + chr1 11874 14409 uc001aaa.3 0 + 11874 14409 0 3 354,109,1189, 0,739,1347, + +-------- + +**About formats** + +**GFF3 format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields: + + 1. seqid - Must be a chromosome or scaffold or contig. + 2. source - The program that generated this feature. + 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". + 4. start - The starting position of the feature in the sequence. The first base is numbered 1. + 5. stop - The ending position of the feature (inclusive). + 6. score - A score between 0 and 1000. If there is no score value, enter ".". + 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). + 8. phase - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'. + 9. attributes - All lines with the same group are linked together into a single item. + +**BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones: + +The first three BED fields (required) are:: + + 1. chrom - The name of the chromosome (e.g. chr1, chrY_random). + 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) + 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval). + +The additional BED fields (optional) are:: + + 4. name - The name of the BED line. + 5. score - A score between 0 and 1000. + 6. strand - Defines the strand - either '+' or '-'. + 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. + 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser. + 9. reserved - This should always be set to zero. + 10. blockCount - The number of blocks (exons) in the BED line. + 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount. + 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount. + +-------- + +This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010 Vipin T. Sreedharan (vipin.ts@tuebingen.mpg.de) + </help> +</tool> |
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| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/galaxy/gff3_to_gtf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/galaxy/gff3_to_gtf.xml Tue Jun 07 17:26:20 2011 -0400 |
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| @@ -0,0 +1,83 @@ +<tool id="fml_gff3togtf" name="GFF3_to_GTF" version="1.0.0"> + <description>converter</description> + <command interpreter="perl">gff3_to_gtf_converter.pl $inf_gff3 $gtf_format + </command> + <inputs> + <param format="gff3" name="inf_gff3" type="data" label="File in GFF3 format" help="GFF3 format file for converting to GTF."/> + </inputs> + <outputs> + <data format="gtf" name="gtf_format" /> + </outputs> + <tests> + <test> + <param name="inf_gff3" value="AceView_ncbi_37.gff3" /> + <output name="gtf_format" file="AceView_gff3_to_gtf.gtf" /> + </test> + <test> + <param name="inf_gff3" value="ENSEMBL_mm9.gff3" /> + <output name="gtf_format" file="ENSEMBL_mm9_gff3_to_gtf.gtf" /> + </test> + </tests> + <help> + +**What it does** + +This tool converts data from GFF3 format to GTF format. + +-------- + +**Example** + +- The following data in GFF3 format:: + + ##gff-version 3 + 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11 + 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859 + 17 protein_coding protein 7256262 7256960 . + . ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751 + 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751 + 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352 + 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751 + 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751 + +- Will be converted to GTF format:: + + 17 protein_coding exon 7255208 7258258 . + . gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; + 17 protein_coding CDS 7256262 7256957 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; protein_id "ENSP00000328352"; + 17 protein_coding start_codon 7256262 7256264 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; + 17 protein_coding stop_codon 7256958 7256960 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; + +-------- + +**About formats** + + +**GFF3 format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields: + + 1. seqid - Must be a chromosome or scaffold. + 2. source - The program that generated this feature. + 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". + 4. start - The starting position of the feature in the sequence. The first base is numbered 1. + 5. stop - The ending position of the feature (inclusive). + 6. score - A score between 0 and 1000. If there is no score value, enter ".". + 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). + 8. phase - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'. + 9. attributes - All lines with the same group are linked together into a single item. + + +**GTF format** Gene Transfer Format, it borrows from GFF, but has additional structure that warrants a separate definition and format name. GTF lines have nine tab-seaparated fields: + + 1. seqname - The name of the sequence. + 2. source - This indicating where the annotation came from. + 3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon' + 4. start - The starting position of the feature in the sequence. The first base is numbered 1. + 5. end - The ending position of the feature (inclusive). + 6. score - The score field indicates a degree of confidence in the feature's existence and coordinates. + 7. strand - Valid entries include '+', '-', or '.' + 8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. + 9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region. + +-------- + +This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010 Vipin T. Sreedharan (vipin.ts@tuebingen.mpg.de) + </help> +</tool> |
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| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/galaxy/gtf_to_gff3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/galaxy/gtf_to_gff3.xml Tue Jun 07 17:26:20 2011 -0400 |
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| @@ -0,0 +1,89 @@ +<tool id="fml_gtf2gff3" name="GTF_to_GFF3" version="1.0.0"> + <description>converter</description> + <command interpreter="python">gtf_to_gff3_converter.py $inf_gtf > $gff3_format + </command> + <inputs> + <param format="gtf" name="inf_gtf" type="data" label="File in GTF format" help="GTF file for converting to GFF3 format."/> + </inputs> + <outputs> + <data format="gff3" name="gff3_format" /> + </outputs> + <tests> + <test> + <param name="inf_gtf" value="UCSC_transcripts.gtf" /> + <output name="gff3_format" file="UCSC_transcripts.gff3" /> + </test> + <test> + <param name="inf_gtf" value="JGI_genes.gtf" /> + <output name="gff3_format" file="JGI_genes.gff3" /> + </test> + <test> + <param name="inf_gtf" value="ENSEMBL_mm9.gtf" /> + <output name="gff3_format" file="ENSEMBL_mm9.gff3" /> + </test> + <test> + <param name="inf_gtf" value="AceView_ncbi_37.gtf" /> + <output name="gff3_format" file="AceView_ncbi_37.gff3" /> + </test> + </tests> + <help> + +**What it does** + +This tool converts data from GTF format to valid GFF3 format. + +-------- + +**Example** + +- The following data in GTF format:: + + 17 protein_coding exon 7255208 7258258 . + . gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; + 17 protein_coding CDS 7256262 7256957 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; protein_id "ENSP00000328352"; + 17 protein_coding start_codon 7256262 7256264 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; + 17 protein_coding stop_codon 7256958 7256960 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; + +- Will be converted to GFF3 format:: + + ##gff-version 3 + 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11 + 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859 + 17 protein_coding protein 7256262 7256960 . + . ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751 + 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751 + 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352 + 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751 + 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751 + +-------- + +**About formats** + +**GTF format** Gene Transfer Format, it borrows from GFF, but has additional structure that warrants a separate definition and format name. GTF lines have nine tab-seaparated fields: + + 1. seqname - The name of the sequence. + 2. source - This indicating where the annotation came from. + 3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon' + 4. start - The starting position of the feature in the sequence. The first base is numbered 1. + 5. end - The ending position of the feature (inclusive). + 6. score - The score field indicates a degree of confidence in the feature's existence and coordinates. + 7. strand - Valid entries include '+', '-', or '.' + 8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. + 9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region. + +**GFF3 format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields: + + 1. seqid - Must be a chromosome or scaffold. + 2. source - The program that generated this feature. + 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". + 4. start - The starting position of the feature in the sequence. The first base is numbered 1. + 5. stop - The ending position of the feature (inclusive). + 6. score - A score between 0 and 1000. If there is no score value, enter ".". + 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). + 8. phase - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'. + 9. attributes - All lines with the same group are linked together into a single item. + +-------- + +This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010 Vipin T. Sreedharan (vipin.ts@tuebingen.mpg.de) + </help> +</tool> |
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| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/scripts/bed_to_gff3_converter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/scripts/bed_to_gff3_converter.py Tue Jun 07 17:26:20 2011 -0400 |
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| @@ -0,0 +1,48 @@ +#!/usr/bin/env python +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 3 of the License, or +# (at your option) any later version. +# +# Written (W) 2010 Vipin T Sreedharan, Friedrich Miescher Laboratory of the Max Planck Society +# Copyright (C) 2010 Max Planck Society +# +# Description : Convert a BED format file to GFF3 format + +import re, sys + +def __main__(): + + try: + bed_fh = open(sys.argv[1], 'rU') + except: + sys.stderr.write('BED format file fail to open, Cannot continue...\n') + sys.stderr.write('USAGE: bed_to_gff3_converter.py <bed file> > *.gff3\n') + sys.exit(-1) + print '##gff-version 3' + for line in bed_fh: + line = line.strip( '\n\r' ).split( '\t' ) + if re.match('#', line[0]):continue + if len(line) != 12: # considering BED lines with 12 fields + line = '\t'.join(line) + sys.stdout.write('Warning: Invalid BED line found- ' + line + '\n') + continue + if len(line[-1].split(',')) != len(line[-2].split(',')):continue # checking the consistency b/w relative start of exon and its length + rstart = line[-1].split(',') + if rstart[-1] == '': rstart.pop() + exon_len = line[-2].split(',') + if exon_len[-1] == '': exon_len.pop() + if len(rstart) != int(line[-3]): continue # checking the number of exons and block count are same + if line[5] != '+' and line[5] != '-':line[5] = '.' # replace the unknown starnd with '.' + # write feature lines to the result file + print line[0] + '\tbed2gff\tgene\t' + str(int(line[1]) + 1) + '\t' + line[2] + '\t' + line[4] + '\t' + line[5] + '\t.\t' + 'ID=Gene:' + line[3] + ';Name=Gene:' + line[3] + print line[0] + '\tbed2gff\ttranscript\t' + str(int(line[1]) + 1) + '\t' + line[2] + '\t' + line[4] + '\t' + line[5] + '\t.\t' + 'ID=' + line[3] + ';Name=' + line[3] + ';Parent=Gene:' + line[3] + st = int(line[1]) + for ex_cnt in range(int(line[-3])): + start = st + int(rstart[ex_cnt]) + 1 + stop = start + int(exon_len[ex_cnt]) - 1 + print line[0] + '\tbed2gff\texon\t' + str(start) + '\t' + str(stop) + '\t' + line[4] + '\t' + line[5] + '\t.\t' + 'Parent=' + line[3] + bed_fh.close() + +if __name__ == "__main__": __main__() |
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| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/scripts/gff3_to_bed_converter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/scripts/gff3_to_bed_converter.py Tue Jun 07 17:26:20 2011 -0400 |
| [ |
| @@ -0,0 +1,79 @@ +#!/usr/bin/env python +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 3 of the License, or +# (at your option) any later version. +# +# Written (W) 2010 Vipin T Sreedharan, Friedrich Miescher Laboratory of the Max Planck Society +# Copyright (C) 2010 Max Planck Society +# +# Description : Convert a genome annotation in GFF3 format to UCSC 12 column Wiggle BED format. BED format typically represents the transcript models. + +import re, sys + +def WriteBED(tinfo, einfo): + + for contig_id, features in tinfo.items(): + for tid, tloc in features.items(): + if tid in einfo: # get corresponding exon info + exon_cnt, exon_len, exon_cod, fex, rstart = 0, '', '', 0, None + if tloc[-1] == '-': + if einfo[tid][0][1] > einfo[tid][-1][1]:einfo[tid].sort() + for ex_ele in einfo[tid]: + if ex_ele[0] != contig_id:continue + exon_cnt += 1 + exon_len += str(int(ex_ele[2])-int(ex_ele[1])+1) + ',' + if fex == 0: # calculate the relative exon start + exon_cod += '0,' + fex = 1 + rstart = int(ex_ele[1]) + else: + exon_cod += str(int(ex_ele[1])-rstart) + ',' + if exon_len: # display bed line + print contig_id + '\t' + tloc[0] + '\t' + tloc[1] + '\t' + tid + '\t' + tloc[2] + '\t' + tloc[-1] + '\t' + tloc[0] + '\t' + tloc[1] + '\t0\t' + str(exon_cnt) + '\t' + exon_len + '\t' + exon_cod + +def ParseAnno(gff_fh): + + tinfo, einfo = dict(), dict() + for gff_line in gff_fh: + gff_line = gff_line.strip('\n\r').split('\t') + if re.match(r'#', gff_line[0]):continue + if re.match(r'>', gff_line[0]):continue + if len(gff_line) == 1: + if re.search(r'\w+', gff_line[0]):continue## GFF files with FASTA sequence together + if len(gff_line) != 9:sys.stderr.write('Warning: Found invalid GFF line\n' + '\t'.join(gff_line) + '\n');continue + if gff_line[3] == '' and gff_line[4] == '':sys.stderr.write('Warning: Found invalid coordinates in GFF line: ' + '\t'.join(gff_line) + '\n');continue + if gff_line[2] == 'transcript' or gff_line[2] == 'scRNA' or gff_line[2] == "mRNA" or gff_line[2] == 'ncRNA' or gff_line[2] == 'miRNA' or gff_line[2] == 'rRNA' or gff_line[2] == 'snoRNA' or gff_line[2] == 'snRNA' or gff_line[2] == 'tRNA' or gff_line[2] == 'pseudogenic_transcript': + col9 = gff_line[-1].split(';') + tid = None + for ele in col9: + if re.search(r'ID=', ele):tid = re.search(r'ID=(.+)', ele).group(1);break + if gff_line[0] in tinfo: + tinfo[gff_line[0]][tid] = (gff_line[3], gff_line[4], gff_line[5], gff_line[6]) + else: + tinfo[gff_line[0]] = {tid:(gff_line[3], gff_line[4], gff_line[5], gff_line[6])} + if gff_line[2] == 'exon': + col9 = gff_line[-1].split(';') + pid = None + for ele in col9: + if re.search(r'Parent=', ele):pid = re.search(r'Parent=(.+)', ele).group(1);break + if pid in einfo: + einfo[pid].append((gff_line[0], int(gff_line[3]), int(gff_line[4]))) + else: + einfo[pid] = [(gff_line[0], int(gff_line[3]), int(gff_line[4]))] + gff_fh.close() + return tinfo, einfo + +if __name__ == "__main__": + + try: + gff_fh = open(sys.argv[1], 'rU') + except: + sys.stderr.write('GFF format file fail to open, Cannot continue...\n') + sys.stderr.write('USAGE: gff3_to_bed_converter.py <gff file> > *.bed\n') + sys.exit(-1) + ## get transcript annotation + tinfo, einfo = ParseAnno(gff_fh) + ## write into bed format + WriteBED(tinfo, einfo) |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/scripts/gff3_to_gtf_converter.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/scripts/gff3_to_gtf_converter.pl Tue Jun 07 17:26:20 2011 -0400 |
| [ |
| @@ -0,0 +1,83 @@ +#!/usr/bin/env perl +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 3 of the License, or +# (at your option) any later version. +# +# Written (W) 2010 Vipin T Sreedharan, Friedrich Miescher Laboratory of the Max Planck Society +# Copyright (C) 2010 Max Planck Society +# +# Description : Convert a GFF3 format file to GTF format. + +use strict; +use warnings; + +use lib '/home/galaxy/perl5/share/perl/5.8.8/'; +use Bio::FeatureIO; + +my $usage = q( +gff3_to_gtf_converter.pl - Program to convert a valid GFF3 format file to GTF format. +USAGE: gff3_to_gtf_converter.pl <GFF3 file name> <output file name> +); + +# requirement check +if (scalar(@ARGV) != 2) { + print $usage; + exit +} + +my $inFile = $ARGV[0]; +my $outFile = $ARGV[1]; + +my $inGFF = Bio::FeatureIO->new( '-file' => "$inFile", + '-format' => 'GFF', + '-version' => 3 ); +my $outGTF = Bio::FeatureIO->new( '-file' => ">$outFile", + '-format' => 'GFF', + '-version' => 2.5); + +my ($gene, $feature_type, $exon_exon_cnt, $cds_exon_cnt) = ('', '', 0, 0); + +while (my $feature = $inGFF->next_feature() ) { + # from a valid GFF3 file try to get transcript information. + if ($feature->type->name eq 'mRNA' || $feature->type->name eq 'miRNA' || $feature->type->name eq 'ncRNA' || $feature->type->name eq 'rRNA' || $feature->type->name eq 'snoRNA' || $feature->type->name eq 'snRNA' || $feature->type->name eq 'tRNA' || $feature->type->name eq 'misc_RNA' || $feature->type->name eq 'processed_transcript' || $feature->type->name eq 'transcript' || $feature->type->name eq 'scRNA') { + my $parent = ($feature->get_Annotations('Parent'))[0]; + $gene = $parent->value; + $cds_exon_cnt = 1; + $exon_exon_cnt = 1; + $feature_type = $feature->type->name; + } + if ($feature->type->name eq 'exon' || $feature->type->name eq 'CDS' ||$feature->type->name eq 'stop_codon' || $feature->type->name eq 'start_codon') { + my $parent = ($feature->get_Annotations('Parent'))[0]; + my $transcript = $parent->value; + + my ($col_exon_number, $protein_id) = ('', ''); + if ($feature->type->name eq 'exon') { + $col_exon_number = Bio::Annotation::SimpleValue->new( '-value' => $exon_exon_cnt, '-tagname' => 'exon_number'); + $exon_exon_cnt++; + } elsif ($feature->type->name eq 'CDS') { + $col_exon_number = Bio::Annotation::SimpleValue->new( '-value' => $cds_exon_cnt, '-tagname' => 'exon_number'); + $cds_exon_cnt++; + my $pid = $transcript; + $pid =~s/Transcript/Protein/; + $protein_id = Bio::Annotation::SimpleValue->new( '-value' => $pid, '-tagname' => 'protein_id'); + } elsif ($feature->type->name eq 'start_codon'){ + $col_exon_number = Bio::Annotation::SimpleValue->new( '-value' => $cds_exon_cnt, '-tagname' => 'exon_number'); + } else { + $col_exon_number = Bio::Annotation::SimpleValue->new( '-value' => $cds_exon_cnt-1, '-tagname' => 'exon_number'); + } + + my $transcript_id = Bio::Annotation::SimpleValue->new( '-value' => $transcript, '-tagname' => 'transcript_id'); + my $gene_id = Bio::Annotation::SimpleValue->new( '-value' => $gene, '-tagname' => 'gene_id'); + my $source_identifer = Bio::Annotation::SimpleValue->new( '-value' => $feature_type, '-tagname' => 'source_id'); + + $feature->add_Annotation($source_identifer); + $feature->add_Annotation($transcript_id); + $feature->add_Annotation($gene_id); + $feature->add_Annotation($col_exon_number); + $feature->add_Annotation($protein_id) if ($feature->type->name eq 'CDS'); + } + $outGTF->write_feature($feature); +} +exit; |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/scripts/gtf_to_gff3_converter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/scripts/gtf_to_gff3_converter.py Tue Jun 07 17:26:20 2011 -0400 |
| [ |
| b'@@ -0,0 +1,233 @@\n+#!/usr/bin/env python\n+#\n+# This program is free software; you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation; either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# Written (W) 2010 Vipin T Sreedharan, Friedrich Miescher Laboratory of the Max Planck Society\n+# Copyright (C) 2010 Max Planck Society\n+#\n+# Description : Convert a GTF format file to GFF3 format, tested extensively on files from following centers NCBI AceView, ENSEMBL, Joint Genome Institute and UCSC Genome Center\n+\n+import re, sys\n+from operator import itemgetter\n+\n+def addCDSphase(strand, cds):\n+ """Add CDS phase to the CDS exons"""\n+ \n+ cds_region, cds_flag = [], 0 \n+ if strand == \'+\':\n+ for cdspos in cds:\n+ if cds_flag == 0:\n+ cdspos = (cdspos[0], cdspos[1], 0)\n+ diff = (cdspos[1]-(cdspos[0]-1))%3\n+ else:\n+ xy = 0\n+ if diff == 0: \n+ cdspos = (cdspos[0], cdspos[1], 0)\n+ elif diff == 1: \n+ cdspos = (cdspos[0], cdspos[1], 2)\n+ xy = 2\n+ elif diff == 2: \n+ cdspos = (cdspos[0], cdspos[1], 1)\n+ xy = 1\n+ diff = ((cdspos[1]-(cdspos[0]-1))-xy)%3\n+ cds_region.append(cdspos)\n+ cds_flag = 1 \n+ elif strand == \'-\':\n+ cds.reverse()\n+ for cdspos in cds: \n+ if cds_flag == 0:\n+ cdspos = (cdspos[0], cdspos[1], 0)\n+ diff = (cdspos[1]-(cdspos[0]-1))%3\n+ else: \n+ xy = 0 \n+ if diff == 0: \n+ cdspos = (cdspos[0], cdspos[1], 0)\n+ elif diff == 1:\n+ cdspos = (cdspos[0], cdspos[1], 2)\n+ xy = 2\n+ elif diff == 2: \n+ cdspos = (cdspos[0], cdspos[1], 1)\n+ xy = 1\n+ diff = ((cdspos[1]-(cdspos[0]-1))-xy)%3\n+ cds_region.append(cdspos)\n+ cds_flag = 1\n+ cds_region.reverse()\n+ return cds_region\n+\n+def buildUTR(cc, ec, strand):\n+ """Build UTR regions from CDS and exon coordiantes"""\n+ \n+ utr5, utr3 = [], []\n+ if strand == \'+\':\n+ cds_s = cc[0][0]\n+ for ex in ec:\n+ if ex[0] <= cds_s and cds_s <= ex[1]:\n+ if ex[0] != cds_s:utr5.append((ex[0], cds_s-1))\n+ break\n+ else:\n+ utr5.append(ex)\n+ cds_e = cc[-1][1]\n+ for i in range(len(ec)):\n+ i += 1\n+ if ec[-i][0] <= cds_e and cds_e <= ec[-i][1]:\n+ if ec[-i][1] != cds_e:utr3.append((cds_e +1, ec[-i][1]))\n+ break\n+ else:\n+ utr3.append(ec[-i]) \n+ utr3.reverse()\n+ elif strand == \'-\':\n+ cds_s = cc[-1][1]\n+ for i in range(len(ec)):\n+ i += 1\n+ if ec[-i][0] <= cds_s and cds_s <= ec[-i][1]:\n+ if ec[-i][1] != cds_s:utr5.append((cds_s+1, ec[-i][1]))\n+ break\n+ else:\n+ utr5.append(ec[-i])\n+ utr5.reverse()\n+ cds_e = cc[0][0] \n+ for ex in ec:\n+ if ex[0] <= cds_e and cds_e <= ex[1]:\n+ if ex[0] != cds_e:utr3.append((ex[0], cds_e-1))\n+ break\n+ else:\n+ utr3.append(ex)\n+ return utr5, utr3\n+\n+def GFFWriter(gtf_file_content):\n+ """Write into GFF3 format"""\n+\n+ for contig, contig_info in sorted(gtf_file_content.items()): # first level, chromosome\n+ for feature, details in contig_info.items(): # second level, gene\n+ source, gene_start, gene_stop, transcript_details, orient, gname = dict(), [], [], dict(), None, None\n+ for ftid, tinfo in details.items(): # third level, transcripts \n+ tinfo[\'exon\'].sort() # ge'..b'gname= name;continue\n+ if re.search(r\'^(transcript_name|transcriptname)$\', tag, re.IGNORECASE):tname= name;continue\n+ if re.search(r\'^(exonNumber|exon_number)$\', tag, re.IGNORECASE):ex_cnt = name;continue\n+\n+ if tid == None:\n+ if gtf_line[2] == \'CDS\':tid = recall # JGI Joint Genome Institute GTF files dont have transcript ID for CDS line\n+ if tid == pid == None:continue # stop_codon icluded in CDS coordinates of JGI GTF files, moreover stop_codon lines dont have any transcript identifications.\n+ if gid == tid:gid = \'Gene:\' + str(gid);tid = \'Transcript:\' + str(tid) # UCSC gene and transcript ID are similar, differentaiting with Gene: and Transcript: tag in the begning \n+ \n+ if gtf_line[0] in gtf_content: # existing chromosome\n+ if gid in gtf_content[gtf_line[0]].keys(): # existing gene \n+ if tid in gtf_content[gtf_line[0]][gid].keys(): # existing transcript\n+ if gtf_line[2] == \'exon\':gtf_content[gtf_line[0]][gid][tid][\'exon\'].append((int(gtf_line[3]), int(gtf_line[4])))\n+ elif gtf_line[2] == \'CDS\':gtf_content[gtf_line[0]][gid][tid][\'CDS\'].append((int(gtf_line[3]), int(gtf_line[4])))\n+ elif gtf_line[2] == \'stop_codon\':gtf_content[gtf_line[0]][gid][tid][\'stop_codon\'].append((int(gtf_line[3]), int(gtf_line[4])))\n+ else: # new transcript \n+ if gtf_line[2] == \'exon\':gtf_content[gtf_line[0]][gid][tid] = dict(exon = [(int(gtf_line[3]), int(gtf_line[4]))], CDS = [], stop_codon = [], info = [gtf_line[1], gtf_line[6], gtf_line[5], gname, tname])\n+ elif gtf_line[2] == \'CDS\':gtf_content[gtf_line[0]][gid][tid] = dict(exon = [], CDS = [(int(gtf_line[3]), int(gtf_line[4]))], stop_codon = [], info = [gtf_line[1], gtf_line[6], gtf_line[5], gname, tname])\n+ elif gtf_line[2] == \'stop_codon\':gtf_content[gtf_line[0]][gid][tid] = dict(exon = [], CDS = [], stop_codon = [(int(gtf_line[3]), int(gtf_line[4]))], info = [gtf_line[1], gtf_line[6], gtf_line[5], gname, tname])\n+ else: # new gene \n+ if gtf_line[2] == \'exon\':gtf_content[gtf_line[0]][gid] = {tid : dict(exon = [(int(gtf_line[3]), int(gtf_line[4]))], CDS = [], stop_codon = [], info = [gtf_line[1], gtf_line[6], gtf_line[5], gname, tname])}\n+ elif gtf_line[2] == \'CDS\':gtf_content[gtf_line[0]][gid] = {tid : dict(exon = [], CDS = [(int(gtf_line[3]), int(gtf_line[4]))], stop_codon = [], info = [gtf_line[1], gtf_line[6], gtf_line[5], gname, tname])}\n+ elif gtf_line[2] == \'stop_codon\':gtf_content[gtf_line[0]][gid] = {tid : dict(exon = [], CDS = [], stop_codon = [(int(gtf_line[3]), int(gtf_line[4]))], info = [gtf_line[1], gtf_line[6], gtf_line[5], gname, tname])}\n+ else: # new chromosome\n+ if gtf_line[2] == \'exon\':gtf_content[gtf_line[0]] = {gid : {tid : dict(exon = [(int(gtf_line[3]), int(gtf_line[4]))], CDS = [], stop_codon = [], info = [gtf_line[1], gtf_line[6], gtf_line[5], gname, tname])}}\n+ elif gtf_line[2] == \'CDS\':gtf_content[gtf_line[0]] = {gid : {tid : dict(exon = [], CDS = [(int(gtf_line[3]), int(gtf_line[4]))], stop_codon = [], info = [gtf_line[1], gtf_line[6], gtf_line[5], gname, tname])}}\n+ elif gtf_line[2] == \'stop_codon\':gtf_content[gtf_line[0]] = {gid : {tid : dict(exon = [], CDS = [], stop_codon = [(int(gtf_line[3]), int(gtf_line[4]))], info = [gtf_line[1], gtf_line[6], gtf_line[5], gname, tname])}}\n+ recall = tid\n+\n+ gtf_fh.close()\n+ return gtf_content\n+\n+def __main__():\n+\n+ try:\n+ gtf_file = sys.argv[1]\n+ except:\n+ sys.stderr.write(\'GTF format file required, Cannot continue...\\n\')\n+ sys.stderr.write(\'USAGE: gtf_to_gff3_converter.py <gtf file> > *.gff3\\n\')\n+ sys.exit(-1)\n+ \n+ gtf_file_content = get_GTF_info(gtf_file)\n+ print \'##gff-version 3\'\n+ GFFWriter(gtf_file_content)\n+\n+if __name__ == "__main__": __main__()\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/AceView_gff3_to_gtf.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/AceView_gff3_to_gtf.gtf Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,2544 @@\n+##gff-version 2.5\n+1\tprotein_coding\tCDS\t12704566\t12704733\t.\t+\t0\tgene_id "AADACL4"; transcript_id "AADACL4.aAug10"; exon_number "1"; protein_id "AADACL4.aAug10";\n+1\tprotein_coding\tCDS\t12711142\t12711358\t.\t+\t0\tgene_id "AADACL4"; transcript_id "AADACL4.aAug10"; exon_number "2"; protein_id "AADACL4.aAug10";\n+1\tprotein_coding\tCDS\t12721802\t12721865\t.\t+\t0\tgene_id "AADACL4"; transcript_id "AADACL4.aAug10"; exon_number "3"; protein_id "AADACL4.aAug10";\n+1\tprotein_coding\tCDS\t12725972\t12726746\t.\t+\t0\tgene_id "AADACL4"; transcript_id "AADACL4.aAug10"; exon_number "4"; protein_id "AADACL4.aAug10";\n+1\tprotein_coding\texon\t12704566\t12704733\t.\t+\t0\tgene_id "AADACL4"; transcript_id "AADACL4.aAug10"; exon_number "1";\n+1\tprotein_coding\texon\t12711142\t12711358\t.\t+\t0\tgene_id "AADACL4"; transcript_id "AADACL4.aAug10"; exon_number "2";\n+1\tprotein_coding\texon\t12721802\t12721865\t.\t+\t0\tgene_id "AADACL4"; transcript_id "AADACL4.aAug10"; exon_number "3";\n+1\tprotein_coding\texon\t12725972\t12727097\t.\t+\t0\tgene_id "AADACL4"; transcript_id "AADACL4.aAug10"; exon_number "4";\n+1\tprotein_coding\tCDS\t12776344\t12776347\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.bAug10"; exon_number "1"; protein_id "AADACL3.bAug10";\n+1\tprotein_coding\tCDS\t12780885\t12780948\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.bAug10"; exon_number "2"; protein_id "AADACL3.bAug10";\n+1\tprotein_coding\tCDS\t12785189\t12785963\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.bAug10"; exon_number "3"; protein_id "AADACL3.bAug10";\n+1\tprotein_coding\texon\t12776119\t12776347\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.bAug10"; exon_number "1";\n+1\tprotein_coding\texon\t12780885\t12780948\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.bAug10"; exon_number "2";\n+1\tprotein_coding\texon\t12785189\t12788726\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.bAug10"; exon_number "3";\n+1\tprotein_coding\tCDS\t12779480\t12779693\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.aAug10"; exon_number "1"; protein_id "AADACL3.aAug10";\n+1\tprotein_coding\tCDS\t12780885\t12780948\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.aAug10"; exon_number "2"; protein_id "AADACL3.aAug10";\n+1\tprotein_coding\tCDS\t12785189\t12785963\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.aAug10"; exon_number "3"; protein_id "AADACL3.aAug10";\n+1\tprotein_coding\texon\t12776119\t12776347\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.aAug10"; exon_number "1";\n+1\tprotein_coding\texon\t12779477\t12779693\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.aAug10"; exon_number "2";\n+1\tprotein_coding\texon\t12780885\t12780948\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.aAug10"; exon_number "3";\n+1\tprotein_coding\texon\t12785189\t12788726\t.\t+\t0\tgene_id "AADACL3"; transcript_id "AADACL3.aAug10"; exon_number "4";\n+10\tprotein_coding\tCDS\t52566489\t52566640\t.\t-\t0\tgene_id "A1CF"; transcript_id "A1CF.fAug10"; exon_number "1"; protein_id "A1CF.fAug10";\n+10\tprotein_coding\tCDS\t52569654\t52569802\t.\t-\t0\tgene_id "A1CF"; transcript_id "A1CF.fAug10"; exon_number "2"; protein_id "A1CF.fAug10";\n+10\tprotein_coding\tCDS\t52570800\t52570936\t.\t-\t0\tgene_id "A1CF"; transcript_id "A1CF.fAug10"; exon_number "3"; protein_id "A1CF.fAug10";\n+10\tprotein_coding\tCDS\t52573617\t52573798\t.\t-\t0\tgene_id "A1CF"; transcript_id "A1CF.fAug10"; exon_number "4"; protein_id "A1CF.fAug10";\n+10\tprotein_coding\tCDS\t52575766\t52576039\t.\t-\t0\tgene_id "A1CF"; transcript_id "A1CF.fAug10"; exon_number "5"; protein_id "A1CF.fAug10";\n+10\tprotein_coding\tCDS\t52580312\t52580409\t.\t-\t0\tgene_id "A1CF"; transcript_id "A1CF.fAug10"; exon_number "6"; protein_id "A1CF.fAug10";\n+10\tprotein_coding\tCDS\t52587891\t52588055\t.\t-\t0\tgene_id "A1CF"; transcript_id "A1CF.fAug10"; exon_number "7"; protein_id "A1CF.fAug10";\n+10\tprotein_coding\tCDS\t52595834\t52596072\t.\t-\t0\tgene_id "A1CF"; transcript_id "A1CF.fAug10"; exon_number "8"; protein_id "A1CF.fAug10";\n+10\tprotein_coding\tCDS\t52601622\t52601752\t.\t-\t0\tgene_id "A1CF"; 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transcript_id "AAA1.gAug10"; exon_number "3";\n+7\ttranscript\texon\t34768349\t34768428\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.gAug10"; exon_number "4";\n+7\ttranscript\texon\t34800724\t34800803\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.gAug10"; exon_number "5";\n+7\ttranscript\texon\t34873773\t34873948\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.gAug10"; exon_number "6";\n+7\ttranscript\texon\t34758474\t34759420\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.hAug10"; exon_number "1";\n+7\ttranscript\texon\t34762896\t34763007\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.hAug10"; exon_number "2";\n+7\ttranscript\texon\t34768349\t34768428\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.hAug10"; exon_number "3";\n+7\ttranscript\texon\t34807954\t34808052\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.hAug10"; exon_number "4";\n+7\ttranscript\texon\t34873773\t34873943\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.hAug10"; exon_number "5";\n+7\ttranscript\texon\t34390034\t34390459\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.iAug10"; exon_number "1";\n+7\ttranscript\texon\t34457191\t34457284\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.iAug10"; exon_number "2";\n+7\ttranscript\texon\t34609324\t34609473\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.iAug10"; exon_number "3";\n+7\ttranscript\texon\t34768349\t34768428\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.iAug10"; exon_number "4";\n+7\ttranscript\texon\t34800724\t34800803\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.iAug10"; exon_number "5";\n+7\tprotein_coding\tCDS\t34457198\t34457284\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.bAug10"; exon_number "1"; protein_id "AAA1.bAug10";\n+7\tprotein_coding\tCDS\t34768349\t34768428\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.bAug10"; exon_number "2"; protein_id "AAA1.bAug10";\n+7\tprotein_coding\tCDS\t34797686\t34797710\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.bAug10"; exon_number "3"; protein_id "AAA1.bAug10";\n+7\tprotein_coding\texon\t34386126\t34390459\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.bAug10"; exon_number "1";\n+7\tprotein_coding\texon\t34457191\t34457284\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.bAug10"; exon_number "2";\n+7\tprotein_coding\texon\t34768349\t34768428\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.bAug10"; exon_number "3";\n+7\tprotein_coding\texon\t34797686\t34797884\t.\t-\t0\tgene_id "AAA1"; transcript_id "AAA1.bAug10"; exon_number "4";\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/AceView_ncbi_37.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/AceView_ncbi_37.gff3 Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,3164 @@\n+##gff-version 3\n+1\tAceView\tgene\t12704566\t12727097\t.\t+\t.\tID=AADACL4;Name=AADACL4\n+1\tAceView\tmRNA\t12704566\t12727097\t.\t+\t.\tID=AADACL4.aAug10;Parent=AADACL4\n+1\tAceView\tCDS\t12704566\t12704733\t.\t+\t0\tParent=AADACL4.aAug10\n+1\tAceView\tCDS\t12711142\t12711358\t.\t+\t0\tParent=AADACL4.aAug10\n+1\tAceView\tCDS\t12721802\t12721865\t.\t+\t2\tParent=AADACL4.aAug10\n+1\tAceView\tCDS\t12725972\t12726746\t.\t+\t1\tParent=AADACL4.aAug10\n+1\tAceView\tthree_prime_UTR\t12726747\t12727097\t.\t+\t.\tParent=AADACL4.aAug10\n+1\tAceView\texon\t12704566\t12704733\t.\t+\t.\tParent=AADACL4.aAug10\n+1\tAceView\texon\t12711142\t12711358\t.\t+\t.\tParent=AADACL4.aAug10\n+1\tAceView\texon\t12721802\t12721865\t.\t+\t.\tParent=AADACL4.aAug10\n+1\tAceView\texon\t12725972\t12727097\t.\t+\t.\tParent=AADACL4.aAug10\n+1\tAceView\tgene\t12776119\t12788726\t.\t+\t.\tID=AADACL3;Name=AADACL3\n+1\tAceView\tmRNA\t12776119\t12788726\t.\t+\t.\tID=AADACL3.bAug10;Parent=AADACL3\n+1\tAceView\tfive_prime_UTR\t12776119\t12776343\t.\t+\t.\tParent=AADACL3.bAug10\n+1\tAceView\tCDS\t12776344\t12776347\t.\t+\t0\tParent=AADACL3.bAug10\n+1\tAceView\tCDS\t12780885\t12780948\t.\t+\t2\tParent=AADACL3.bAug10\n+1\tAceView\tCDS\t12785189\t12785963\t.\t+\t1\tParent=AADACL3.bAug10\n+1\tAceView\tthree_prime_UTR\t12785964\t12788726\t.\t+\t.\tParent=AADACL3.bAug10\n+1\tAceView\texon\t12776119\t12776347\t.\t+\t.\tParent=AADACL3.bAug10\n+1\tAceView\texon\t12780885\t12780948\t.\t+\t.\tParent=AADACL3.bAug10\n+1\tAceView\texon\t12785189\t12788726\t.\t+\t.\tParent=AADACL3.bAug10\n+1\tAceView\tmRNA\t12776119\t12788726\t.\t+\t.\tID=AADACL3.aAug10;Parent=AADACL3\n+1\tAceView\tfive_prime_UTR\t12776119\t12776347\t.\t+\t.\tParent=AADACL3.aAug10\n+1\tAceView\tfive_prime_UTR\t12779477\t12779479\t.\t+\t.\tParent=AADACL3.aAug10\n+1\tAceView\tCDS\t12779480\t12779693\t.\t+\t0\tParent=AADACL3.aAug10\n+1\tAceView\tCDS\t12780885\t12780948\t.\t+\t2\tParent=AADACL3.aAug10\n+1\tAceView\tCDS\t12785189\t12785963\t.\t+\t1\tParent=AADACL3.aAug10\n+1\tAceView\tthree_prime_UTR\t12785964\t12788726\t.\t+\t.\tParent=AADACL3.aAug10\n+1\tAceView\texon\t12776119\t12776347\t.\t+\t.\tParent=AADACL3.aAug10\n+1\tAceView\texon\t12779477\t12779693\t.\t+\t.\tParent=AADACL3.aAug10\n+1\tAceView\texon\t12780885\t12780948\t.\t+\t.\tParent=AADACL3.aAug10\n+1\tAceView\texon\t12785189\t12788726\t.\t+\t.\tParent=AADACL3.aAug10\n+10\tAceView\tgene\t52566307\t52588060\t.\t-\t.\tID=A1CF;Name=A1CF\n+10\tAceView\tmRNA\t52566307\t52645387\t.\t-\t.\tID=A1CF.fAug10;Parent=A1CF\n+10\tAceView\tfive_prime_UTR\t52619701\t52619745\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\tfive_prime_UTR\t52622649\t52622741\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\tfive_prime_UTR\t52623793\t52623840\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\tfive_prime_UTR\t52645341\t52645387\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\tCDS\t52566489\t52566640\t.\t-\t2\tParent=A1CF.fAug10\n+10\tAceView\tCDS\t52569654\t52569802\t.\t-\t1\tParent=A1CF.fAug10\n+10\tAceView\tCDS\t52570800\t52570936\t.\t-\t0\tParent=A1CF.fAug10\n+10\tAceView\tCDS\t52573617\t52573798\t.\t-\t2\tParent=A1CF.fAug10\n+10\tAceView\tCDS\t52575766\t52576039\t.\t-\t0\tParent=A1CF.fAug10\n+10\tAceView\tCDS\t52580312\t52580409\t.\t-\t2\tParent=A1CF.fAug10\n+10\tAceView\tCDS\t52587891\t52588055\t.\t-\t2\tParent=A1CF.fAug10\n+10\tAceView\tCDS\t52595834\t52596072\t.\t-\t1\tParent=A1CF.fAug10\n+10\tAceView\tCDS\t52601622\t52601752\t.\t-\t0\tParent=A1CF.fAug10\n+10\tAceView\tCDS\t52603748\t52603882\t.\t-\t0\tParent=A1CF.fAug10\n+10\tAceView\tCDS\t52619602\t52619700\t.\t-\t0\tParent=A1CF.fAug10\n+10\tAceView\tthree_prime_UTR\t52566307\t52566488\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52566307\t52566640\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52569654\t52569802\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52570800\t52570936\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52573617\t52573798\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52575766\t52576039\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52580312\t52580409\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52587891\t52588055\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52595834\t52596072\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52601622\t52601752\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52603748\t52603882\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52619602\t52619745\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52622649\t52622741\t.\t-\t.\tParent=A1CF.fAug10\n+10\tAceView\texon\t52623793\t52623840\t.\t-\t.\tP'..b'743462\t34800803\t.\t-\t.\tID=AAA1.cAug10;Parent=AAA1\n+7\tAceView\tfive_prime_UTR\t34800803\t34800803\t.\t-\t.\tParent=AAA1.cAug10\n+7\tAceView\tCDS\t34743797\t34743811\t.\t-\t0\tParent=AAA1.cAug10\n+7\tAceView\tCDS\t34768349\t34768428\t.\t-\t2\tParent=AAA1.cAug10\n+7\tAceView\tCDS\t34800724\t34800802\t.\t-\t0\tParent=AAA1.cAug10\n+7\tAceView\tthree_prime_UTR\t34743462\t34743796\t.\t-\t.\tParent=AAA1.cAug10\n+7\tAceView\texon\t34743462\t34743811\t.\t-\t.\tParent=AAA1.cAug10\n+7\tAceView\texon\t34768349\t34768428\t.\t-\t.\tParent=AAA1.cAug10\n+7\tAceView\texon\t34800724\t34800803\t.\t-\t.\tParent=AAA1.cAug10\n+7\tAceView\ttranscript\t34386126\t34797884\t.\t-\t.\tID=AAA1.eAug10;Parent=AAA1\n+7\tAceView\texon\t34386126\t34390459\t.\t-\t.\tParent=AAA1.eAug10\n+7\tAceView\texon\t34457191\t34457284\t.\t-\t.\tParent=AAA1.eAug10\n+7\tAceView\texon\t34609324\t34609473\t.\t-\t.\tParent=AAA1.eAug10\n+7\tAceView\texon\t34768349\t34768428\t.\t-\t.\tParent=AAA1.eAug10\n+7\tAceView\texon\t34797686\t34797884\t.\t-\t.\tParent=AAA1.eAug10\n+7\tAceView\tmRNA\t34607864\t34797884\t.\t-\t.\tID=AAA1.aAug10;Parent=AAA1\n+7\tAceView\tfive_prime_UTR\t34797711\t34797884\t.\t-\t.\tParent=AAA1.aAug10\n+7\tAceView\tCDS\t34609384\t34609473\t.\t-\t0\tParent=AAA1.aAug10\n+7\tAceView\tCDS\t34768349\t34768428\t.\t-\t2\tParent=AAA1.aAug10\n+7\tAceView\tCDS\t34797686\t34797710\t.\t-\t0\tParent=AAA1.aAug10\n+7\tAceView\tthree_prime_UTR\t34607864\t34607984\t.\t-\t.\tParent=AAA1.aAug10\n+7\tAceView\tthree_prime_UTR\t34609324\t34609383\t.\t-\t.\tParent=AAA1.aAug10\n+7\tAceView\texon\t34607864\t34607984\t.\t-\t.\tParent=AAA1.aAug10\n+7\tAceView\texon\t34609324\t34609473\t.\t-\t.\tParent=AAA1.aAug10\n+7\tAceView\texon\t34768349\t34768428\t.\t-\t.\tParent=AAA1.aAug10\n+7\tAceView\texon\t34797686\t34797884\t.\t-\t.\tParent=AAA1.aAug10\n+7\tAceView\tmRNA\t34682839\t34800803\t.\t-\t.\tID=AAA1.dAug10;Parent=AAA1\n+7\tAceView\tfive_prime_UTR\t34800803\t34800803\t.\t-\t.\tParent=AAA1.dAug10\n+7\tAceView\tCDS\t34682958\t34682963\t.\t-\t0\tParent=AAA1.dAug10\n+7\tAceView\tCDS\t34768349\t34768428\t.\t-\t2\tParent=AAA1.dAug10\n+7\tAceView\tCDS\t34800724\t34800802\t.\t-\t0\tParent=AAA1.dAug10\n+7\tAceView\tthree_prime_UTR\t34682839\t34682957\t.\t-\t.\tParent=AAA1.dAug10\n+7\tAceView\texon\t34682839\t34682963\t.\t-\t.\tParent=AAA1.dAug10\n+7\tAceView\texon\t34768349\t34768428\t.\t-\t.\tParent=AAA1.dAug10\n+7\tAceView\texon\t34800724\t34800803\t.\t-\t.\tParent=AAA1.dAug10\n+7\tAceView\ttranscript\t34758479\t34873948\t.\t-\t.\tID=AAA1.gAug10;Parent=AAA1\n+7\tAceView\texon\t34758479\t34759420\t.\t-\t.\tParent=AAA1.gAug10\n+7\tAceView\texon\t34760254\t34760397\t.\t-\t.\tParent=AAA1.gAug10\n+7\tAceView\texon\t34762896\t34763007\t.\t-\t.\tParent=AAA1.gAug10\n+7\tAceView\texon\t34768349\t34768428\t.\t-\t.\tParent=AAA1.gAug10\n+7\tAceView\texon\t34800724\t34800803\t.\t-\t.\tParent=AAA1.gAug10\n+7\tAceView\texon\t34873773\t34873948\t.\t-\t.\tParent=AAA1.gAug10\n+7\tAceView\ttranscript\t34758474\t34873943\t.\t-\t.\tID=AAA1.hAug10;Parent=AAA1\n+7\tAceView\texon\t34758474\t34759420\t.\t-\t.\tParent=AAA1.hAug10\n+7\tAceView\texon\t34762896\t34763007\t.\t-\t.\tParent=AAA1.hAug10\n+7\tAceView\texon\t34768349\t34768428\t.\t-\t.\tParent=AAA1.hAug10\n+7\tAceView\texon\t34807954\t34808052\t.\t-\t.\tParent=AAA1.hAug10\n+7\tAceView\texon\t34873773\t34873943\t.\t-\t.\tParent=AAA1.hAug10\n+7\tAceView\ttranscript\t34390034\t34800803\t.\t-\t.\tID=AAA1.iAug10;Parent=AAA1\n+7\tAceView\texon\t34390034\t34390459\t.\t-\t.\tParent=AAA1.iAug10\n+7\tAceView\texon\t34457191\t34457284\t.\t-\t.\tParent=AAA1.iAug10\n+7\tAceView\texon\t34609324\t34609473\t.\t-\t.\tParent=AAA1.iAug10\n+7\tAceView\texon\t34768349\t34768428\t.\t-\t.\tParent=AAA1.iAug10\n+7\tAceView\texon\t34800724\t34800803\t.\t-\t.\tParent=AAA1.iAug10\n+7\tAceView\tmRNA\t34386126\t34797884\t.\t-\t.\tID=AAA1.bAug10;Parent=AAA1\n+7\tAceView\tfive_prime_UTR\t34797711\t34797884\t.\t-\t.\tParent=AAA1.bAug10\n+7\tAceView\tCDS\t34457198\t34457284\t.\t-\t0\tParent=AAA1.bAug10\n+7\tAceView\tCDS\t34768349\t34768428\t.\t-\t2\tParent=AAA1.bAug10\n+7\tAceView\tCDS\t34797686\t34797710\t.\t-\t0\tParent=AAA1.bAug10\n+7\tAceView\tthree_prime_UTR\t34386126\t34390459\t.\t-\t.\tParent=AAA1.bAug10\n+7\tAceView\tthree_prime_UTR\t34457191\t34457197\t.\t-\t.\tParent=AAA1.bAug10\n+7\tAceView\texon\t34386126\t34390459\t.\t-\t.\tParent=AAA1.bAug10\n+7\tAceView\texon\t34457191\t34457284\t.\t-\t.\tParent=AAA1.bAug10\n+7\tAceView\texon\t34768349\t34768428\t.\t-\t.\tParent=AAA1.bAug10\n+7\tAceView\texon\t34797686\t34797884\t.\t-\t.\tParent=AAA1.bAug10\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/AceView_ncbi_37.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/AceView_ncbi_37.gtf Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,3989 @@\n+11\tAceView\texon\t111933358\t111934981\t.\t-\t0\tgene_id 2-oxoacid_dh; Gene_type cDNA_supported; transcript_id 2-oxoacid_dh.aAug10-unspliced; exon_number 1\n+19\tAceView\tCDS\t58859154\t58859210\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.aAug10; product_id A1BGAS.aAug10; exon_number 1\n+19\tAceView\texon\t58859153\t58859210\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.aAug10; exon_number 1\n+19\tAceView\tintron\t58859211\t58864686\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.aAug10; type gt_ag\n+19\tAceView\tCDS\t58864687\t58864840\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.aAug10; product_id A1BGAS.aAug10; exon_number 2\n+19\tAceView\texon\t58864687\t58864840\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.aAug10; exon_number 2\n+19\tAceView\tintron\t58864841\t58865079\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.aAug10; type gt_ag\n+19\tAceView\tCDS\t58865080\t58865114\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.aAug10; product_id A1BGAS.aAug10; exon_number 3\n+19\tAceView\texon\t58865080\t58865223\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.aAug10; exon_number 3\n+19\tAceView\tstop_codon\t58865115\t58865117\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.aAug10; product_id A1BGAS.aAug10;\n+19\tAceView\tintron\t58865224\t58865734\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.aAug10; type gt_ag\n+19\tAceView\texon\t58865735\t58866090\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.aAug10; exon_number 4\n+19\tAceView\tstart_codon\t58864404\t58864406\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.bAug10; product_id A1BGAS.bAug10;\n+19\tAceView\tCDS\t58864404\t58864410\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.bAug10; product_id A1BGAS.bAug10; exon_number 1\n+19\tAceView\texon\t58862110\t58864410\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.bAug10; exon_number 1\n+19\tAceView\tintron\t58864411\t58864744\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.bAug10; type gt_ag\n+19\tAceView\tCDS\t58864745\t58864840\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.bAug10; product_id A1BGAS.bAug10; exon_number 2\n+19\tAceView\texon\t58864745\t58864840\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.bAug10; exon_number 2\n+19\tAceView\tintron\t58864841\t58865079\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.bAug10; type gt_ag\n+19\tAceView\tCDS\t58865080\t58865114\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.bAug10; product_id A1BGAS.bAug10; exon_number 3\n+19\tAceView\texon\t58865080\t58865223\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.bAug10; exon_number 3\n+19\tAceView\tstop_codon\t58865115\t58865117\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.bAug10; product_id A1BGAS.bAug10;\n+19\tAceView\tintron\t58865224\t58865734\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.bAug10; type gt_ag\n+19\tAceView\texon\t58865735\t58866548\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.bAug10; exon_number 4\n+19\tAceView\texon\t58859122\t58859210\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.cAug10; exon_number 1\n+19\tAceView\tintron\t58859211\t58864686\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.cAug10; type gt_ag\n+19\tAceView\texon\t58864687\t58864840\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.cAug10; exon_number 2\n+19\tAceView\tintron\t58864841\t58865079\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.cAug10; type gt_ag\n+19\tAceView\tstart_codon\t58865831\t58865833\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; transcript_id A1BGAS.cAug10; product_id A1BGAS.cAug10;\n+19\tAceView\tCDS\t58865831\t58866547\t.\t+\t0\tgene_id A1BGAS; Gene_type cDNA_supported; tran'..b'codon\t219129739\t219129741\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.gAug10; product_id AAMP.gAug10;\n+2\tAceView\tintron\t219129332\t219129738\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.gAug10; type gt_ag\n+2\tAceView\texon\t219128853\t219129331\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.gAug10; exon_number 11\n+2\tAceView\tstart_codon\t219134807\t219134809\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; product_id AAMP.hAug10;\n+2\tAceView\tCDS\t219134689\t219134809\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; product_id AAMP.hAug10; exon_number 1\n+2\tAceView\texon\t219134689\t219134843\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; exon_number 1\n+2\tAceView\tintron\t219134258\t219134688\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; type gt_ag\n+2\tAceView\tCDS\t219134105\t219134257\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; product_id AAMP.hAug10; exon_number 2\n+2\tAceView\texon\t219134105\t219134257\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; exon_number 2\n+2\tAceView\tintron\t219132337\t219134104\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; type gt_ag\n+2\tAceView\tCDS\t219132217\t219132336\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; product_id AAMP.hAug10; exon_number 3\n+2\tAceView\texon\t219132217\t219132336\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; exon_number 3\n+2\tAceView\tintron\t219131710\t219132216\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; type gt_ag\n+2\tAceView\tCDS\t219131570\t219131709\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; product_id AAMP.hAug10; exon_number 4\n+2\tAceView\texon\t219131570\t219131709\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; exon_number 4\n+2\tAceView\tintron\t219131311\t219131569\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; type gt_ag\n+2\tAceView\tCDS\t219131166\t219131310\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; product_id AAMP.hAug10; exon_number 5\n+2\tAceView\texon\t219131166\t219131310\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; exon_number 5\n+2\tAceView\tintron\t219130871\t219131165\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; type gt_ag\n+2\tAceView\tCDS\t219130787\t219130870\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; product_id AAMP.hAug10; exon_number 6\n+2\tAceView\texon\t219130787\t219130870\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; exon_number 6\n+2\tAceView\tintron\t219130670\t219130786\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; type gt_ag\n+2\tAceView\tCDS\t219130392\t219130669\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; product_id AAMP.hAug10; exon_number 7\n+2\tAceView\texon\t219130302\t219130669\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; exon_number 7\n+2\tAceView\tstop_codon\t219130389\t219130391\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; product_id AAMP.hAug10;\n+2\tAceView\tintron\t219130185\t219130301\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; type gt_ag\n+2\tAceView\texon\t219130094\t219130184\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; exon_number 8\n+2\tAceView\tintron\t219129898\t219130093\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; type gt_ag\n+2\tAceView\texon\t219129743\t219129897\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; exon_number 9\n+2\tAceView\tintron\t219129332\t219129742\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; type gt_ag\n+2\tAceView\texon\t219128853\t219129331\t.\t-\t0\tgene_id AAMP; Gene_type cDNA_supported; transcript_id AAMP.hAug10; exon_number 10\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/Aly_JGI.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/Aly_JGI.bed Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,252 @@\n+scaffold_1\t10652\t11944\tTranscript:909750\t.\t-\t10652\t11944\t0\t5\t60,225,159,360,132,\t0,130,392,608,1161,\n+scaffold_1\t464358\t467635\tTranscript:470161\t.\t+\t464358\t467635\t0\t18\t202,63,72,108,81,54,126,90,126,108,117,57,81,5,174,10,20,31,\t0,599,744,929,1130,1329,1606,1827,2037,2253,2453,2649,2797,2915,2978,3174,3209,3247,\n+scaffold_1\t548765\t550572\tTranscript:918872\t.\t-\t548765\t550572\t0\t4\t170,274,174,28,\t0,593,965,1780,\n+scaffold_1\t80941\t82330\tTranscript:470071\t.\t+\t80941\t82330\t0\t2\t277,1014,\t0,376,\n+scaffold_1\t483425\t484126\tTranscript:311324\t.\t+\t483425\t484126\t0\t3\t72,216,54,\t0,343,648,\n+scaffold_1\t124594\t126229\tTranscript:470077\t.\t-\t124594\t126229\t0\t2\t792,700,\t0,936,\n+scaffold_1\t122468\t124310\tTranscript:470076\t.\t+\t122468\t124310\t0\t4\t1626,84,4,79,\t0,1653,1749,1764,\n+scaffold_1\t118008\t119066\tTranscript:470075\t.\t+\t118008\t119066\t0\t6\t49,732,57,44,56,29,\t0,66,819,899,960,1030,\n+scaffold_1\t90714\t113497\tTranscript:470074\t.\t-\t90714\t113497\t0\t22\t358,90,91,197,78,117,96,126,97,71,99,84,171,129,33,97,51,79,82,56,90,75,\t0,18818,19001,19212,19496,19665,19860,20042,20257,20536,20684,20856,21022,21382,21651,21776,21947,22094,22283,22441,22603,22709,\n+scaffold_1\t621551\t622441\tTranscript:909905\t.\t-\t621551\t622441\t0\t5\t85,140,120,77,151,\t0,175,386,578,740,\n+scaffold_1\t134679\t139817\tTranscript:470079\t.\t-\t134679\t139817\t0\t20\t19,354,129,144,126,126,93,133,132,135,108,204,89,150,154,222,186,123,101,172,\t0,42,474,701,922,1186,1410,1591,2068,2300,2516,2754,3045,3252,3555,3824,4128,4399,4621,4967,\n+scaffold_1\t127652\t134697\tTranscript:470078\t.\t+\t127652\t134697\t0\t11\t1166,318,355,423,293,274,500,322,358,650,825,\t0,1371,1874,2318,2863,3443,4043,4627,5028,5477,6221,\n+scaffold_1\t798586\t799140\tTranscript:470261\t.\t-\t798586\t799140\t0\t1\t555,\t0,\n+scaffold_1\t684011\t686672\tTranscript:909919\t.\t-\t684011\t686672\t0\t7\t81,96,78,139,68,72,129,\t0,250,454,1428,1680,2360,2533,\n+scaffold_1\t156948\t159348\tTranscript:311256\t.\t+\t156948\t159348\t0\t8\t195,177,171,182,212,120,479,237,\t0,384,637,888,1149,1393,1594,2164,\n+scaffold_1\t560362\t562206\tTranscript:470187\t.\t-\t560362\t562206\t0\t5\t42,10,290,190,1058,\t0,68,97,508,787,\n+scaffold_1\t860953\t874764\tTranscript:311407\t.\t-\t860953\t874764\t0\t19\t1236,147,307,309,3006,1651,1115,103,700,1166,115,66,192,174,57,136,86,73,182,\t0,1347,1588,2052,2707,5983,7729,8952,9162,10011,11333,11619,11827,12166,12484,12621,12933,13180,13630,\n+scaffold_1\t771817\t774951\tTranscript:909946\t.\t+\t771817\t774951\t0\t11\t108,198,76,72,88,256,116,221,19,72,256,\t0,231,535,682,855,1025,1350,1548,2129,2732,2879,\n+scaffold_1\t479138\t481385\tTranscript:333544\t.\t-\t479138\t481385\t0\t5\t792,141,246,297,108,\t0,874,1318,1748,2140,\n+scaffold_1\t765430\t766468\tTranscript:918940\t.\t-\t765430\t766468\t0\t2\t529,96,\t0,943,\n+scaffold_1\t766738\t768326\tTranscript:918941\t.\t-\t766738\t768326\t0\t3\t211,573,73,\t0,578,1516,\n+scaffold_1\t849099\t851591\tTranscript:470280\t.\t+\t849099\t851591\t0\t15\t76,3,107,44,78,193,31,59,74,87,62,29,136,100,30,\t0,111,179,357,767,954,1237,1349,1498,1683,1859,2016,2146,2311,2463,\n+scaffold_1\t57579\t57871\tTranscript:918741\t.\t+\t57579\t57871\t0\t1\t293,\t0,\n+scaffold_1\t58865\t72177\tTranscript:918742\t.\t+\t58865\t72177\t0\t49\t113,298,229,340,114,129,192,195,138,123,254,104,95,225,162,73,68,146,109,147,48,129,243,138,86,106,96,153,183,230,103,126,45,195,127,101,135,84,147,132,48,147,62,154,192,105,135,201,280,\t0,209,584,904,1435,1635,1838,2119,2442,2671,2877,3232,3571,3753,4317,4563,4746,4949,5205,5406,5644,5766,6016,6374,6597,6778,7127,7380,7687,7945,8270,8456,8667,8886,9339,9568,9964,10175,10675,10910,11151,11293,11507,11767,12025,12306,12503,12726,13033,\n+scaffold_1\t356318\t357400\tTranscript:470139\t.\t-\t356318\t357400\t0\t2\t727,329,\t0,754,\n+scaffold_1\t786367\t786721\tTranscript:918948\t.\t+\t786367\t786721\t0\t1\t355,\t0,\n+scaffold_1\t787193\t787397\tTranscript:918949\t.\t+\t787193\t787397\t0\t1\t205,\t0,\n+scaffold_1\t511272\t518844\tTranscript:333551\t.\t-\t511272\t518844\t0\t21\t178,407,165,906,191,98,180,629,96,162,183,151,234,161,123,173,220,395,211,114,912,\t0,277,781,1027,2017,2290,2433,2661,3383,3564,3812,4083,4319,4644,4887,5097,5359,5667,'..b'66,3239,3467,3671,3861,4147,4363,4706,4918,5333,\n+scaffold_1\t3311\t6198\tTranscript:470048\t.\t-\t3311\t6198\t0\t9\t180,196,273,201,108,7,378,220,568,\t0,202,499,853,1172,1419,1540,2008,2320,\n+scaffold_1\t9512\t10567\tTranscript:470049\t.\t+\t9512\t10567\t0\t3\t53,82,695,\t0,64,361,\n+scaffold_1\t605536\t607891\tTranscript:470198\t.\t+\t605536\t607891\t0\t2\t765,1020,\t0,1336,\n+scaffold_1\t652374\t653539\tTranscript:470212\t.\t-\t652374\t653539\t0\t2\t302,779,\t0,387,\n+scaffold_1\t650407\t652252\tTranscript:470210\t.\t+\t650407\t652252\t0\t4\t44,59,162,1193,\t0,71,447,653,\n+scaffold_1\t436171\t436800\tTranscript:311313\t.\t-\t436171\t436800\t0\t3\t125,91,105,\t0,320,525,\n+scaffold_1\t428322\t429820\tTranscript:311310\t.\t-\t428322\t429820\t0\t7\t264,33,90,44,64,152,100,\t0,304,434,682,800,1084,1399,\n+scaffold_1\t152834\t155670\tTranscript:909785\t.\t-\t152834\t155670\t0\t2\t1675,650,\t0,2187,\n+scaffold_1\t266834\t270418\tTranscript:470119\t.\t-\t266834\t270418\t0\t8\t237,716,244,328,235,195,103,217,\t0,337,1181,1516,2329,2822,3099,3368,\n+scaffold_1\t759661\t760663\tTranscript:470240\t.\t+\t759661\t760663\t0\t6\t141,48,531,103,15,69,\t0,157,223,768,896,934,\n+scaffold_1\t441904\t443720\tTranscript:311315\t.\t+\t441904\t443720\t0\t2\t993,627,\t0,1190,\n+scaffold_1\t246920\t248384\tTranscript:470115\t.\t+\t246920\t248384\t0\t9\t62,353,296,141,98,45,17,18,35,\t0,93,533,905,1131,1248,1320,1372,1430,\n+scaffold_1\t501318\t503489\tTranscript:918864\t.\t+\t501318\t503489\t0\t6\t224,63,117,400,152,171,\t0,353,605,1211,1738,2001,\n+scaffold_1\t236778\t241721\tTranscript:470110\t.\t+\t236778\t241721\t0\t16\t103,180,159,112,120,152,183,35,163,54,93,143,71,84,294,60,\t0,114,768,1022,1245,1446,1715,1992,2454,2779,3173,3418,4243,4395,4571,4884,\n+scaffold_1\t243695\t245459\tTranscript:470113\t.\t-\t243695\t245459\t0\t6\t44,166,111,106,296,330,\t0,68,317,838,1049,1435,\n+scaffold_1\t330470\t334264\tTranscript:909830\t.\t+\t330470\t334264\t0\t3\t785,1961,167,\t0,1600,3628,\n+scaffold_1\t313347\t315496\tTranscript:918815\t.\t-\t313347\t315496\t0\t4\t1048,161,132,191,\t0,1315,1707,1959,\n+scaffold_1\t46396\t48761\tTranscript:470065\t.\t+\t46396\t48761\t0\t9\t164,76,89,90,45,70,140,89,172,\t0,297,454,641,850,991,1267,2009,2194,\n+scaffold_1\t365041\t365523\tTranscript:909838\t.\t-\t365041\t365523\t0\t3\t97,88,67,\t0,207,416,\n+scaffold_1\t367696\t369417\tTranscript:909839\t.\t-\t367696\t369417\t0\t8\t56,76,78,105,35,46,98,52,\t0,195,411,905,1212,1368,1514,1670,\n+scaffold_1\t779234\t780531\tTranscript:470252\t.\t-\t779234\t780531\t0\t5\t39,196,122,348,72,\t0,68,345,860,1226,\n+scaffold_1\t768374\t770507\tTranscript:311385\t.\t+\t768374\t770507\t0\t10\t87,66,75,145,47,58,50,57,248,61,\t0,187,401,562,791,924,1055,1197,1336,2073,\n+scaffold_1\t328181\t328380\tTranscript:918819\t.\t+\t328181\t328380\t0\t1\t200,\t0,\n+scaffold_1\t816662\t816932\tTranscript:918958\t.\t+\t816662\t816932\t0\t1\t271,\t0,\n+scaffold_1\t928527\t930332\tTranscript:470297\t.\t+\t928527\t930332\t0\t8\t70,161,58,309,49,95,80,115,\t0,91,692,829,1236,1365,1538,1691,\n+scaffold_1\t113969\t115315\tTranscript:918756\t.\t-\t113969\t115315\t0\t1\t1347,\t0,\n+scaffold_1\t915290\t920350\tTranscript:470295\t.\t+\t915290\t920350\t0\t11\t515,539,69,198,132,87,441,168,231,116,401,\t0,612,1269,1908,2192,2873,3050,3591,3934,4388,4660,\n+scaffold_1\t731564\t731809\tTranscript:918928\t.\t-\t731564\t731809\t0\t1\t246,\t0,\n+scaffold_1\t835648\t840282\tTranscript:470277\t.\t-\t835648\t840282\t0\t15\t32,47,96,81,145,272,123,159,282,189,184,142,244,636,320,\t0,68,133,312,500,728,1086,1294,1572,2023,2474,2846,3211,3532,4315,\n+scaffold_1\t628623\t630888\tTranscript:918899\t.\t-\t628623\t630888\t0\t6\t531,85,208,48,168,476,\t0,616,930,1217,1528,1790,\n+scaffold_1\t800563\t803042\tTranscript:918952\t.\t-\t800563\t803042\t0\t9\t95,97,101,189,158,232,136,104,291,\t0,235,433,623,894,1134,1449,1701,2189,\n+scaffold_1\t617112\t618613\tTranscript:918895\t.\t+\t617112\t618613\t0\t7\t100,316,53,73,105,81,176,\t0,218,634,797,960,1155,1326,\n+scaffold_1\t601736\t602094\tTranscript:918890\t.\t-\t601736\t602094\t0\t1\t359,\t0,\n+scaffold_1\t602514\t603658\tTranscript:918891\t.\t+\t602514\t603658\t0\t3\t510,145,81,\t0,792,1064,\n+scaffold_1\t930976\t935010\tTranscript:470299\t.\t+\t930976\t935010\t0\t13\t548,281,83,404,194,181,125,90,79,77,107,157,111,\t0,688,1271,1460,1997,2278,2610,2903,3099,3272,3549,3754,3924,\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/Aly_JGI.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/Aly_JGI.gff3 Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,3996 @@\n+##gff-version 3\n+##sequence-region scaffold_1 1 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.1__253__AT1G03190.1\n+scaffold_1\tJGI_Filtered\texon\t934248\t934324\t.\t+\t.\tID=exon:470299;Parent=Transcript:470299\n+scaffold_1\tJGI_Filtered\tCDS\t934248\t934324\t.\t+\t0\tID=CDS:470299;Parent=Transcript:470299;Name=fgenesh2_kg.1__253__AT1G03190.1\n+scaffold_1\tJGI_Filtered\texon\t934525\t934631\t.\t+\t.\tID=exon:470299;Parent=Transcript:470299\n+scaffold_1\tJGI_Filtered\tCDS\t934525\t934631\t.\t+\t2\tID=CDS:470299;Parent=Transcript:470299;Name=fgenesh2_kg.1__253__AT1G03190.1\n+scaffold_1\tJGI_Filtered\texon\t934730\t934886\t.\t+\t.\tID=exon:470299;Parent=Transcript:470299\n+scaffold_1\tJGI_Filtered\tCDS\t934730\t934851\t.\t+\t1\tID=CDS:470299;Parent=Transcript:470299;Name=fgenesh2_kg.1__253__AT1G03190.1\n+scaffold_1\tJGI_Filtered\texon\t934900\t935010\t.\t+\t.\tID=exon:470299;Parent=Transcript:470299\n+scaffold_1\tJGI_Filtered\tthree_prime_UTR\t934852\t934886\t.\t+\t.\tID=three_prime_UTR:470299;Parent=Transcript:470299\n+scaffold_1\tJGI_Filtered\tthree_prime_UTR\t934900\t935010\t.\t+\t.\tID=three_prime_UTR:470299;Parent=Transcript:470299\n+scaffold_1\tJGI_Filtered\tgene\t938460\t939704\t.\t+\t.\tID=fgenesh1_pm.C_scaffold_1000202;Name=fgenesh1_pm.C_scaffold_1000202\n+scaffold_1\tJGI_Filtered\tmRNA\t938460\t939704\t.\t+\t.\tID=Transcript:311422;Name=Transcript:311422;Parent=fgenesh1_pm.C_scaffold_1000202\n+scaffold_1\tJGI_Filtered\texon\t938460\t938693\t.\t+\t.\tID=exon:311422;Parent=Transcript:311422\n+scaffold_1\tJGI_Filtered\tCDS\t938460\t938693\t.\t+\t0\tID=CDS:311422;Parent=Transcript:311422;Name=fgenesh1_pm.C_scaffold_1000202\n+scaffold_1\tJGI_Filtered\texon\t938841\t939104\t.\t+\t.\tID=exon:311422;Parent=Transcript:311422\n+scaffold_1\tJGI_Filtered\tCDS\t938841\t939104\t.\t+\t0\tID=CDS:311422;Parent=Transcript:311422;Name=fgenesh1_pm.C_scaffold_1000202\n+scaffold_1\tJGI_Filtered\texon\t939200\t939361\t.\t+\t.\tID=exon:311422;Parent=Transcript:311422\n+scaffold_1\tJGI_Filtered\tCDS\t939200\t939361\t.\t+\t0\tID=CDS:311422;Parent=Transcript:311422;Name=fgenesh1_pm.C_scaffold_1000202\n+scaffold_1\tJGI_Filtered\texon\t939394\t939477\t.\t+\t.\tID=exon:311422;Parent=Transcript:311422\n+scaffold_1\tJGI_Filtered\tCDS\t939394\t939477\t.\t+\t0\tID=CDS:311422;Parent=Transcript:311422;Name=fgenesh1_pm.C_scaffold_1000202\n+scaffold_1\tJGI_Filtered\texon\t939597\t939704\t.\t+\t.\tID=exon:311422;Parent=Transcript:311422\n+scaffold_1\tJGI_Filtered\tCDS\t939597\t939704\t.\t+\t0\tID=CDS:311422;Parent=Transcript:311422;Name=fgenesh1_pm.C_scaffold_1000202\n+scaffold_1\tJGI_Filtered\tgene\t940106\t941321\t.\t-\t.\tID=scaffold_100268.1;Name=scaffold_100268.1\n+scaffold_1\tJGI_Filtered\tmRNA\t940106\t941321\t.\t-\t.\tID=Transcript:918987;Name=Transcript:918987;Parent=scaffold_100268.1\n+scaffold_1\tJGI_Filtered\tthree_prime_UTR\t940106\t940125\t.\t-\t.\tID=three_prime_UTR:918987;Parent=Transcript:918987\n+scaffold_1\tJGI_Filtered\texon\t940106\t940528\t.\t-\t.\tID=exon:918987;Parent=Transcript:918987\n+scaffold_1\tJGI_Filtered\tCDS\t940126\t940528\t.\t-\t0\tID=CDS:918987;Parent=Transcript:918987;Name=scaffold_100268.1\n+scaffold_1\tJGI_Filtered\texon\t940628\t940686\t.\t-\t.\tID=exon:918987;Parent=Transcript:918987\n+scaffold_1\tJGI_Filtered\tCDS\t940628\t940686\t.\t-\t1\tID=CDS:918987;Parent=Transcript:918987;Name=scaffold_100268.1\n+scaffold_1\tJGI_Filtered\texon\t941262\t941321\t.\t-\t.\tID=exon:918987;Parent=Transcript:918987\n+scaffold_1\tJGI_Filtered\tCDS\t941262\t941300\t.\t-\t0\tID=CDS:918987;Parent=Transcript:918987;Name=scaffold_100268.1\n+scaffold_1\tJGI_Filtered\tfive_prime_UTR\t941301\t941321\t.\t-\t.\tID=five_prime_UTR:918987;Parent=Transcript:918987\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/ENSEMBL_mm9.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/ENSEMBL_mm9.gff3 Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,4424 @@\n+##gff-version 3\n+18\tlincRNA\tgene\t3336414\t3366861\t.\t+\t.\tID=ENSMUSG00000091488;Name=AC124336.2\n+18\tlincRNA\ttranscript\t3336414\t3366861\t.\t+\t.\tID=ENSMUST00000171726;Parent=ENSMUSG00000091488;Name=AC124336.2-201\n+18\tlincRNA\texon\t3336414\t3337176\t.\t+\t.\tParent=ENSMUST00000171726\n+18\tlincRNA\texon\t3365925\t3366861\t.\t+\t.\tParent=ENSMUST00000171726\n+18\tprotein_coding\tgene\t9314042\t9450148\t.\t-\t.\tID=ENSMUSG00000024286;Name=Ccny\n+18\tprotein_coding\tmRNA\t9314042\t9450148\t.\t-\t.\tID=ENSMUST00000053917;Parent=ENSMUSG00000024286;Name=Ccny-201\n+18\tprotein_coding\tfive_prime_UTR\t9449670\t9450148\t.\t-\t.\tParent=ENSMUST00000053917\n+18\tprotein_coding\tCDS\t9316554\t9316670\t.\t-\t0\tParent=ENSMUST00000053917\n+18\tprotein_coding\tCDS\t9319407\t9319569\t.\t-\t1\tParent=ENSMUST00000053917\n+18\tprotein_coding\tCDS\t9332782\t9332948\t.\t-\t0\tParent=ENSMUST00000053917\n+18\tprotein_coding\tCDS\t9345192\t9345311\t.\t-\t0\tParent=ENSMUST00000053917\n+18\tprotein_coding\tCDS\t9345412\t9345469\t.\t-\t1\tParent=ENSMUST00000053917\n+18\tprotein_coding\tCDS\t9349386\t9349421\t.\t-\t1\tParent=ENSMUST00000053917\n+18\tprotein_coding\tCDS\t9353405\t9353505\t.\t-\t0\tParent=ENSMUST00000053917\n+18\tprotein_coding\tCDS\t9377792\t9377826\t.\t-\t2\tParent=ENSMUST00000053917\n+18\tprotein_coding\tCDS\t9386733\t9386807\t.\t-\t2\tParent=ENSMUST00000053917\n+18\tprotein_coding\tCDS\t9449516\t9449669\t.\t-\t0\tParent=ENSMUST00000053917\n+18\tprotein_coding\tthree_prime_UTR\t9314042\t9316553\t.\t-\t.\tParent=ENSMUST00000053917\n+18\tprotein_coding\texon\t9314042\t9316670\t.\t-\t.\tParent=ENSMUST00000053917\n+18\tprotein_coding\texon\t9319407\t9319569\t.\t-\t.\tParent=ENSMUST00000053917\n+18\tprotein_coding\texon\t9332782\t9332948\t.\t-\t.\tParent=ENSMUST00000053917\n+18\tprotein_coding\texon\t9345192\t9345311\t.\t-\t.\tParent=ENSMUST00000053917\n+18\tprotein_coding\texon\t9345412\t9345469\t.\t-\t.\tParent=ENSMUST00000053917\n+18\tprotein_coding\texon\t9349386\t9349421\t.\t-\t.\tParent=ENSMUST00000053917\n+18\tprotein_coding\texon\t9353405\t9353505\t.\t-\t.\tParent=ENSMUST00000053917\n+18\tprotein_coding\texon\t9377792\t9377826\t.\t-\t.\tParent=ENSMUST00000053917\n+18\tprotein_coding\texon\t9386733\t9386807\t.\t-\t.\tParent=ENSMUST00000053917\n+18\tprotein_coding\texon\t9449516\t9450148\t.\t-\t.\tParent=ENSMUST00000053917\n+18\tprotein_coding\tmRNA\t9314042\t9450148\t.\t-\t.\tID=ENSMUST00000115867;Parent=ENSMUSG00000024286;Name=Ccny-202\n+18\tprotein_coding\tfive_prime_UTR\t9449670\t9450148\t.\t-\t.\tParent=ENSMUST00000115867\n+18\tprotein_coding\tCDS\t9316554\t9316670\t.\t-\t0\tParent=ENSMUST00000115867\n+18\tprotein_coding\tCDS\t9319407\t9319569\t.\t-\t1\tParent=ENSMUST00000115867\n+18\tprotein_coding\tCDS\t9332782\t9332948\t.\t-\t0\tParent=ENSMUST00000115867\n+18\tprotein_coding\tCDS\t9345192\t9345311\t.\t-\t0\tParent=ENSMUST00000115867\n+18\tprotein_coding\tCDS\t9345412\t9345469\t.\t-\t1\tParent=ENSMUST00000115867\n+18\tprotein_coding\tCDS\t9349386\t9349421\t.\t-\t1\tParent=ENSMUST00000115867\n+18\tprotein_coding\tCDS\t9353405\t9353505\t.\t-\t0\tParent=ENSMUST00000115867\n+18\tprotein_coding\tCDS\t9377792\t9377826\t.\t-\t2\tParent=ENSMUST00000115867\n+18\tprotein_coding\tCDS\t9449516\t9449669\t.\t-\t0\tParent=ENSMUST00000115867\n+18\tprotein_coding\tthree_prime_UTR\t9314042\t9316553\t.\t-\t.\tParent=ENSMUST00000115867\n+18\tprotein_coding\texon\t9314042\t9316670\t.\t-\t.\tParent=ENSMUST00000115867\n+18\tprotein_coding\texon\t9319407\t9319569\t.\t-\t.\tParent=ENSMUST00000115867\n+18\tprotein_coding\texon\t9332782\t9332948\t.\t-\t.\tParent=ENSMUST00000115867\n+18\tprotein_coding\texon\t9345192\t9345311\t.\t-\t.\tParent=ENSMUST00000115867\n+18\tprotein_coding\texon\t9345412\t9345469\t.\t-\t.\tParent=ENSMUST00000115867\n+18\tprotein_coding\texon\t9349386\t9349421\t.\t-\t.\tParent=ENSMUST00000115867\n+18\tprotein_coding\texon\t9353405\t9353505\t.\t-\t.\tParent=ENSMUST00000115867\n+18\tprotein_coding\texon\t9377792\t9377826\t.\t-\t.\tParent=ENSMUST00000115867\n+18\tprotein_coding\texon\t9449516\t9450148\t.\t-\t.\tParent=ENSMUST00000115867\n+18\tmiRNA\tgene\t10782897\t10782983\t.\t-\t.\tID=ENSMUSG00000065399;Name=Mir133a-1\n+18\tmiRNA\ttranscript\t10782897\t10782983\t.\t-\t.\tID=ENSMUST00000083465;Parent=ENSMUSG00000065399;Name=Mir133a-1-201\n+18\tmiRNA\texon\t10782897\t10782983\t.\t-\t.\tParent=ENSMUST00000083465\n+18\tprotein_coding\tgene\t9726195\t9726668\t.\t-\t.\tID='..b'694\n+NT_166402\tprotein_coding\texon\t36964\t37064\t.\t+\t.\tParent=ENSMUST00000096694\n+NT_166402\tprotein_coding\texon\t37217\t38054\t.\t+\t.\tParent=ENSMUST00000096694\n+NT_166433\tprotein_coding\tgene\t28587\t52512\t.\t+\t.\tID=ENSMUSG00000078423;Name=AC007307.2\n+NT_166433\tprotein_coding\tmRNA\t28587\t52512\t.\t+\t.\tID=ENSMUST00000105217;Parent=ENSMUSG00000078423;Name=AC007307.2-201\n+NT_166433\tprotein_coding\tfive_prime_UTR\t28587\t28657\t.\t+\t.\tParent=ENSMUST00000105217\n+NT_166433\tprotein_coding\tCDS\t28658\t28798\t.\t+\t0\tParent=ENSMUST00000105217\n+NT_166433\tprotein_coding\tCDS\t31129\t31299\t.\t+\t0\tParent=ENSMUST00000105217\n+NT_166433\tprotein_coding\tCDS\t32196\t32249\t.\t+\t0\tParent=ENSMUST00000105217\n+NT_166433\tprotein_coding\tthree_prime_UTR\t32250\t32270\t.\t+\t.\tParent=ENSMUST00000105217\n+NT_166433\tprotein_coding\tthree_prime_UTR\t51920\t52512\t.\t+\t.\tParent=ENSMUST00000105217\n+NT_166433\tprotein_coding\texon\t28587\t28798\t.\t+\t.\tParent=ENSMUST00000105217\n+NT_166433\tprotein_coding\texon\t31129\t31299\t.\t+\t.\tParent=ENSMUST00000105217\n+NT_166433\tprotein_coding\texon\t32196\t32270\t.\t+\t.\tParent=ENSMUST00000105217\n+NT_166433\tprotein_coding\texon\t51920\t52512\t.\t+\t.\tParent=ENSMUST00000105217\n+NT_166433\tprotein_coding\tgene\t47745\t52514\t.\t+\t.\tID=ENSMUSG00000078424;Name=AC007307.3\n+NT_166433\tprotein_coding\tmRNA\t47745\t52514\t.\t+\t.\tID=ENSMUST00000105218;Parent=ENSMUSG00000078424;Name=AC007307.3-201\n+NT_166433\tprotein_coding\tfive_prime_UTR\t47745\t47746\t.\t+\t.\tParent=ENSMUST00000105218\n+NT_166433\tprotein_coding\tCDS\t47747\t47845\t.\t+\t0\tParent=ENSMUST00000105218\n+NT_166433\tprotein_coding\tCDS\t50322\t50492\t.\t+\t0\tParent=ENSMUST00000105218\n+NT_166433\tprotein_coding\tCDS\t51351\t51404\t.\t+\t0\tParent=ENSMUST00000105218\n+NT_166433\tprotein_coding\tthree_prime_UTR\t51405\t51425\t.\t+\t.\tParent=ENSMUST00000105218\n+NT_166433\tprotein_coding\tthree_prime_UTR\t51920\t52514\t.\t+\t.\tParent=ENSMUST00000105218\n+NT_166433\tprotein_coding\texon\t47745\t47845\t.\t+\t.\tParent=ENSMUST00000105218\n+NT_166433\tprotein_coding\texon\t50322\t50492\t.\t+\t.\tParent=ENSMUST00000105218\n+NT_166433\tprotein_coding\texon\t51351\t51425\t.\t+\t.\tParent=ENSMUST00000105218\n+NT_166433\tprotein_coding\texon\t51920\t52514\t.\t+\t.\tParent=ENSMUST00000105218\n+NT_166433\tprotein_coding\tmRNA\t47928\t52514\t.\t+\t.\tID=ENSMUST00000105219;Parent=ENSMUSG00000078424;Name=AC007307.3-202\n+NT_166433\tprotein_coding\tfive_prime_UTR\t47928\t47985\t.\t+\t.\tParent=ENSMUST00000105219\n+NT_166433\tprotein_coding\tCDS\t47986\t48129\t.\t+\t0\tParent=ENSMUST00000105219\n+NT_166433\tprotein_coding\tCDS\t50322\t50492\t.\t+\t0\tParent=ENSMUST00000105219\n+NT_166433\tprotein_coding\tCDS\t51351\t51404\t.\t+\t0\tParent=ENSMUST00000105219\n+NT_166433\tprotein_coding\tthree_prime_UTR\t51405\t51425\t.\t+\t.\tParent=ENSMUST00000105219\n+NT_166433\tprotein_coding\tthree_prime_UTR\t51920\t52514\t.\t+\t.\tParent=ENSMUST00000105219\n+NT_166433\tprotein_coding\texon\t47928\t48129\t.\t+\t.\tParent=ENSMUST00000105219\n+NT_166433\tprotein_coding\texon\t50322\t50492\t.\t+\t.\tParent=ENSMUST00000105219\n+NT_166433\tprotein_coding\texon\t51351\t51425\t.\t+\t.\tParent=ENSMUST00000105219\n+NT_166433\tprotein_coding\texon\t51920\t52514\t.\t+\t.\tParent=ENSMUST00000105219\n+NT_166433\tprotein_coding\tgene\t11955\t18898\t.\t+\t.\tID=ENSMUSG00000000702;Name=AC007307.1\n+NT_166433\tprotein_coding\tmRNA\t11955\t18898\t.\t+\t.\tID=ENSMUST00000105216;Parent=ENSMUSG00000000702;Name=AC007307.1-201\n+NT_166433\tprotein_coding\tfive_prime_UTR\t11955\t12025\t.\t+\t.\tParent=ENSMUST00000105216\n+NT_166433\tprotein_coding\tCDS\t12026\t12166\t.\t+\t0\tParent=ENSMUST00000105216\n+NT_166433\tprotein_coding\tCDS\t16677\t16841\t.\t+\t0\tParent=ENSMUST00000105216\n+NT_166433\tprotein_coding\tCDS\t17745\t17789\t.\t+\t0\tParent=ENSMUST00000105216\n+NT_166433\tprotein_coding\tthree_prime_UTR\t17790\t17814\t.\t+\t.\tParent=ENSMUST00000105216\n+NT_166433\tprotein_coding\tthree_prime_UTR\t18309\t18898\t.\t+\t.\tParent=ENSMUST00000105216\n+NT_166433\tprotein_coding\texon\t11955\t12166\t.\t+\t.\tParent=ENSMUST00000105216\n+NT_166433\tprotein_coding\texon\t16677\t16841\t.\t+\t.\tParent=ENSMUST00000105216\n+NT_166433\tprotein_coding\texon\t17745\t17814\t.\t+\t.\tParent=ENSMUST00000105216\n+NT_166433\tprotein_coding\texon\t18309\t18898\t.\t+\t.\tParent=ENSMUST00000105216\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/ENSEMBL_mm9.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/ENSEMBL_mm9.gtf Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,3974 @@\n+NT_166433\tprotein_coding\texon\t11955\t12166\t.\t+\t.\t gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "1"; gene_name "AC007307.1"; transcript_name "AC007307.1-201";\n+NT_166433\tprotein_coding\tCDS\t12026\t12166\t.\t+\t0\t gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "1"; gene_name "AC007307.1"; transcript_name "AC007307.1-201"; protein_id "ENSMUSP00000100851";\n+NT_166433\tprotein_coding\tstart_codon\t12026\t12028\t.\t+\t0\t gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "1"; gene_name "AC007307.1"; transcript_name "AC007307.1-201";\n+NT_166433\tprotein_coding\texon\t16677\t16841\t.\t+\t.\t gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "2"; gene_name "AC007307.1"; transcript_name "AC007307.1-201";\n+NT_166433\tprotein_coding\tCDS\t16677\t16841\t.\t+\t0\t gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "2"; gene_name "AC007307.1"; transcript_name "AC007307.1-201"; protein_id "ENSMUSP00000100851";\n+NT_166433\tprotein_coding\texon\t17745\t17814\t.\t+\t.\t gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "3"; gene_name "AC007307.1"; transcript_name "AC007307.1-201";\n+NT_166433\tprotein_coding\tCDS\t17745\t17786\t.\t+\t0\t gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "3"; gene_name "AC007307.1"; transcript_name "AC007307.1-201"; protein_id "ENSMUSP00000100851";\n+NT_166433\tprotein_coding\tstop_codon\t17787\t17789\t.\t+\t0\t gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "3"; gene_name "AC007307.1"; transcript_name "AC007307.1-201";\n+NT_166433\tprotein_coding\texon\t18309\t18898\t.\t+\t.\t gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "4"; gene_name "AC007307.1"; transcript_name "AC007307.1-201";\n+NT_166433\tprotein_coding\texon\t28587\t28798\t.\t+\t.\t gene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "1"; gene_name "AC007307.2"; transcript_name "AC007307.2-201";\n+NT_166433\tprotein_coding\tCDS\t28658\t28798\t.\t+\t0\t gene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "1"; gene_name "AC007307.2"; transcript_name "AC007307.2-201"; protein_id "ENSMUSP00000100852";\n+NT_166433\tprotein_coding\tstart_codon\t28658\t28660\t.\t+\t0\t gene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "1"; gene_name "AC007307.2"; transcript_name "AC007307.2-201";\n+NT_166433\tprotein_coding\texon\t31129\t31299\t.\t+\t.\t gene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "2"; gene_name "AC007307.2"; transcript_name "AC007307.2-201";\n+NT_166433\tprotein_coding\tCDS\t31129\t31299\t.\t+\t0\t gene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "2"; gene_name "AC007307.2"; transcript_name "AC007307.2-201"; protein_id "ENSMUSP00000100852";\n+NT_166433\tprotein_coding\texon\t32196\t32270\t.\t+\t.\t gene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "3"; gene_name "AC007307.2"; transcript_name "AC007307.2-201";\n+NT_166433\tprotein_coding\tCDS\t32196\t32246\t.\t+\t0\t gene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "3"; gene_name "AC007307.2"; transcript_name "AC007307.2-201"; protein_id "ENSMUSP00000100852";\n+NT_166433\tprotein_coding\tstop_codon\t32247\t32249\t.\t+\t0\t gene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "3"; gene_name "AC007307.2"; transcript_name "AC007307.2-201";\n+NT_166433\tprotein_coding\texon\t51920\t52512\t.\t+\t.\t gene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "4"; gene_name "AC007307.2"; transcript_name "AC007307.2-201";\n+NT_166433\tprotein_coding\texon\t47745\t47845\t.\t+\t.\t gene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105218"; exon_number "1"; gene_name "AC007307.3"; transcript_name "AC007307.3-201";\n+NT_166433\tprotein_coding\tCDS\t47747\t47845\t.\t+\t0\t gene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105218"; exon_number "1"; g'..b'32"; gene_name "Lama3"; transcript_name "Lama3-202";\n+18\tprotein_coding\tCDS\t12726175\t12726341\t.\t+\t0\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "32"; gene_name "Lama3"; transcript_name "Lama3-202"; protein_id "ENSMUSP00000111524";\n+18\tprotein_coding\texon\t12730409\t12730592\t.\t+\t.\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "33"; gene_name "Lama3"; transcript_name "Lama3-202";\n+18\tprotein_coding\tCDS\t12730409\t12730592\t.\t+\t1\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "33"; gene_name "Lama3"; transcript_name "Lama3-202"; protein_id "ENSMUSP00000111524";\n+18\tprotein_coding\texon\t12732723\t12732863\t.\t+\t.\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "34"; gene_name "Lama3"; transcript_name "Lama3-202";\n+18\tprotein_coding\tCDS\t12732723\t12732863\t.\t+\t0\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "34"; gene_name "Lama3"; transcript_name "Lama3-202"; protein_id "ENSMUSP00000111524";\n+18\tprotein_coding\texon\t12736261\t12736420\t.\t+\t.\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "35"; gene_name "Lama3"; transcript_name "Lama3-202";\n+18\tprotein_coding\tCDS\t12736261\t12736420\t.\t+\t0\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "35"; gene_name "Lama3"; transcript_name "Lama3-202"; protein_id "ENSMUSP00000111524";\n+18\tprotein_coding\texon\t12736523\t12736653\t.\t+\t.\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "36"; gene_name "Lama3"; transcript_name "Lama3-202";\n+18\tprotein_coding\tCDS\t12736523\t12736653\t.\t+\t2\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "36"; gene_name "Lama3"; transcript_name "Lama3-202"; protein_id "ENSMUSP00000111524";\n+18\tprotein_coding\texon\t12738795\t12738888\t.\t+\t.\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "37"; gene_name "Lama3"; transcript_name "Lama3-202";\n+18\tprotein_coding\tCDS\t12738795\t12738888\t.\t+\t0\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "37"; gene_name "Lama3"; transcript_name "Lama3-202"; protein_id "ENSMUSP00000111524";\n+18\tprotein_coding\texon\t12740202\t12740321\t.\t+\t.\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "38"; gene_name "Lama3"; transcript_name "Lama3-202";\n+18\tprotein_coding\tCDS\t12740202\t12740321\t.\t+\t2\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "38"; gene_name "Lama3"; transcript_name "Lama3-202"; protein_id "ENSMUSP00000111524";\n+18\tprotein_coding\texon\t12741027\t12741522\t.\t+\t.\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "39"; gene_name "Lama3"; transcript_name "Lama3-202";\n+18\tprotein_coding\tCDS\t12741027\t12741169\t.\t+\t2\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "39"; gene_name "Lama3"; transcript_name "Lama3-202"; protein_id "ENSMUSP00000111524";\n+18\tprotein_coding\tstop_codon\t12741170\t12741172\t.\t+\t0\t gene_id "ENSMUSG00000024421"; transcript_id "ENSMUST00000115858"; exon_number "39"; gene_name "Lama3"; transcript_name "Lama3-202";\n+18\tprotein_coding\texon\t12657194\t12657637\t.\t-\t.\t gene_id "ENSMUSG00000090309"; transcript_id "ENSMUST00000172267"; exon_number "1"; gene_name "AC102131.1"; transcript_name "AC102131.1-201";\n+18\tprotein_coding\tCDS\t12657197\t12657637\t.\t-\t0\t gene_id "ENSMUSG00000090309"; transcript_id "ENSMUST00000172267"; exon_number "1"; gene_name "AC102131.1"; transcript_name "AC102131.1-201"; protein_id "ENSMUSP00000129942";\n+18\tprotein_coding\tstop_codon\t12657194\t12657196\t.\t-\t0\t gene_id "ENSMUSG00000090309"; transcript_id "ENSMUST00000172267"; exon_number "1"; gene_name "AC102131.1"; transcript_name "AC102131.1-201";\n+18\trRNA\texon\t12736933\t12737046\t.\t-\t.\t gene_id "ENSMUSG00000088342"; transcript_id "ENSMUST00000157717"; exon_number "1"; gene_name "5S_rRNA.42"; transcript_name "5S_rRNA.42-201";\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/ENSEMBL_mm9_gff3_to_gtf.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/ENSEMBL_mm9_gff3_to_gtf.gtf Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,3709 @@\n+##gff-version 2.5\n+18\ttranscript\texon\t3336414\t3337176\t.\t+\t0\tgene_id "ENSMUSG00000091488"; transcript_id "ENSMUST00000171726"; exon_number "1";\n+18\ttranscript\texon\t3365925\t3366861\t.\t+\t0\tgene_id "ENSMUSG00000091488"; transcript_id "ENSMUST00000171726"; exon_number "2";\n+18\tprotein_coding\tCDS\t9316554\t9316670\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "1"; protein_id "ENSMUST00000053917";\n+18\tprotein_coding\tCDS\t9319407\t9319569\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "2"; protein_id "ENSMUST00000053917";\n+18\tprotein_coding\tCDS\t9332782\t9332948\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "3"; protein_id "ENSMUST00000053917";\n+18\tprotein_coding\tCDS\t9345192\t9345311\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "4"; protein_id "ENSMUST00000053917";\n+18\tprotein_coding\tCDS\t9345412\t9345469\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "5"; protein_id "ENSMUST00000053917";\n+18\tprotein_coding\tCDS\t9349386\t9349421\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "6"; protein_id "ENSMUST00000053917";\n+18\tprotein_coding\tCDS\t9353405\t9353505\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "7"; protein_id "ENSMUST00000053917";\n+18\tprotein_coding\tCDS\t9377792\t9377826\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "8"; protein_id "ENSMUST00000053917";\n+18\tprotein_coding\tCDS\t9386733\t9386807\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "9"; protein_id "ENSMUST00000053917";\n+18\tprotein_coding\tCDS\t9449516\t9449669\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "10"; protein_id "ENSMUST00000053917";\n+18\tprotein_coding\texon\t9314042\t9316670\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "1";\n+18\tprotein_coding\texon\t9319407\t9319569\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "2";\n+18\tprotein_coding\texon\t9332782\t9332948\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "3";\n+18\tprotein_coding\texon\t9345192\t9345311\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "4";\n+18\tprotein_coding\texon\t9345412\t9345469\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "5";\n+18\tprotein_coding\texon\t9349386\t9349421\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "6";\n+18\tprotein_coding\texon\t9353405\t9353505\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "7";\n+18\tprotein_coding\texon\t9377792\t9377826\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "8";\n+18\tprotein_coding\texon\t9386733\t9386807\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "9";\n+18\tprotein_coding\texon\t9449516\t9450148\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000053917"; exon_number "10";\n+18\tprotein_coding\tCDS\t9316554\t9316670\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000115867"; exon_number "1"; protein_id "ENSMUST00000115867";\n+18\tprotein_coding\tCDS\t9319407\t9319569\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000115867"; exon_number "2"; protein_id "ENSMUST00000115867";\n+18\tprotein_coding\tCDS\t9332782\t9332948\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000115867"; exon_number "3"; protein_id "ENSMUST00000115867";\n+18\tprotein_coding\tCDS\t9345192\t9345311\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000115867"; exon_number "4"; protein_id "ENSMUST00000115867";\n+18\tprotein_coding\tCDS\t9345412\t9345469\t.\t-\t0\tgene_id "ENSMUSG00000024286"; transcript_id "ENSMUST00000115867"; exon_number "5"; protein_id "ENSMUST00000115867";\n+18\t'..b'nscript_id "ENSMUST00000105217"; exon_number "1"; protein_id "ENSMUST00000105217";\n+NT_166433\tprotein_coding\tCDS\t31129\t31299\t.\t+\t0\tgene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "2"; protein_id "ENSMUST00000105217";\n+NT_166433\tprotein_coding\tCDS\t32196\t32249\t.\t+\t0\tgene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "3"; protein_id "ENSMUST00000105217";\n+NT_166433\tprotein_coding\texon\t28587\t28798\t.\t+\t0\tgene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "1";\n+NT_166433\tprotein_coding\texon\t31129\t31299\t.\t+\t0\tgene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "2";\n+NT_166433\tprotein_coding\texon\t32196\t32270\t.\t+\t0\tgene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "3";\n+NT_166433\tprotein_coding\texon\t51920\t52512\t.\t+\t0\tgene_id "ENSMUSG00000078423"; transcript_id "ENSMUST00000105217"; exon_number "4";\n+NT_166433\tprotein_coding\tCDS\t47747\t47845\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105218"; exon_number "1"; protein_id "ENSMUST00000105218";\n+NT_166433\tprotein_coding\tCDS\t50322\t50492\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105218"; exon_number "2"; protein_id "ENSMUST00000105218";\n+NT_166433\tprotein_coding\tCDS\t51351\t51404\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105218"; exon_number "3"; protein_id "ENSMUST00000105218";\n+NT_166433\tprotein_coding\texon\t47745\t47845\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105218"; exon_number "1";\n+NT_166433\tprotein_coding\texon\t50322\t50492\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105218"; exon_number "2";\n+NT_166433\tprotein_coding\texon\t51351\t51425\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105218"; exon_number "3";\n+NT_166433\tprotein_coding\texon\t51920\t52514\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105218"; exon_number "4";\n+NT_166433\tprotein_coding\tCDS\t47986\t48129\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105219"; exon_number "1"; protein_id "ENSMUST00000105219";\n+NT_166433\tprotein_coding\tCDS\t50322\t50492\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105219"; exon_number "2"; protein_id "ENSMUST00000105219";\n+NT_166433\tprotein_coding\tCDS\t51351\t51404\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105219"; exon_number "3"; protein_id "ENSMUST00000105219";\n+NT_166433\tprotein_coding\texon\t47928\t48129\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105219"; exon_number "1";\n+NT_166433\tprotein_coding\texon\t50322\t50492\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105219"; exon_number "2";\n+NT_166433\tprotein_coding\texon\t51351\t51425\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105219"; exon_number "3";\n+NT_166433\tprotein_coding\texon\t51920\t52514\t.\t+\t0\tgene_id "ENSMUSG00000078424"; transcript_id "ENSMUST00000105219"; exon_number "4";\n+NT_166433\tprotein_coding\tCDS\t12026\t12166\t.\t+\t0\tgene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "1"; protein_id "ENSMUST00000105216";\n+NT_166433\tprotein_coding\tCDS\t16677\t16841\t.\t+\t0\tgene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "2"; protein_id "ENSMUST00000105216";\n+NT_166433\tprotein_coding\tCDS\t17745\t17789\t.\t+\t0\tgene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "3"; protein_id "ENSMUST00000105216";\n+NT_166433\tprotein_coding\texon\t11955\t12166\t.\t+\t0\tgene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "1";\n+NT_166433\tprotein_coding\texon\t16677\t16841\t.\t+\t0\tgene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "2";\n+NT_166433\tprotein_coding\texon\t17745\t17814\t.\t+\t0\tgene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "3";\n+NT_166433\tprotein_coding\texon\t18309\t18898\t.\t+\t0\tgene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "4";\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/JGI_genes.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/JGI_genes.gff3 Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,4626 @@\n+##gff-version 3\n+scaffold_1\tJGI\tgene\t1237411\t1237623\t.\t+\t.\tID=e_gw2.1.2098.1;Name=e_gw2.1.2098.1\n+scaffold_1\tJGI\tmRNA\t1237411\t1237623\t.\t+\t.\tID=1027156;Parent=e_gw2.1.2098.1\n+scaffold_1\tJGI\tCDS\t1237411\t1237456\t.\t+\t0\tParent=1027156\n+scaffold_1\tJGI\tCDS\t1237502\t1237623\t.\t+\t2\tParent=1027156\n+scaffold_1\tJGI\texon\t1237411\t1237456\t.\t+\t.\tParent=1027156\n+scaffold_1\tJGI\texon\t1237502\t1237623\t.\t+\t.\tParent=1027156\n+scaffold_1\tJGI\tgene\t5902548\t5912971\t.\t+\t.\tID=estExt_Genewise2Plus.C_10864;Name=estExt_Genewise2Plus.C_10864\n+scaffold_1\tJGI\tmRNA\t5902548\t5912971\t.\t+\t.\tID=1045793;Parent=estExt_Genewise2Plus.C_10864\n+scaffold_1\tJGI\tCDS\t5902548\t5902888\t.\t+\t0\tParent=1045793\n+scaffold_1\tJGI\tCDS\t5902966\t5909048\t.\t+\t1\tParent=1045793\n+scaffold_1\tJGI\tCDS\t5909123\t5910952\t.\t+\t2\tParent=1045793\n+scaffold_1\tJGI\tCDS\t5911034\t5911827\t.\t+\t2\tParent=1045793\n+scaffold_1\tJGI\tCDS\t5911903\t5912205\t.\t+\t0\tParent=1045793\n+scaffold_1\tJGI\tCDS\t5912269\t5912760\t.\t+\t0\tParent=1045793\n+scaffold_1\tJGI\tthree_prime_UTR\t5912761\t5912971\t.\t+\t.\tParent=1045793\n+scaffold_1\tJGI\texon\t5902548\t5902888\t.\t+\t.\tParent=1045793\n+scaffold_1\tJGI\texon\t5902966\t5909048\t.\t+\t.\tParent=1045793\n+scaffold_1\tJGI\texon\t5909123\t5910952\t.\t+\t.\tParent=1045793\n+scaffold_1\tJGI\texon\t5911034\t5911827\t.\t+\t.\tParent=1045793\n+scaffold_1\tJGI\texon\t5911903\t5912205\t.\t+\t.\tParent=1045793\n+scaffold_1\tJGI\texon\t5912269\t5912971\t.\t+\t.\tParent=1045793\n+scaffold_1\tJGI\tgene\t5701930\t5702697\t.\t-\t.\tID=fgenesh2_pg.1_#_81;Name=fgenesh2_pg.1_#_81\n+scaffold_1\tJGI\tmRNA\t5701930\t5702697\t.\t-\t.\tID=1066497;Parent=fgenesh2_pg.1_#_81\n+scaffold_1\tJGI\tCDS\t5701930\t5702605\t.\t-\t1\tParent=1066497\n+scaffold_1\tJGI\tCDS\t5702660\t5702697\t.\t-\t0\tParent=1066497\n+scaffold_1\tJGI\texon\t5701930\t5702605\t.\t-\t.\tParent=1066497\n+scaffold_1\tJGI\texon\t5702660\t5702697\t.\t-\t.\tParent=1066497\n+scaffold_1\tJGI\tgene\t6192379\t6193551\t.\t-\t.\tID=estExt_Genewise2Plus.C_10944;Name=estExt_Genewise2Plus.C_10944\n+scaffold_1\tJGI\tmRNA\t6192379\t6193551\t.\t-\t.\tID=1045858;Parent=estExt_Genewise2Plus.C_10944\n+scaffold_1\tJGI\tfive_prime_UTR\t6193484\t6193551\t.\t-\t.\tParent=1045858\n+scaffold_1\tJGI\tCDS\t6192379\t6192999\t.\t-\t0\tParent=1045858\n+scaffold_1\tJGI\tCDS\t6193076\t6193367\t.\t-\t1\tParent=1045858\n+scaffold_1\tJGI\tCDS\t6193440\t6193483\t.\t-\t0\tParent=1045858\n+scaffold_1\tJGI\texon\t6192379\t6192999\t.\t-\t.\tParent=1045858\n+scaffold_1\tJGI\texon\t6193076\t6193367\t.\t-\t.\tParent=1045858\n+scaffold_1\tJGI\texon\t6193440\t6193551\t.\t-\t.\tParent=1045858\n+scaffold_1\tJGI\tgene\t5709177\t5710596\t.\t-\t.\tID=fgenesh2_pg.1_#_84;Name=fgenesh2_pg.1_#_84\n+scaffold_1\tJGI\tmRNA\t5709177\t5710596\t.\t-\t.\tID=1066500;Parent=fgenesh2_pg.1_#_84\n+scaffold_1\tJGI\tCDS\t5709177\t5709216\t.\t-\t1\tParent=1066500\n+scaffold_1\tJGI\tCDS\t5709320\t5710164\t.\t-\t0\tParent=1066500\n+scaffold_1\tJGI\tCDS\t5710228\t5710596\t.\t-\t0\tParent=1066500\n+scaffold_1\tJGI\texon\t5709177\t5709216\t.\t-\t.\tParent=1066500\n+scaffold_1\tJGI\texon\t5709320\t5710164\t.\t-\t.\tParent=1066500\n+scaffold_1\tJGI\texon\t5710228\t5710596\t.\t-\t.\tParent=1066500\n+scaffold_1\tJGI\tgene\t3582929\t3583102\t.\t+\t.\tID=e_gw2.1.2720.1;Name=e_gw2.1.2720.1\n+scaffold_1\tJGI\tmRNA\t3582929\t3583102\t.\t+\t.\tID=1026247;Parent=e_gw2.1.2720.1\n+scaffold_1\tJGI\tCDS\t3582929\t3583102\t.\t+\t0\tParent=1026247\n+scaffold_1\tJGI\texon\t3582929\t3583102\t.\t+\t.\tParent=1026247\n+scaffold_1\tJGI\tgene\t5061339\t5072066\t.\t-\t.\tID=gm1.335_g;Name=gm1.335_g\n+scaffold_1\tJGI\tmRNA\t5061339\t5072066\t.\t-\t.\tID=204986;Parent=gm1.335_g\n+scaffold_1\tJGI\tCDS\t5061339\t5061410\t.\t-\t0\tParent=204986\n+scaffold_1\tJGI\tCDS\t5070743\t5070801\t.\t-\t2\tParent=204986\n+scaffold_1\tJGI\tCDS\t5071914\t5071951\t.\t-\t1\tParent=204986\n+scaffold_1\tJGI\tCDS\t5072047\t5072066\t.\t-\t0\tParent=204986\n+scaffold_1\tJGI\texon\t5061339\t5061410\t.\t-\t.\tParent=204986\n+scaffold_1\tJGI\texon\t5070743\t5070801\t.\t-\t.\tParent=204986\n+scaffold_1\tJGI\texon\t5071914\t5071951\t.\t-\t.\tParent=204986\n+scaffold_1\tJGI\texon\t5072047\t5072066\t.\t-\t.\tParent=204986\n+scaffold_1\tJGI\tgene\t6220485\t6222489\t.\t+\t.\tID=gm1.515_g;Name=gm1.515_g\n+scaffold_1\tJGI\tmRNA\t6220485\t6222489\t.\t+\t.\tID=205166;Parent=gm1.515_g\n+scaffold_1\tJGI\tCDS\t6220485\t6220508\t.\t+\t0\tParent=205166\n+scaffold_1\tJGI\tCDS\t6220551\t622'..b'Genemark2.C_10474\n+scaffold_1\tJGI\tmRNA\t6068472\t6069874\t.\t-\t.\tID=1090684;Parent=estExt_Genemark2.C_10474\n+scaffold_1\tJGI\tCDS\t6068473\t6068941\t.\t-\t1\tParent=1090684\n+scaffold_1\tJGI\tCDS\t6068976\t6069014\t.\t-\t1\tParent=1090684\n+scaffold_1\tJGI\tCDS\t6069080\t6069105\t.\t-\t0\tParent=1090684\n+scaffold_1\tJGI\tCDS\t6069143\t6069420\t.\t-\t2\tParent=1090684\n+scaffold_1\tJGI\tCDS\t6069507\t6069611\t.\t-\t2\tParent=1090684\n+scaffold_1\tJGI\tCDS\t6069662\t6069669\t.\t-\t1\tParent=1090684\n+scaffold_1\tJGI\tCDS\t6069778\t6069797\t.\t-\t0\tParent=1090684\n+scaffold_1\tJGI\tCDS\t6069836\t6069874\t.\t-\t0\tParent=1090684\n+scaffold_1\tJGI\tthree_prime_UTR\t6068472\t6068472\t.\t-\t.\tParent=1090684\n+scaffold_1\tJGI\texon\t6068472\t6068941\t.\t-\t.\tParent=1090684\n+scaffold_1\tJGI\texon\t6068976\t6069014\t.\t-\t.\tParent=1090684\n+scaffold_1\tJGI\texon\t6069080\t6069105\t.\t-\t.\tParent=1090684\n+scaffold_1\tJGI\texon\t6069143\t6069420\t.\t-\t.\tParent=1090684\n+scaffold_1\tJGI\texon\t6069507\t6069611\t.\t-\t.\tParent=1090684\n+scaffold_1\tJGI\texon\t6069662\t6069669\t.\t-\t.\tParent=1090684\n+scaffold_1\tJGI\texon\t6069778\t6069797\t.\t-\t.\tParent=1090684\n+scaffold_1\tJGI\texon\t6069836\t6069874\t.\t-\t.\tParent=1090684\n+scaffold_1\tJGI\tgene\t6222830\t6223956\t.\t-\t.\tID=fgenesh2_kg.1_#_199_#_Contig10010;Name=fgenesh2_kg.1_#_199_#_Contig10010\n+scaffold_1\tJGI\tmRNA\t6222830\t6223956\t.\t-\t.\tID=1059305;Parent=fgenesh2_kg.1_#_199_#_Contig10010\n+scaffold_1\tJGI\tfive_prime_UTR\t6223850\t6223956\t.\t-\t.\tParent=1059305\n+scaffold_1\tJGI\tCDS\t6223123\t6223377\t.\t-\t0\tParent=1059305\n+scaffold_1\tJGI\tCDS\t6223466\t6223513\t.\t-\t0\tParent=1059305\n+scaffold_1\tJGI\tCDS\t6223599\t6223636\t.\t-\t2\tParent=1059305\n+scaffold_1\tJGI\tCDS\t6223717\t6223849\t.\t-\t0\tParent=1059305\n+scaffold_1\tJGI\tthree_prime_UTR\t6222830\t6223122\t.\t-\t.\tParent=1059305\n+scaffold_1\tJGI\texon\t6222830\t6223377\t.\t-\t.\tParent=1059305\n+scaffold_1\tJGI\texon\t6223466\t6223513\t.\t-\t.\tParent=1059305\n+scaffold_1\tJGI\texon\t6223599\t6223636\t.\t-\t.\tParent=1059305\n+scaffold_1\tJGI\texon\t6223717\t6223956\t.\t-\t.\tParent=1059305\n+scaffold_1\tJGI\tgene\t6194330\t6196070\t.\t+\t.\tID=fgenesh2_kg.1_#_188_#_Contig951;Name=fgenesh2_kg.1_#_188_#_Contig951\n+scaffold_1\tJGI\tmRNA\t6194330\t6196070\t.\t+\t.\tID=1059294;Parent=fgenesh2_kg.1_#_188_#_Contig951\n+scaffold_1\tJGI\tfive_prime_UTR\t6194330\t6194523\t.\t+\t.\tParent=1059294\n+scaffold_1\tJGI\tCDS\t6194524\t6194757\t.\t+\t0\tParent=1059294\n+scaffold_1\tJGI\tCDS\t6194844\t6195164\t.\t+\t0\tParent=1059294\n+scaffold_1\tJGI\tthree_prime_UTR\t6195165\t6195696\t.\t+\t.\tParent=1059294\n+scaffold_1\tJGI\tthree_prime_UTR\t6195774\t6196070\t.\t+\t.\tParent=1059294\n+scaffold_1\tJGI\texon\t6194330\t6194757\t.\t+\t.\tParent=1059294\n+scaffold_1\tJGI\texon\t6194844\t6195696\t.\t+\t.\tParent=1059294\n+scaffold_1\tJGI\texon\t6195774\t6196070\t.\t+\t.\tParent=1059294\n+scaffold_1\tJGI\tgene\t4208772\t4210540\t.\t-\t.\tID=gm1.273_g;Name=gm1.273_g\n+scaffold_1\tJGI\tmRNA\t4208772\t4210540\t.\t-\t.\tID=204924;Parent=gm1.273_g\n+scaffold_1\tJGI\tCDS\t4208772\t4208899\t.\t-\t2\tParent=204924\n+scaffold_1\tJGI\tCDS\t4208964\t4209686\t.\t-\t2\tParent=204924\n+scaffold_1\tJGI\tCDS\t4209714\t4209734\t.\t-\t2\tParent=204924\n+scaffold_1\tJGI\tCDS\t4209782\t4210451\t.\t-\t0\tParent=204924\n+scaffold_1\tJGI\tCDS\t4210511\t4210540\t.\t-\t0\tParent=204924\n+scaffold_1\tJGI\texon\t4208772\t4208899\t.\t-\t.\tParent=204924\n+scaffold_1\tJGI\texon\t4208964\t4209686\t.\t-\t.\tParent=204924\n+scaffold_1\tJGI\texon\t4209714\t4209734\t.\t-\t.\tParent=204924\n+scaffold_1\tJGI\texon\t4209782\t4210451\t.\t-\t.\tParent=204924\n+scaffold_1\tJGI\texon\t4210511\t4210540\t.\t-\t.\tParent=204924\n+scaffold_1\tJGI\tgene\t5585408\t5590273\t.\t+\t.\tID=estExt_fgenesh2_pm.C_10049;Name=estExt_fgenesh2_pm.C_10049\n+scaffold_1\tJGI\tmRNA\t5585408\t5590273\t.\t+\t.\tID=1073299;Parent=estExt_fgenesh2_pm.C_10049\n+scaffold_1\tJGI\tfive_prime_UTR\t5585408\t5585504\t.\t+\t.\tParent=1073299\n+scaffold_1\tJGI\tCDS\t5585505\t5585741\t.\t+\t0\tParent=1073299\n+scaffold_1\tJGI\tCDS\t5585815\t5586858\t.\t+\t0\tParent=1073299\n+scaffold_1\tJGI\tthree_prime_UTR\t5586859\t5587647\t.\t+\t.\tParent=1073299\n+scaffold_1\tJGI\tthree_prime_UTR\t5587746\t5590273\t.\t+\t.\tParent=1073299\n+scaffold_1\tJGI\texon\t5585408\t5585741\t.\t+\t.\tParent=1073299\n+scaffold_1\tJGI\texon\t5585815\t5587647\t.\t+\t.\tParent=1073299\n+scaffold_1\tJGI\texon\t5587746\t5590273\t.\t+\t.\tParent=1073299\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/JGI_genes.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/JGI_genes.gtf Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,3994 @@\n+scaffold_1\tJGI\texon\t7\t12\t.\t+\t.\tname "fgenesh2_pg.1_#_1"; transcriptId 1066417\n+scaffold_1\tJGI\tCDS\t7\t12\t.\t+\t0\tname "fgenesh2_pg.1_#_1"; proteinId 1066417; exonNumber 1\n+scaffold_1\tJGI\tstart_codon\t7\t9\t.\t+\t0\tname "fgenesh2_pg.1_#_1"\n+scaffold_1\tJGI\texon\t363\t902\t.\t+\t.\tname "fgenesh2_pg.1_#_1"; transcriptId 1066417\n+scaffold_1\tJGI\tCDS\t363\t902\t.\t+\t0\tname "fgenesh2_pg.1_#_1"; proteinId 1066417; exonNumber 2\n+scaffold_1\tJGI\texon\t954\t1160\t.\t+\t.\tname "fgenesh2_pg.1_#_1"; transcriptId 1066417\n+scaffold_1\tJGI\tCDS\t954\t1160\t.\t+\t0\tname "fgenesh2_pg.1_#_1"; proteinId 1066417; exonNumber 3\n+scaffold_1\tJGI\tstop_codon\t1158\t1160\t.\t+\t0\tname "fgenesh2_pg.1_#_1"\n+scaffold_1\tJGI\texon\t17310\t18075\t.\t-\t.\tname "estExt_Genewise2Plus.C_10002"; transcriptId 1045566\n+scaffold_1\tJGI\tCDS\t17597\t18075\t.\t-\t2\tname "estExt_Genewise2Plus.C_10002"; proteinId 1045566; exonNumber 3\n+scaffold_1\tJGI\tstop_codon\t17597\t17599\t.\t-\t0\tname "estExt_Genewise2Plus.C_10002"\n+scaffold_1\tJGI\texon\t18135\t18268\t.\t-\t.\tname "estExt_Genewise2Plus.C_10002"; transcriptId 1045566\n+scaffold_1\tJGI\tCDS\t18135\t18268\t.\t-\t1\tname "estExt_Genewise2Plus.C_10002"; proteinId 1045566; exonNumber 2\n+scaffold_1\tJGI\texon\t18353\t19188\t.\t-\t.\tname "estExt_Genewise2Plus.C_10002"; transcriptId 1045566\n+scaffold_1\tJGI\tCDS\t18353\t19188\t.\t-\t0\tname "estExt_Genewise2Plus.C_10002"; proteinId 1045566; exonNumber 1\n+scaffold_1\tJGI\tstart_codon\t19186\t19188\t.\t-\t0\tname "estExt_Genewise2Plus.C_10002"\n+scaffold_1\tJGI\texon\t29168\t29186\t.\t-\t.\tname "estExt_Genemark2.C_10004"; transcriptId 1090574\n+scaffold_1\tJGI\texon\t31979\t32005\t.\t-\t.\tname "estExt_Genemark2.C_10004"; transcriptId 1090574\n+scaffold_1\tJGI\texon\t32085\t32211\t.\t-\t.\tname "estExt_Genemark2.C_10004"; transcriptId 1090574\n+scaffold_1\tJGI\tCDS\t32170\t32211\t.\t-\t0\tname "estExt_Genemark2.C_10004"; proteinId 1090574; exonNumber 3\n+scaffold_1\tJGI\tstop_codon\t32170\t32172\t.\t-\t0\tname "estExt_Genemark2.C_10004"\n+scaffold_1\tJGI\texon\t32249\t32298\t.\t-\t.\tname "estExt_Genemark2.C_10004"; transcriptId 1090574\n+scaffold_1\tJGI\tCDS\t32249\t32298\t.\t-\t2\tname "estExt_Genemark2.C_10004"; proteinId 1090574; exonNumber 2\n+scaffold_1\tJGI\texon\t39594\t39912\t.\t-\t.\tname "estExt_Genemark2.C_10004"; transcriptId 1090574\n+scaffold_1\tJGI\tCDS\t39594\t39912\t.\t-\t0\tname "estExt_Genemark2.C_10004"; proteinId 1090574; exonNumber 1\n+scaffold_1\tJGI\texon\t48024\t49977\t.\t-\t.\tname "fgenesh2_kg.1_#_3_#_Contig2893"; transcriptId 1059109\n+scaffold_1\tJGI\tCDS\t48459\t49977\t.\t-\t1\tname "fgenesh2_kg.1_#_3_#_Contig2893"; proteinId 1059109; exonNumber 4\n+scaffold_1\tJGI\tstop_codon\t48459\t48461\t.\t-\t0\tname "fgenesh2_kg.1_#_3_#_Contig2893"\n+scaffold_1\tJGI\texon\t50732\t50830\t.\t-\t.\tname "fgenesh2_kg.1_#_3_#_Contig2893"; transcriptId 1059109\n+scaffold_1\tJGI\tCDS\t50732\t50830\t.\t-\t1\tname "fgenesh2_kg.1_#_3_#_Contig2893"; proteinId 1059109; exonNumber 3\n+scaffold_1\tJGI\texon\t50924\t51099\t.\t-\t.\tname "fgenesh2_kg.1_#_3_#_Contig2893"; transcriptId 1059109\n+scaffold_1\tJGI\tCDS\t50924\t51099\t.\t-\t0\tname "fgenesh2_kg.1_#_3_#_Contig2893"; proteinId 1059109; exonNumber 2\n+scaffold_1\tJGI\texon\t51227\t51548\t.\t-\t.\tname "fgenesh2_kg.1_#_3_#_Contig2893"; transcriptId 1059109\n+scaffold_1\tJGI\tCDS\t51227\t51403\t.\t-\t0\tname "fgenesh2_kg.1_#_3_#_Contig2893"; proteinId 1059109; exonNumber 1\n+scaffold_1\tJGI\tstart_codon\t51401\t51403\t.\t-\t0\tname "fgenesh2_kg.1_#_3_#_Contig2893"\n+scaffold_1\tJGI\texon\t62584\t62802\t.\t+\t.\tname "e_gw2.1.1272.1"; transcriptId 1026707\n+scaffold_1\tJGI\tCDS\t62584\t62802\t.\t+\t0\tname "e_gw2.1.1272.1"; proteinId 1026707; exonNumber 1\n+scaffold_1\tJGI\tstop_codon\t62800\t62802\t.\t+\t0\tname "e_gw2.1.1272.1"\n+scaffold_1\tJGI\texon\t82115\t82306\t.\t-\t.\tname "e_gw2.1.1271.1"; transcriptId 1026712\n+scaffold_1\tJGI\tCDS\t82115\t82306\t.\t-\t0\tname "e_gw2.1.1271.1"; proteinId 1026712; exonNumber 1\n+scaffold_1\tJGI\tstop_codon\t82115\t82117\t.\t-\t0\tname "e_gw2.1.1271.1"\n+scaffold_1\tJGI\texon\t120058\t120311\t.\t-\t.\tname "fgenesh2_kg.1_#_6_#_Contig4211"; transcriptId 1059112\n+scaffold_1\tJGI\tCDS\t120203\t120311\t.\t-\t1\tname "fgenesh2_kg.1_#_6_#_Contig4211"; proteinId 1059112; exonNumber 5\n+scaffol'..b'n\t6530335\t6530597\t.\t-\t.\tname "estExt_fgenesh2_pg.C_10280"; transcriptId 1078583\n+scaffold_1\tJGI\tCDS\t6530335\t6530597\t.\t-\t1\tname "estExt_fgenesh2_pg.C_10280"; proteinId 1078583; exonNumber 2\n+scaffold_1\tJGI\texon\t6530713\t6530971\t.\t-\t.\tname "estExt_fgenesh2_pg.C_10280"; transcriptId 1078583\n+scaffold_1\tJGI\tCDS\t6530713\t6530909\t.\t-\t0\tname "estExt_fgenesh2_pg.C_10280"; proteinId 1078583; exonNumber 1\n+scaffold_1\tJGI\tstart_codon\t6530907\t6530909\t.\t-\t0\tname "estExt_fgenesh2_pg.C_10280"\n+scaffold_1\tJGI\texon\t6530961\t6531797\t.\t-\t.\tname "estExt_fgenesh2_pg.C_10281"; transcriptId 1078584\n+scaffold_1\tJGI\tCDS\t6531507\t6531797\t.\t-\t0\tname "estExt_fgenesh2_pg.C_10281"; proteinId 1078584; exonNumber 2\n+scaffold_1\tJGI\tstop_codon\t6531507\t6531509\t.\t-\t0\tname "estExt_fgenesh2_pg.C_10281"\n+scaffold_1\tJGI\texon\t6531869\t6532149\t.\t-\t.\tname "estExt_fgenesh2_pg.C_10281"; transcriptId 1078584\n+scaffold_1\tJGI\tCDS\t6531869\t6532027\t.\t-\t0\tname "estExt_fgenesh2_pg.C_10281"; proteinId 1078584; exonNumber 1\n+scaffold_1\tJGI\tstart_codon\t6532025\t6532027\t.\t-\t0\tname "estExt_fgenesh2_pg.C_10281"\n+scaffold_1\tJGI\texon\t6532672\t6535468\t.\t+\t.\tname "estExt_Genemark2.C_10601"; transcriptId 1090763\n+scaffold_1\tJGI\tCDS\t6532672\t6535468\t.\t+\t0\tname "estExt_Genemark2.C_10601"; proteinId 1090763; exonNumber 1\n+scaffold_1\tJGI\tstart_codon\t6532672\t6532674\t.\t+\t0\tname "estExt_Genemark2.C_10601"\n+scaffold_1\tJGI\texon\t6535501\t6536357\t.\t+\t.\tname "estExt_Genemark2.C_10601"; transcriptId 1090763\n+scaffold_1\tJGI\tCDS\t6535501\t6536357\t.\t+\t2\tname "estExt_Genemark2.C_10601"; proteinId 1090763; exonNumber 2\n+scaffold_1\tJGI\texon\t6536382\t6536530\t.\t+\t.\tname "estExt_Genemark2.C_10601"; transcriptId 1090763\n+scaffold_1\tJGI\tCDS\t6536382\t6536530\t.\t+\t0\tname "estExt_Genemark2.C_10601"; proteinId 1090763; exonNumber 3\n+scaffold_1\tJGI\texon\t6536577\t6536589\t.\t+\t.\tname "estExt_Genemark2.C_10601"; transcriptId 1090763\n+scaffold_1\tJGI\tCDS\t6536577\t6536589\t.\t+\t1\tname "estExt_Genemark2.C_10601"; proteinId 1090763; exonNumber 4\n+scaffold_1\tJGI\tstop_codon\t6536587\t6536589\t.\t+\t0\tname "estExt_Genemark2.C_10601"\n+scaffold_1\tJGI\texon\t6536649\t6537413\t.\t-\t.\tname "fgenesh2_kg.1_#_289_#_Contig6235"; transcriptId 1059395\n+scaffold_1\tJGI\tCDS\t6536793\t6537413\t.\t-\t0\tname "fgenesh2_kg.1_#_289_#_Contig6235"; proteinId 1059395; exonNumber 2\n+scaffold_1\tJGI\tstop_codon\t6536793\t6536795\t.\t-\t0\tname "fgenesh2_kg.1_#_289_#_Contig6235"\n+scaffold_1\tJGI\texon\t6537494\t6537976\t.\t-\t.\tname "fgenesh2_kg.1_#_289_#_Contig6235"; transcriptId 1059395\n+scaffold_1\tJGI\tCDS\t6537494\t6537910\t.\t-\t0\tname "fgenesh2_kg.1_#_289_#_Contig6235"; proteinId 1059395; exonNumber 1\n+scaffold_1\tJGI\tstart_codon\t6537908\t6537910\t.\t-\t0\tname "fgenesh2_kg.1_#_289_#_Contig6235"\n+scaffold_1\tJGI\texon\t6537938\t6537972\t.\t+\t.\tname "gm1.603_g"; transcriptId 205254\n+scaffold_1\tJGI\tCDS\t6537938\t6537972\t.\t+\t0\tname "gm1.603_g"; proteinId 205254; exonNumber 1\n+scaffold_1\tJGI\tstart_codon\t6537938\t6537940\t.\t+\t0\tname "gm1.603_g"\n+scaffold_1\tJGI\texon\t6538014\t6538046\t.\t+\t.\tname "gm1.603_g"; transcriptId 205254\n+scaffold_1\tJGI\tCDS\t6538014\t6538046\t.\t+\t1\tname "gm1.603_g"; proteinId 205254; exonNumber 2\n+scaffold_1\tJGI\texon\t6538107\t6538156\t.\t+\t.\tname "gm1.603_g"; transcriptId 205254\n+scaffold_1\tJGI\tCDS\t6538107\t6538156\t.\t+\t1\tname "gm1.603_g"; proteinId 205254; exonNumber 3\n+scaffold_1\tJGI\texon\t6538201\t6538314\t.\t+\t.\tname "gm1.603_g"; transcriptId 205254\n+scaffold_1\tJGI\tCDS\t6538201\t6538314\t.\t+\t2\tname "gm1.603_g"; proteinId 205254; exonNumber 4\n+scaffold_1\tJGI\texon\t6538367\t6538787\t.\t+\t.\tname "gm1.603_g"; transcriptId 205254\n+scaffold_1\tJGI\tCDS\t6538367\t6538787\t.\t+\t2\tname "gm1.603_g"; proteinId 205254; exonNumber 5\n+scaffold_1\tJGI\texon\t6538843\t6539173\t.\t+\t.\tname "gm1.603_g"; transcriptId 205254\n+scaffold_1\tJGI\tCDS\t6538843\t6539173\t.\t+\t1\tname "gm1.603_g"; proteinId 205254; exonNumber 6\n+scaffold_1\tJGI\texon\t6539217\t6539489\t.\t+\t.\tname "gm1.603_g"; transcriptId 205254\n+scaffold_1\tJGI\tCDS\t6539217\t6539489\t.\t+\t0\tname "gm1.603_g"; proteinId 205254; exonNumber 7\n+scaffold_1\tJGI\tstop_codon\t6539487\t6539489\t.\t+\t0\tname "gm1.603_g"\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/MB7_3R.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/MB7_3R.bed Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,241 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|
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/MB7_3R.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/MB7_3R.gff3 Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,3971 @@\n+##gff-version 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tMB7\texon\t1139660\t1140027\t0\t-\t.\tParent=CG32464-RB\n+3R\tMB7\texon\t1148710\t1148847\t0\t-\t.\tParent=CG32464-RB\n+3R\tMB7\texon\t1149387\t1149566\t0\t-\t.\tParent=CG32464-RB\n+3R\tMB7\tthree_prime_UTR\t1098665\t1099668\t0\t-\t.\tParent=CG32464-RB\n+3R\tMB7\tstop_codon\t1099669\t1099671\t0\t-\t0\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1099669\t1099804\t0\t-\t1\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1099871\t1100040\t0\t-\t0\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1100457\t1100616\t0\t-\t1\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1100688\t1100809\t0\t-\t0\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1118362\t1118563\t0\t-\t1\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1118720\t1118882\t0\t-\t2\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1118941\t1119092\t0\t-\t1\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1119784\t1119956\t0\t-\t0\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1120028\t1120577\t0\t-\t1\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1121363\t1121517\t0\t-\t0\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1121579\t1121685\t0\t-\t2\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1121869\t1122357\t0\t-\t2\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1123924\t1124211\t0\t-\t2\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1125192\t1125295\t0\t-\t1\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1129833\t1129904\t0\t-\t1\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1138711\t1139219\t0\t-\t0\tParent=CG32464-RB\n+3R\tMB7\tCDS\t1139660\t1139920\t0\t-\t0\tParent=CG32464-RB\n+3R\tMB7\tstart_codon\t1139918\t1139920\t0\t-\t0\tParent=CG32464-RB\n+3R\tMB7\tfive_prime_UTR\t1139921\t1140027\t0\t-\t.\tParent=CG32464-RB\n+3R\tMB7\tfive_prime_UTR\t1148710\t1148847\t0\t-\t.\tParent=CG32464-RB\n+3R\tMB7\tfive_prime_UTR\t1149387\t1149566\t0\t-\t.\tParent=CG32464-RB\n+3R\tMB7\tmRNA\t1098665\t1149566\t3\t-\t.\tID=CG32464-RU;Parent=CG32464;Name=CG32464-RU\n+3R\tMB7\texon\t1098665\t1099804\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1099871\t1100040\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1100457\t1100616\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1100688\t1100809\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1118362\t1118563\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1118720\t1118882\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1118941\t1119092\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1119784\t1119956\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1120028\t1120577\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1121363\t1121517\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1121579\t1121685\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1121869\t1122357\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1123924\t1124211\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1125192\t1125295\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1138711\t1139219\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1139660\t1140027\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1148710\t1148847\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\texon\t1149387\t1149566\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\tthree_prime_UTR\t1098665\t1099668\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\tstop_codon\t1099669\t1099671\t0\t-\t0\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1099669\t1099804\t0\t-\t1\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1099871\t1100040\t0\t-\t0\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1100457\t1100616\t0\t-\t1\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1100688\t1100809\t0\t-\t0\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1118362\t1118563\t0\t-\t1\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1118720\t1118882\t0\t-\t2\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1118941\t1119092\t0\t-\t1\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1119784\t1119956\t0\t-\t0\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1120028\t1120577\t0\t-\t1\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1121363\t1121517\t0\t-\t0\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1121579\t1121685\t0\t-\t2\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1121869\t1122357\t0\t-\t2\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1123924\t1124211\t0\t-\t2\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1125192\t1125295\t0\t-\t1\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1138711\t1139219\t0\t-\t0\tParent=CG32464-RU\n+3R\tMB7\tCDS\t1139660\t1139920\t0\t-\t0\tParent=CG32464-RU\n+3R\tMB7\tstart_codon\t1139918\t1139920\t0\t-\t0\tParent=CG32464-RU\n+3R\tMB7\tfive_prime_UTR\t1139921\t1140027\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\tfive_prime_UTR\t1148710\t1148847\t0\t-\t.\tParent=CG32464-RU\n+3R\tMB7\tfive_prime_UTR\t1149387\t1149566\t0\t-\t.\tParent=CG32464-RU\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/UCSC_transcripts.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/UCSC_transcripts.gff3 Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,129 @@\n+##gff-version 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tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\tCDS\t879078\t879188\t.\t+\t0\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\tCDS\t879288\t879533\t.\t+\t0\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t861322\t861393\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t865535\t865716\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t866419\t866469\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t871152\t871276\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t874420\t874509\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t874655\t874840\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t876524\t876686\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t877516\t877631\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t877790\t877868\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t877939\t878438\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t878633\t878757\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t879078\t879188\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\texon\t879288\t879533\t.\t+\t.\tParent=Transcript:CCDS2.2\n+chr1\thg19_ccdsGene\tgene\t901912\t909955\t.\t+\t.\tID=Gene:CCDS4.1;Name=Gene:CCDS4.1\n+chr1\thg19_ccdsGene\tmRNA\t901912\t909955\t0.000000\t+\t.\tID=Transcript:CCDS4.1;Parent=Gene:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t901912\t901994\t.\t+\t0\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t902084\t902183\t.\t+\t1\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t905657\t905803\t.\t+\t0\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t905901\t905981\t.\t+\t0\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t906066\t906138\t.\t+\t0\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t906259\t906386\t.\t+\t2\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t906493\t906588\t.\t+\t0\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t906704\t906784\t.\t+\t0\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t907455\t907530\t.\t+\t0\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t907668\t907804\t.\t+\t2\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t908241\t908390\t.\t+\t0\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t908566\t908706\t.\t+\t0\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t908880\t909020\t.\t+\t0\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t909213\t909431\t.\t+\t0\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t909696\t909744\t.\t+\t0\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\tCDS\t909822\t909955\t.\t+\t2\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t901912\t901994\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t902084\t902183\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t905657\t905803\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t905901\t905981\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t906066\t906138\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t906259\t906386\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t906493\t906588\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t906704\t906784\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t907455\t907530\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t907668\t907804\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t908241\t908390\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t908566\t908706\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t908880\t909020\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t909213\t909431\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t909696\t909744\t.\t+\t.\tParent=Transcript:CCDS4.1\n+chr1\thg19_ccdsGene\texon\t909822\t909955\t.\t+\t.\tParent=Transcript:CCDS4.1\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/UCSC_transcripts.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/UCSC_transcripts.gtf Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,129 @@\n+chr1\thg19_ccdsGene\tstart_codon\t861322\t861324\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t861322\t861393\t0.000000\t+\t0\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t861322\t861393\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t865535\t865716\t0.000000\t+\t0\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t865535\t865716\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t866419\t866469\t0.000000\t+\t1\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t866419\t866469\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t871152\t871276\t0.000000\t+\t1\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t871152\t871276\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t874420\t874509\t0.000000\t+\t2\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t874420\t874509\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t874655\t874840\t0.000000\t+\t2\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t874655\t874840\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t876524\t876686\t0.000000\t+\t2\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t876524\t876686\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t877516\t877631\t0.000000\t+\t1\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t877516\t877631\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t877790\t877868\t0.000000\t+\t2\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t877790\t877868\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t877939\t878438\t0.000000\t+\t1\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t877939\t878438\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t878633\t878757\t0.000000\t+\t2\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t878633\t878757\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t879078\t879188\t0.000000\t+\t0\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t879078\t879188\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tCDS\t879288\t879530\t0.000000\t+\t0\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tstop_codon\t879531\t879533\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\texon\t879288\t879533\t0.000000\t+\t.\tgene_id "CCDS2.2"; transcript_id "CCDS2.2"; \n+chr1\thg19_ccdsGene\tstop_codon\t880074\t880076\t0.000000\t-\t.\tgene_id "CCDS3.1"; transcript_id "CCDS3.1"; \n+chr1\thg19_ccdsGene\tCDS\t880077\t880180\t0.000000\t-\t2\tgene_id "CCDS3.1"; 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\n+chr1\thg19_ccdsGene\tCDS\t901912\t901994\t0.000000\t+\t0\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t901912\t901994\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t902084\t902183\t0.000000\t+\t1\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t902084\t902183\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t905657\t905803\t0.000000\t+\t0\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t905657\t905803\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t905901\t905981\t0.000000\t+\t0\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t905901\t905981\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t906066\t906138\t0.000000\t+\t0\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t906066\t906138\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t906259\t906386\t0.000000\t+\t2\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t906259\t906386\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t906493\t906588\t0.000000\t+\t0\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t906493\t906588\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t906704\t906784\t0.000000\t+\t0\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t906704\t906784\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t907455\t907530\t0.000000\t+\t0\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t907455\t907530\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t907668\t907804\t0.000000\t+\t2\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t907668\t907804\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t908241\t908390\t0.000000\t+\t0\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t908241\t908390\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t908566\t908706\t0.000000\t+\t0\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t908566\t908706\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t908880\t909020\t0.000000\t+\t0\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t908880\t909020\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t909213\t909431\t0.000000\t+\t0\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t909213\t909431\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t909696\t909744\t0.000000\t+\t0\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t909696\t909744\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tCDS\t909822\t909952\t0.000000\t+\t2\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\tstop_codon\t909953\t909955\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+chr1\thg19_ccdsGene\texon\t909822\t909955\t0.000000\t+\t.\tgene_id "CCDS4.1"; transcript_id "CCDS4.1"; \n+\n' |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/ccds_genes.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/ccds_genes.bed Tue Jun 07 17:26:20 2011 -0400 |
| b |
| @@ -0,0 +1,20 @@ +chr1 92149295 92327088 CCDS30770.1 0 - 92149295 92327088 0 16 119,108,42,121,300,159,141,153,338,190,148,169,184,138,185,61, 0,11933,14350,24924,28504,32497,32829,35573,36154,38216,43920,46066,51037,74874,113548,177732, +chr1 67000041 67208778 CCDS30744.1 0 + 67000041 67208778 0 25 10,64,25,72,57,55,176,12,12,25,52,86,93,75,501,128,127,60,112,156,133,203,65,165,23, 0,91488,98711,101585,105418,108451,109185,126154,133171,136636,137585,138922,142645,145319,147510,154789,155831,161075,184935,194905,199389,204976,206299,206913,208714, +chr1 8384389 8404073 CCDS30577.1 0 + 8384389 8404073 0 8 397,93,225,728,154,177,206,267, 0,968,1488,5879,11107,13486,15163,19417, +chr1 16767256 16785385 CCDS44067.1 0 + 16767256 16785385 0 8 14,101,105,82,109,178,76,49, 0,2870,7108,7298,8331,11076,15056,18080, +chr1 16767256 16785491 CCDS44066.1 0 + 16767256 16785491 0 7 92,101,105,82,109,178,155, 0,2870,7108,7298,8331,11076,18080, +chr1 16767256 16785385 CCDS173.1 0 + 16767256 16785385 0 8 92,101,105,82,109,178,76,49, 0,2870,7108,7298,8331,11076,15056,18080, +chr1 25072044 25167428 CCDS256.1 0 + 25072044 25167428 0 6 72,110,126,107,182,165, 0,52188,68540,81456,94306,95219, +chr1 33547850 33585783 CCDS375.1 0 + 33547850 33585783 0 9 105,174,173,135,166,163,113,215,139, 0,1704,9800,11032,12298,14457,15817,35652,37794, +chr1 48999844 50489468 CCDS44137.1 0 - 48999844 50489468 0 14 121,27,97,163,153,112,115,90,40,217,95,125,123,34, 0,717,5469,52831,56660,100320,119164,128979,333018,511411,711597,1163140,1317223,1489590, +chr1 100661810 100715376 CCDS767.1 0 - 100661810 100715376 0 11 168,72,192,78,167,217,122,182,76,124,51, 0,9975,10190,14439,18562,19728,22371,34478,39181,44506,53515, +chr1 150981108 151006710 CCDS977.1 0 + 150981108 151006710 0 8 39,93,203,185,159,95,159,429, 0,9179,9834,15978,16882,18600,20153,25173, +chr1 175914288 176176114 CCDS44279.1 0 - 175914288 176176114 0 19 18,45,161,125,118,117,82,109,144,136,115,58,77,69,120,65,98,60,407, 0,2042,41790,43135,44209,82419,98033,98557,101028,135999,140623,171471,189857,203853,217716,218674,230757,239480,261419, +chr1 175914288 176176114 CCDS30944.1 0 - 175914288 176176114 0 20 18,45,161,125,118,117,82,109,144,136,115,58,77,60,69,120,77,98,60,407, 0,2042,41790,43135,44209,82419,98033,98557,101028,135999,140623,171471,189857,191335,203853,217716,218662,230757,239480,261419, +chr1 184446643 184588690 CCDS1362.1 0 + 184446643 184588690 0 5 94,95,77,61,39, 0,30078,113229,120891,142008, +chr1 226420201 226496888 CCDS1553.1 0 - 226420201 226496888 0 15 106,98,180,126,81,102,120,134,158,126,134,105,95,33,79, 0,595,843,6470,18338,33032,33712,35456,45274,53832,55163,63341,65218,68672,76608, +chr1 1982069 2116448 CCDS37.1 0 + 1982069 2116448 0 18 71,122,90,51,86,132,82,53,189,98,87,136,88,120,80,90,116,88, 0,4810,5853,8910,84631,93579,95396,98241,100159,105364,118887,121424,121670,123266,124123,124593,133952,134291, +chr1 2075777 2116448 CCDS41229.1 0 + 2075777 2116448 0 13 3,82,53,189,98,87,136,88,120,80,90,116,88, 0,1688,4533,6451,11656,25179,27716,27962,29558,30415,30885,40244,40583, +chr1 2985823 3350375 CCDS44048.1 0 + 2985823 3350375 0 17 37,350,51,135,103,208,148,154,1417,85,170,78,170,175,237,175,78, 0,116865,174827,315892,327231,333531,335479,336235,342124,345303,348568,349407,356321,356791,361612,362706,364474, +chr1 2985823 3350375 CCDS41236.1 0 + 2985823 3350375 0 17 37,350,51,135,103,208,148,154,1417,85,170,78,170,175,237,175,135, 0,116865,174827,315892,327231,333531,335479,336235,342124,345303,348568,349407,356321,356791,361612,362706,364417, +chr1 6285139 6295971 CCDS61.1 0 - 6285139 6295971 0 5 183,218,170,89,195, 0,6822,8394,9806,10637, |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/ccds_genes.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/ccds_genes.gff3 Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,290 @@\n+##gff-version 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|
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/hs_2009.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/hs_2009.bed Tue Jun 07 17:26:20 2011 -0400 |
| b |
| @@ -0,0 +1,58 @@ +chr1 11873 14409 uc001aaa.3 0 + 11873 11873 0 3 354,109,1189, 0,739,1347, +chr1 11873 14409 uc010nxq.1 0 + 12189 13639 0 3 354,127,1007, 0,721,1529, +chr1 11873 14409 uc010nxr.1 0 + 11873 11873 0 3 354,52,1189, 0,772,1347, +chr1 14362 16765 uc009vis.2 0 - 14362 14362 0 4 467,69,147,159, 0,607,1433,2244, +chr1 16857 17751 uc009vjc.1 0 - 16857 16857 0 2 198,519, 0,375, +chr1 15795 18061 uc009vjd.2 0 - 15795 15795 0 5 152,159,198,136,456, 0,811,1062,1437,1810, +chr1 14362 19759 uc009vit.2 0 - 14362 14362 0 9 467,69,152,159,198,510,147,99,847, 0,607,1433,2244,2495,2870,3552,3905,4550, +chr1 14362 19759 uc001aae.3 0 - 14362 14362 0 10 467,69,152,159,198,136,137,147,99,847, 0,607,1433,2244,2495,2870,3243,3552,3905,4550, +chr1 14362 19759 uc009viu.2 0 - 14362 14362 0 10 467,69,152,159,198,510,147,102,54,847, 0,607,1433,2244,2495,2870,3552,3905,4138,4550, +chr1 16857 19759 uc001aai.1 0 - 16857 16857 0 6 198,136,137,147,112,847, 0,375,748,1057,1410,2055, +chr1 14362 24901 uc001aab.3 0 - 14362 14362 0 10 467,69,152,159,202,136,137,147,112,164, 0,607,1433,2244,2491,2870,3243,3552,3905,10375, +chr1 14362 29370 uc001aah.3 0 - 14362 14362 0 11 467,69,152,159,198,136,137,147,99,154,50, 0,607,1433,2244,2495,2870,3243,3552,3905,10375,14958, +chr1 14362 29370 uc009vir.2 0 - 14362 14362 0 10 467,69,152,159,198,510,147,99,154,50, 0,607,1433,2244,2495,2870,3552,3905,10375,14958, +chr1 14362 29370 uc009viq.2 0 - 14362 14362 0 7 467,152,159,198,456,154,50, 0,1433,2244,2495,3243,10375,14958, +chr1 14362 29370 uc001aac.3 0 - 14362 14362 0 11 467,69,152,159,198,110,137,147,102,154,50, 0,607,1433,2244,2495,2896,3243,3552,3905,10375,14958, +chr1 14406 29370 uc009viv.2 0 - 14406 14406 0 7 2359,198,136,137,147,154,50, 0,2451,2826,3199,3508,10331,14914, +chr1 14406 29370 uc009viw.2 0 - 14406 14406 0 7 2359,198,510,147,99,154,50, 0,2451,2826,3508,3861,10331,14914, +chr1 15602 29370 uc009vix.2 0 - 15602 15602 0 7 345,159,198,136,147,154,50, 0,1004,1255,1630,2312,9135,13718, +chr1 16606 29370 uc009viz.2 0 - 16606 16606 0 8 159,202,136,137,147,112,154,50, 0,247,626,999,1308,1661,8131,12714, +chr1 16606 29370 uc009viy.2 0 - 16606 16606 0 9 159,198,136,137,147,95,58,154,50, 0,251,626,999,1308,1661,1890,8131,12714, +chr1 16857 29370 uc010nxs.1 0 - 16857 16857 0 8 198,136,137,147,99,227,154,50, 0,375,748,1057,1410,2055,7880,12463, +chr1 17232 29370 uc009vje.2 0 - 17232 17232 0 4 510,147,99,50, 0,682,1035,12088, +chr1 17605 29370 uc009vjf.2 0 - 17605 17605 0 7 137,147,95,58,227,154,50, 0,309,662,891,1307,7132,11715, +chr1 16857 29961 uc009vjb.1 0 - 16857 16857 0 7 198,136,137,147,112,154,138, 0,375,748,1057,1410,7880,12966, +chr1 34611 36081 uc001aak.2 0 - 34611 34611 0 3 563,205,361, 0,665,1109, +chr1 69090 70008 uc001aal.1 0 + 69090 70008 0 1 918, 0, +chr1 137838 139228 uc001aam.3 0 - 137838 137838 0 1 1390, 0, +chr1 89294 237877 uc010nxt.1 0 - 89294 89294 0 2 1110,1263, 0,147320, +chr1 321083 321114 uc001aaq.1 0 + 321083 321083 0 1 31, 0, +chr1 321145 321223 uc001aar.1 0 + 321145 321145 0 1 78, 0, +chr1 322036 326938 uc009vjk.2 0 + 324342 325605 0 3 192,58,2500, 0,2251,2402, +chr1 323891 328580 uc001aav.3 0 + 323891 323891 0 4 169,58,2500,1545, 0,396,547,3144, +chr1 323891 328580 uc001aau.2 0 + 324342 325605 0 3 169,58,4142, 0,396,547, +chr1 367658 368595 uc010nxu.1 0 + 367658 368594 0 1 937, 0, +chr1 420205 421839 uc001aax.1 0 + 420205 420205 0 3 91,267,444, 0,786,1190, +chr1 566461 568045 uc001aaz.2 0 + 566461 566461 0 1 1584, 0, +chr1 568148 568842 uc001aba.1 0 + 568148 568148 0 1 694, 0, +chr1 568843 568912 uc001abb.2 0 + 568843 568843 0 1 69, 0, +chr1 569326 570349 uc001abc.2 0 + 569326 569326 0 1 1023, 0, +chr1 621097 622034 uc010nxv.1 0 - 621098 622034 0 1 937, 0, +chr1 661139 665731 uc001abe.3 0 - 664484 665108 0 3 4045,58,169, 0,4138,4423, +chr1 668401 668479 uc001abi.1 0 - 668401 668401 0 1 78, 0, +chr1 668510 668541 uc001abj.2 0 - 668510 668510 0 1 31, 0, +chr1 661139 670994 uc009vjm.2 0 - 664484 665108 0 3 4045,58,192, 0,7547,9663, +chr1 671807 671885 uc010nxw.1 0 - 671807 671807 0 1 78, 0, +chr1 671916 671947 uc001abl.2 0 - 671916 671916 0 1 31, 0, +chr1 661139 679736 uc002khh.2 0 - 661139 661139 0 7 4045,58,191,233,58,65,162, 0,4138,6257,14043,14369,17526,18435, +chr1 674239 679736 uc001abm.2 0 - 674239 674239 0 5 165,233,58,65,162, 0,943,1269,4426,5335, +chr1 700236 714006 uc001abo.2 0 - 700236 700236 0 7 391,59,66,216,132,110,343, 0,1472,3691,4640,8119,9314,13427, +chr1 761586 762902 uc010nxx.1 0 - 762079 762571 0 1 1316, 0, +chr1 763063 788902 uc009vjn.1 0 + 763063 763063 0 4 92,102,184,132, 0,1319,24243,25707, +chr1 763063 788997 uc001abp.1 0 + 763063 763063 0 6 92,102,153,184,96,227, 0,1319,19970,24243,24987,25707, +chr1 763063 788997 uc001abq.1 0 + 763063 763063 0 5 92,102,184,96,227, 0,1319,24243,24987,25707, +chr1 763063 788997 uc009vjo.1 0 + 763063 763063 0 4 92,102,96,227, 0,1319,24987,25707, +chr1 763063 789740 uc001abr.1 0 + 763063 763063 0 7 92,102,153,184,96,132,784, 0,1319,19970,24243,24987,25707,25893, +chr1 791897 794579 uc001abs.2 0 + 791897 791897 0 1 2682, 0, +chr1 803452 812182 uc001abt.3 0 - 803452 803452 0 3 603,1044,57, 0,6039,8673, +chr1 846814 850328 uc001abu.1 0 + 846814 846814 0 2 39,3004, 0,510, |
| b |
| diff -r 000000000000 -r ed53dca1c6ff fml_gff_converter_programs/t/hs_2009.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_converter_programs/t/hs_2009.gff3 Tue Jun 07 17:26:20 2011 -0400 |
| b |
| b'@@ -0,0 +1,375 @@\n+##gff-version 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|