README.rst
setup.cfg
setup.py
bin/gtftk
docs/Makefile
docs/__init__.py
docs/source/#H3K4me3_cond_1.bed#
docs/source/ENCFF112BHN_H3K4me3_K562_sub.bed
docs/source/ENCFF112BHN_H3K4me3_K562_tiny.bed
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docs/source/ENCFF431HAA_H3K36me3_K562_sub.bw
docs/source/ENCFF742FDS_H3K4me3_K562_sub.bw
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docs/source/H3K4me3_cond_1.bed
docs/source/H3K4me3_cond_2.bed
docs/source/H3K4me3_cond_3.bed
docs/source/about.rst
docs/source/add_attr_to_pos.tab
docs/source/airway_love.txt.gz
docs/source/annotation.rst
docs/source/api.rst
docs/source/bwig_coverage.rst
docs/source/conf.py
docs/source/conversion.rst
docs/source/coordinates.rst
docs/source/coverage.bed
docs/source/coverage.rst
docs/source/developers.rst
docs/source/editing.rst
docs/source/example_01.png
docs/source/example_01b.png
docs/source/example_02.png
docs/source/example_05.png
docs/source/example_06.png
docs/source/example_06b.png
docs/source/example_07.png
docs/source/example_08.png
docs/source/example_13.png
docs/source/example_pa_01.pdf
docs/source/example_pa_02.pdf
docs/source/example_pa_03.pdf
docs/source/example_pa_04.pdf
docs/source/gtftk_args.rst
docs/source/hg38.genome
docs/source/hg38.genome.back
docs/source/index.rst
docs/source/information.rst
docs/source/installation.rst
docs/source/mini_real.gtf.gz
docs/source/mini_real_coding_pot.tab
docs/source/mini_real_control_1.txt
docs/source/mini_real_counts_ENCFF630HEX.tsv
docs/source/mini_real_gn_list_hg38.txt
docs/source/mini_real_noov_rnd_tx.gtf.gz
docs/source/mini_real_promoter.zip
docs/source/mini_real_tx.zip
docs/source/miscellaneous.rst
docs/source/selection.rst
docs/source/sequence.rst
docs/source/simple.1.bt2
docs/source/simple.2.bt2
docs/source/simple.2.bw
docs/source/simple.3.bt2
docs/source/simple.3.bw
docs/source/simple.4.bt2
docs/source/simple.bam
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docs/source/simple.fa
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docs/source/simple.geneList
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docs/source/simple.gtf
docs/source/simple.join
docs/source/simple.join_mat
docs/source/simple.join_mat_2
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pygtftk/Line.py
pygtftk/__init__.py
pygtftk/arg_formatter.py
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pygtftk/biomart.py
pygtftk/cmd_manager.py
pygtftk/cmd_object.py
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pygtftk/data/simple/__init__.py
pygtftk/data/simple/add_attr_to_pos.tab
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pygtftk/data/simple_02/simple_02.gtf
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pygtftk/data/simple_02/simple_02.join_mat
pygtftk/data/simple_02/simple_02.map
pygtftk/data/simple_02/simple_02.reads.fq
pygtftk/data/simple_02/simple_02.rev.1.bt2
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pygtftk/data/simple_02/simple_02_nbe.gtf
pygtftk/data/simple_02/simple_02_nbe.gtf.old
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pygtftk/data/simple_03/__init__.py
pygtftk/data/simple_03/simple_short_long.gtf
pygtftk/data/simple_04/__init__.py
pygtftk/data/simple_04/simple.chromInfo
pygtftk/data/simple_04/simple_04.fa
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pygtftk/data/simple_05/__init__.py
pygtftk/data/simple_05/simple_rm.gtf
pygtftk/data/simple_06/simple_06.gtf
pygtftk/data/tiny_real/ENCFF112BHN_H3K4me3_K562_tiny.bed
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pygtftk/data/tiny_real/__init__.py
pygtftk/data/tiny_real/airway_love.txt.gz
pygtftk/data/tiny_real/hg38.genome
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pygtftk/data/tiny_real/mini_real_control_1.txt
pygtftk/data/tiny_real/mini_real_counts_ENCFF630HEX.tsv
pygtftk/data/tiny_real/mini_real_gn_list_hg38.txt
pygtftk/data/tiny_real/tiny_real.gtf.gz
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pygtftk/plugins/add_exon_nb.py
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pygtftk/plugins/seqid_list.py
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pygtftk/rtools/__init__.py
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pygtftk/src/__init__.py
pygtftk/src/libgtftk/README.md
pygtftk/src/libgtftk/__init__.py
pygtftk/src/libgtftk/blast_reader.c
pygtftk/src/libgtftk/column.c
pygtftk/src/libgtftk/config.h
pygtftk/src/libgtftk/globals.c
pygtftk/src/libgtftk/gtf_reader.c
pygtftk/src/libgtftk/libgtftk.c
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pygtftk/src/libgtftk/command/__init__.py
pygtftk/src/libgtftk/command/add_attr_column.c
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pygtftk/src/libgtftk/command/add_attributes.c
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pygtftk/src/libgtftk/command/add_prefix.c
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pygtftk/src/libgtftk/command/del_attributes.c
pygtftk/src/libgtftk/command/extract_data.c
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pygtftk/src/libgtftk/command/free_raw_data.c
pygtftk/src/libgtftk/command/get_list.c
pygtftk/src/libgtftk/command/get_sequences.c
pygtftk/src/libgtftk/command/get_type.c
pygtftk/src/libgtftk/command/load_blast.c
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pygtftk/src/libgtftk/command/print_bed.c
pygtftk/src/libgtftk/command/select_by_genomic_location.c
pygtftk/src/libgtftk/command/select_by_key.c
pygtftk/src/libgtftk/command/select_by_number_of_exon.c
pygtftk/src/libgtftk/command/select_by_positions.c
pygtftk/src/libgtftk/command/select_by_transcript_size.c
pygtftk/src/libgtftk/command/select_transcript.c
pygtftk/stats/intersect/__init__.py
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