Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
R		R
0入口.py		0入口.py
210_mafft.py		210_mafft.py
210_mafft_2.py		210_mafft_2.py
210_mafft_ortholog.py		210_mafft_ortholog.py
CD_HIT.py		CD_HIT.py
Directory_creater.py		Directory_creater.py
OrthoFinder.py		OrthoFinder.py
OrthoFinder_extract_sequence_from_Orthogroups.py		OrthoFinder_extract_sequence_from_Orthogroups.py
README.md		README.md
alignment_call_snp_HaplotypeCaller.py		alignment_call_snp_HaplotypeCaller.py
alignment_call_snp_mummer.py		alignment_call_snp_mummer.py
alignment_extract_fst_prepare_contig_length.py		alignment_extract_fst_prepare_contig_length.py
alignment_extract_orthologs.py		alignment_extract_orthologs.py
alignment_extract_orthologs_2.py		alignment_extract_orthologs_2.py
alignment_extract_orthologs_mafft.py		alignment_extract_orthologs_mafft.py
alignment_extract_orthologs_mafft_slop.py		alignment_extract_orthologs_mafft_slop.py
alignment_extract_orthologs_mafft_slop_2.py		alignment_extract_orthologs_mafft_slop_2.py
alignment_extract_orthologs_mafft_slop_2_210.py		alignment_extract_orthologs_mafft_slop_2_210.py
alignment_extract_orthologs_mafft_slop_2_filter.py		alignment_extract_orthologs_mafft_slop_2_filter.py
alignment_extract_orthologs_mafft_slop_2_filter_210.py		alignment_extract_orthologs_mafft_slop_2_filter_210.py
alignment_extract_orthologs_mafft_slop_2_filter_210_2.py		alignment_extract_orthologs_mafft_slop_2_filter_210_2.py
alignment_extract_orthologs_mafft_slop_mgg_key.py		alignment_extract_orthologs_mafft_slop_mgg_key.py
alignment_extract_orthologs_mafft_slop_mgg_key_210.py		alignment_extract_orthologs_mafft_slop_mgg_key_210.py
annotation_eggnog_cog.py		annotation_eggnog_cog.py
annotation_eggnog_cog_2.py		annotation_eggnog_cog_2.py
annotation_interpro.py		annotation_interpro.py
annotation_interpro_147.py		annotation_interpro_147.py
annotation_interproscan_go_pfam.py		annotation_interproscan_go_pfam.py
annotation_interproscan_go_pfam_2.py		annotation_interproscan_go_pfam_2.py
annotation_kegg_id.py		annotation_kegg_id.py
annotation_kegg_id_2.py		annotation_kegg_id_2.py
annotation_secreted_proteins.py		annotation_secreted_proteins.py
annotation_secreted_proteins_2.py		annotation_secreted_proteins_2.py
annotation_secreted_proteins_2_rice_division.py		annotation_secreted_proteins_2_rice_division.py
blast_70_15_mgg_Augustus.py		blast_70_15_mgg_Augustus.py
calculate_dnds.py		calculate_dnds.py
calculate_dnds_2.py		calculate_dnds_2.py
clade_color.py		clade_color.py
clade_color_5clade.py		clade_color_5clade.py
clade_different_secreted_protein.py		clade_different_secreted_protein.py
cluster.py		cluster.py
cluster_orthofinder.py		cluster_orthofinder.py
cluster_orthofinder_5clade.py		cluster_orthofinder_5clade.py
cluster_orthofinder_5clade_blastn.py		cluster_orthofinder_5clade_blastn.py
compare_zhong.py		compare_zhong.py
copy_contig.py		copy_contig.py
copy_for_protein.py		copy_for_protein.py
enrichment_clade_different_eggnog_cog.py		enrichment_clade_different_eggnog_cog.py
enrichment_clade_different_interproscan_go_pfam.py		enrichment_clade_different_interproscan_go_pfam.py
enrichment_clade_different_kegg.py		enrichment_clade_different_kegg.py
extract_nucleic.py		extract_nucleic.py
extract_nucleic_2.py		extract_nucleic_2.py
extract_sequence_from_Orthogroups.py		extract_sequence_from_Orthogroups.py
extract_strain_id.py		extract_strain_id.py
fgenesh_GFF.py		fgenesh_GFF.py
fgenesh_gff_to_targer_dir.py		fgenesh_gff_to_targer_dir.py
fgenesh_result_to_fasta.py		fgenesh_result_to_fasta.py
fgenesh_result_to_fasta_2.py		fgenesh_result_to_fasta_2.py
fgenesh_result_to_fasta_3.py		fgenesh_result_to_fasta_3.py
fgenesh_result_to_fasta_4.py		fgenesh_result_to_fasta_4.py
fgenesh_result_to_fasta_5.py		fgenesh_result_to_fasta_5.py
fgenesh_result_to_fasta_pro.py		fgenesh_result_to_fasta_pro.py
fgenesh_result_to_fasta_vertify.py		fgenesh_result_to_fasta_vertify.py
filter_too_small_sequence.py		filter_too_small_sequence.py
general.py		general.py
linsdu.py		linsdu.py
mafft.py		mafft.py
mafft_gene.py		mafft_gene.py
mafft_gene_理解并行计算.py		mafft_gene_理解并行计算.py
nucleotide_diversity.py		nucleotide_diversity.py
pav.py		pav.py
pav_R_part.py		pav_R_part.py
pav_R_part_2.py		pav_R_part_2.py
pav_R_part_2_blastn.py		pav_R_part_2_blastn.py
pav_contig_present.py		pav_contig_present.py
pav_contig_present_for_pan_data_2.py		pav_contig_present_for_pan_data_2.py
pav_contig_present_for_pan_data_2_blast_gth.py		pav_contig_present_for_pan_data_2_blast_gth.py
pav_contig_present_for_pan_data_2_blast_only.py		pav_contig_present_for_pan_data_2_blast_only.py
qc_contig_by_busco.py		qc_contig_by_busco.py
qc_contig_read_busco.py		qc_contig_read_busco.py
set_minus.py		set_minus.py
set_minus_cut.py		set_minus_cut.py
set_minus_orthofinder.py		set_minus_orthofinder.py
set_minus_with_cluster.py		set_minus_with_cluster.py
slow_sub_2.py		slow_sub_2.py
test.py		test.py
test2.py		test2.py
test_gffutil.py		test_gffutil.py
test_gffutil_for_update.py		test_gffutil_for_update.py
test_gffutils.py		test_gffutils.py
test_orthofinder.py		test_orthofinder.py
test_segmentUnionLength.py		test_segmentUnionLength.py
trim_N.py		trim_N.py
uniformize_gene_to_protein.py		uniformize_gene_to_protein.py
upset.py		upset.py
zhe-mummer-2-vcf.py		zhe-mummer-2-vcf.py
zhe_MUMmerSNPs2VCF.py		zhe_MUMmerSNPs2VCF.py

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RiceBlastPanGenome

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入口文件是 0入口.py，其他py文件作为函数在 0入口.py 中被调用。
R文件夹中的R脚本嵌入在需要调用它的python脚本中，使用python包rpy2调用。

WangZhe-1/RiceBlastPanGenome

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