├── .gitignore ├── LICENSE ├── README.md ├── biology └── bio_plasmid_get_insert.pl ├── blast ├── auto_blast ├── auto_makeblastdb ├── blast_best_hit.py ├── blast_best_hit_outfmt6.py └── fasta_rename_head_before_blast.pl ├── enzyme ├── embossre.enz ├── enzs.list ├── restrict_check_digested_sequence_number.pl ├── restrict_choose_enzyme_for_identify_genomes.pl ├── restrict_with_T_tail.pl ├── restrict_with_far_away_digest_site.pl └── restrict_without_digest_site_in_sequences.pl ├── file_formats ├── add_annotations_to_myva.pl ├── bam2gff.py ├── extract_cds_from_glimmer_predict_result.pl ├── extract_features_from_genbank_file.py ├── extract_sequence_from_genbank_file.pl ├── genbank_filter.py ├── gff2fa.py ├── gff_frame_start_coverage.plot.R ├── gff_frame_start_coverage.py └── gff_intersect.py ├── for_education ├── Parsing grouped data in multi-line.pl ├── extract_cds_by_gff.pl ├── fasta_common_seqs2.pl ├── fasta_extract_sequence_by_id_file.pl ├── join_table.pl └── simple_statistics.pl ├── not_used ├── csv2tab ├── csv_join ├── csv_join_paired_lines.py ├── csv_split_paired_lines.py ├── fasta_seq_gc_content_plot.py └── fasta_seq_length_plot.py ├── plot ├── README.md ├── example │ ├── data.tsv │ ├── data.tsv.dist.png │ ├── data.txt.png │ ├── heatmap.png │ └── plot_barplot.png ├── plot_distribution.R └── plot_distribution.py ├── protein └── protein_batch_compute_pI.pl ├── sequence ├── README.md ├── fasta2tab ├── fasta_common_seqs.pl ├── fasta_extract_by_pattern.pl ├── fasta_extract_randomly.pl ├── fasta_gc_skew.plot.R ├── fasta_gc_skew.py ├── fasta_locate_motif.pl ├── fasta_remove_duplicates.pl ├── fasta_rename_duplicated_names.pl ├── fasta_reset_start_position_for_circular_genome.pl ├── fasta_sliding_window.pl ├── fasta_trim_aligned_fasta.pl ├── fastq2tab ├── fastq_extract_paired_reads.pl ├── fastx_mapping_with_bwa.pl ├── fastx_pwm.py ├── fastx_tm.py ├── fastx_translate.py ├── run_clustalo.pl ├── sample │ ├── gc_skew.png │ ├── seq.fa │ └── seq.fq.gz ├── seqcomp ├── seqrc ├── seqrev ├── tab2fasta └── tab2fastq ├── taxon └── taxon_fetch.py └── util └── unzipGBK /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shenwei356/bio_scripts/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shenwei356/bio_scripts/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shenwei356/bio_scripts/HEAD/README.md -------------------------------------------------------------------------------- /biology/bio_plasmid_get_insert.pl: -------------------------------------------------------------------------------- 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