]> git.donarmstrong.com Git - biopieces.git/tree - bp_bin/
added .biopiecesrc
[biopieces.git] / bp_bin /
drwxr-xr-x   ..
-rw-r--r-- 88 00README
-rwxr-xr-x 2373 add_ident
-rwxr-xr-x 2600 align_pair_seq
-rwxr-xr-x 2645 align_seq
-rwxr-xr-x 2011 analyze_bed
-rwxr-xr-x 3942 analyze_seq
-rwxr-xr-x 2794 analyze_tags
-rwxr-xr-x 5079 analyze_vals
-rwxr-xr-x 3318 assemble_tag_contigs
-rwxr-xr-x 2200 bioscript
-rwxr-xr-x 5812 biostat
-rwxr-xr-x 8049 blast_seq
-rwxr-xr-x 5039 blat_seq
-rwxr-xr-x 6288 bowtie_seq
-rwxr-xr-x 2809 calc_bit_scores
-rwxr-xr-x 3444 calc_fixedstep
-rwxr-xr-x 2281 complement_seq
-rwxr-xr-x 2708 compute
-rwxr-xr-x 2640 count_records
-rwxr-xr-x 3549 count_vals
-rwxr-xr-x 2896 create_blast_db
-rwxr-xr-x 3087 create_bowtie_index
-rwxr-xr-x 3157 create_vmatch_index
-rwxr-xr-x 2899 create_weight_matrix
-rwxr-xr-x 3644 extract_seq
-rwxr-xr-x 2399 flip_tab
-rwxr-xr-x 2505 fold_seq
-rwxr-xr-x 5319 format_genome
-rwxr-xr-x 6184 get_genome_align
-rwxr-xr-x 5156 get_genome_phastcons
-rwxr-xr-x 8263 get_genome_seq
-rwxr-xr-x 9081 grab
-rwxr-xr-x 2148 head_records
-rwxr-xr-x 3386 indel_seq
-rwxr-xr-x 2542 invert_align
-rwxr-xr-x 2498 length_seq
-rwxr-xr-x 2254 length_vals
-rwxr-xr-x 2004 list_biopieces
-rwxr-xr-x 2425 list_genomes
-rwxr-xr-x 2217 list_mysql_databases
lrwxrwxrwx 34 lowercase_seq -> ../code_python/Cjung/lowercase_seq
-rwxr-xr-x 2884 match_seq
-rwxr-xr-x 3015 max_vals
-rwxr-xr-x 2994 mean_vals
-rwxr-xr-x 2934 median_vals
-rwxr-xr-x 5981 merge_records
-rwxr-xr-x 2630 merge_vals
-rwxr-xr-x 3015 min_vals
-rwxr-xr-x 3274 mutate_seq
-rwxr-xr-x 2786 oligo_freq
-rwxr-xr-x 6686 patscan_seq
-rwxr-xr-x 4293 plot_chrdist
-rwxr-xr-x 3801 plot_histogram
-rwxr-xr-x 3118 plot_karyogram
-rwxr-xr-x 3620 plot_lendist
-rwxr-xr-x 6983 plot_matches
-rwxr-xr-x 5076 plot_phastcons_profiles
-rwxr-xr-x 2571 plot_seqlogo
-rwxr-xr-x 2263 print_wiki
-rwxr-xr-x 2994 random_records
-rwxr-xr-x 3140 read_2bit
-rwxr-xr-x 3078 read_bed
-rwxr-xr-x 3757 read_blast_tab
-rwxr-xr-x 4137 read_embl
-rwxr-xr-x 2713 read_fasta
-rwxr-xr-x 3215 read_fastq
-rwxr-xr-x 2729 read_fixedstep
-rwxr-xr-x 2621 read_gff
-rwxr-xr-x 2967 read_mysql
-rwxr-xr-x 2761 read_psl
-rwxr-xr-x 4043 read_soft
-rwxr-xr-x 3655 read_solexa
-rwxr-xr-x 3514 read_solid
-rwxr-xr-x 3297 read_stockholm
-rwxr-xr-x 3942 read_tab
-rwxr-xr-x 2693 read_ucsc_config
-rwxr-xr-x 3772 remove_adaptor
-rwxr-xr-x 2033 remove_indels
-rwxr-xr-x 2551 remove_keys
-rwxr-xr-x 4012 remove_mysql_tables
-rwxr-xr-x 4974 remove_ucsc_tracks
-rwxr-xr-x 2277 rename_keys
-rwxr-xr-x 1977 reverse_seq
-rwxr-xr-x 2010 shuffle_seq
-rwxr-xr-x 4804 soap_seq
-rwxr-xr-x 3058 sort_records
-rwxr-xr-x 3176 split_bed
-rwxr-xr-x 3649 split_seq
-rwxr-xr-x 2962 split_vals
-rwxr-xr-x 2788 sum_vals
-rwxr-xr-x 860 swapcase_seq
-rwxr-xr-x 2931 tile_seq
-rwxr-xr-x 2707 translate_seq
-rwxr-xr-x 2745 transliterate_seq
-rwxr-xr-x 2982 transliterate_vals
-rwxr-xr-x 2829 uniq_vals
-rwxr-xr-x 8771 upload_to_ucsc
-rwxr-xr-x 1971 uppercase_seq
-rwxr-xr-x 8104 vmatch_seq
-rwxr-xr-x 3217 write_2bit
-rwxr-xr-x 3283 write_align
-rwxr-xr-x 3147 write_bed
-rwxr-xr-x 4371 write_blast
-rwxr-xr-x 2820 write_fasta
-rwxr-xr-x 2683 write_fastq
-rwxr-xr-x 2671 write_fixedstep
-rwxr-xr-x 10283 write_mysql
-rwxr-xr-x 2753 write_psl
-rwxr-xr-x 2910 write_solid
-rwxr-xr-x 4803 write_tab
-rwxr-xr-x 2480 write_ucsc_config