| from termcolor import colored | |
| def seq2colored_seq(seq, color_table): | |
| """Return sequence with colors, according to color_table {sub_sequence: color_name}, e.g, {'A': 'red'}. | |
| """ | |
| result = '' | |
| for x in seq: | |
| if x in color_table: |
| (eval-when-compile (require 'cl)) | |
| ;;; Quote selected region as python-list. | |
| (defun quote-as-list () | |
| ;; a t g c | |
| ;; -> ["a", "t", "g", "c"] | |
| (interactive) | |
| ;; cut region as `seq` | |
| (setq seq (buffer-substring (region-beginning) (region-end))) |
| (eval-when-compile (require 'cl)) | |
| (defun quote-as-dict () | |
| "Quote selected region as python-dict. | |
| a t g c | |
| -> {'a': 't', 'g': 'c'} | |
| " | |
| (interactive) |
| #!/bin/sh | |
| ## Split-window if there is only one pane, else select-pane. | |
| ## | |
| ## Set key-binding to run this script, in .tmux.conf, like, | |
| ## bind -n C-t run "/path/to/tmux-split-or-select-pane.sh" | |
| # check if more than one pane exists | |
| tmux list-panes > /tmp/tmux.list-panes | |
| awk '{if ($1!="0:") {exit 1}}' /tmp/tmux.list-panes |
| #!/usr/bin/env python | |
| # -*- coding: utf-8 -*- | |
| import argparse | |
| import subprocess | |
| def _main(): | |
| parser = argparse.ArgumentParser() | |
| args = parser.parse_args() |
| for c in 'hello, world\n\0': | |
| print format(ord(c), 'b').rjust(8, '0') | |
| # 01101000 | |
| # 01100101 | |
| # 01101100 | |
| # 01101100 | |
| # 01101111 | |
| # 00101100 | |
| # 00100000 |
| #!/bin/bash | |
| # USAGE: md5check [files] | |
| # | |
| # example: ./md5check *.gz | |
| if [ $# -eq 0 ]; then | |
| echo "USAGE: md5check [files]" | |
| exit 0 | |
| fi |
| def get_contigs(bam_path): | |
| """Get contig information by `samtools view -H` | |
| Arg: | |
| bam_path: path to a bam-file | |
| RetVal: | |
| ['chr1', 'chr2', ..., 'chrM'] | |
| """ |
| #!/usr/bin/env python | |
| # -*- coding: utf-8 -*- | |
| from collections import Counter | |
| import fileinput | |
| def _main(): | |
| """ | |
| Usage example: |
#How to use blast from command-line, on Mac OS X.
Download executables (binary) of blast-commands for Mac OS X.
$ curl -O ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+.dmg
or
$ wget ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+.dmg