brantfaircloth

# get singleton reads names from assembly stats:

grep Singleton 454ReadStatus.txt > singles.txt

# if you assembled using fasta+qual files, use faSomeRecords from kent source:

faSomeRecords ../reads/schisto.454reads.combined.fsa singles.txt singles.fa

# if you assembled using SFF files:

brantfaircloth

• assemble data and output an AMOS file (-amos_file yes)

• download and build http://sourceforge.net/projects/amos/

• convert the afg file output by velvet to a bnk file

   ~/src/amos-3.0.0/src/Bank/bank-transact -m my.afg -b my.bnk -c
  

• get short-version, depth-of-coverage output

   ~/src/amos-3.0.0/src/Validation/analyze-read-depth my.bnk -d
  

brantfaircloth

# this works just fine w/ multiprocess...
# now with more flushing

import sys
import time

sys.stdout.write("This is running")
sys.stdout.flush()
for i in range(5):
    sys.stdout.write(".")

brantfaircloth

rows = ['A','B','C','D','E','F','G','H']
columns = ['1','2','3','4','5','6','7','8','9','10','11','12']

[['{0}:{1}'.format(r,c) for c in columns] for r in rows]

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#!/bin/bash
#
# postgresbak - psql backup for xxx.yyy.zzz.qqq
#
# Created by Brant Faircloth on 2009-04-06.
# Copyright (c) 2009 Brant Faircloth. All rights reserved.
# 
# Run by cron w/ 
# 0	0	*	*	*	/path/to/script/postgresbak.sh
#

brantfaircloth

#!/bin/bash
#
# mysqlbak - mysql backup for xxx.yyy.zzz.qqq
#
# Created by Brant Faircloth on 2009-04-06.
# Copyright (c) 2009 Brant Faircloth. All rights reserved.
#
# Run by cron w/ 
# 0	0	*	*	*	/path/to/script/mysqlbak.sh
#

brantfaircloth

#!/bin/bash
#
# duplicity_backup_to_s3.sh
#
# Created by Brant Faircloth on 2011-05-05.
# Copyright (c) 2011 Brant Faircloth. All rights reserved.
#
# Run by cron w/ 
# 0	2	*	*	*	/path/to/duplicity_backup_to_s3.sh 2>&1 >> /var/log/duplicity/etc.log
#

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• start an image:

    ec2-run-instances --key keypair ami-74f0061d \
        --instance-type=c1.xlarge \
        --block-device-mapping '/dev/sda2=ephemeral0' \
        --block-device-mapping '/dev/sda3=ephemeral1'
  

• log in

ssh -i ec2-keypair ec2-user@ec2-xxx-yy-zz-qqq.compute-1.amazonaws.com

brantfaircloth

text = Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
csv = "Query id","Subject id","% identity","alignment length","mismatches","gap openings","q. start","q. end","s. start","s. end","e-value","bit score"

brantfaircloth

#!/usr/bin/env ruby

# Note:  original hint from Florian Pilz @ http://stackoverflow.com/questions/4307192/is-it-possible-to-hook-a-git-commit-to-the-save-on-textmate.  Slightly updated with git path (homebrew) and change to git_answer.

filename = ENV["TM_FILEPATH"].split("/").last

require ENV['TM_SUPPORT_PATH'] + '/lib/ui'
message = TextMate::UI.request_string(:title => "Committing changes of #{filename}", :prompt => "Please enter the commit message for your changes.")
`/usr/local/bin/git add #{ENV["TM_FILEPATH"]} 2>&1`
commit = `/usr/local/bin/git commit -m "#{message}" 2>&1`