Mitchell Stanton-Cook mscook
mscook
/ gist:4174156
Created
November 30, 2012 06:39
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| diff --git a/bin/bg7 b/bin/bg7 | |
| old mode 100644 | |
| new mode 100755 | |
| index f5173ba..1b84cab | |
| --- a/bin/bg7 | |
| +++ b/bin/bg7 | |
| @@ -29,7 +29,8 @@ runs bg7 version 0.9. Params are: | |
| -G | --genbank_data: xml with extra data for your project needed for .gbk output (things like | |
| locus name, Gen bank division tag, etc). There's a template for this at | |
| ${BG7_HOME}/resources/ |
mscook
/ example_fabric_class_task.py
Created
June 12, 2013 14:02
How to use classes to define fabric tasks
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| from fabric.api import task | |
| from fabric.tasks import Task | |
| class MyTask(Task): | |
| name = "deploy" | |
| def run(self, environment, domain="whatever.com"): | |
| run("git clone foo") | |
| sudo("service apache2 restart") | |
| instance = MyTask() |
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| import sys | |
| import textwrap | |
| """ | |
| Usage: | |
| chunk_mfa.py input.fa 500 | |
| """ |
mscook
/ nesoni_stats.py
Created
January 22, 2014 05:46
Want to extract out mapping stats from a nesoni run?
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| # Mitchell Stanton-Cook | |
| # m.stantoncook@gmail.com | |
| # github.com/mscook | |
| import glob | |
| """ | |
| (> XXXXX 47,065 unmapped pairs | |
| (> XXXXX 19,785 unmapped reads | |
| (> XXXXX 5,098,912 reads/pairs with alignments |
mscook
/ kranken_run_parse.py
Created
March 13, 2014 06:23
Parse kraken analysis of assemblies flagging those for further analysis
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| import glob | |
| import sys | |
| import os | |
| from Bio import Entrez | |
| Entrez.email = "Beatson.Lab@gmail.com" | |
mscook
/ fix_order.py
Created
March 17, 2014 05:02
Need to tidy up Mauve ordering run (should not prefix "ordered" and should be in uppercase)
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| import glob | |
| import os | |
| inf = glob.glob("*/*.fas") | |
| for f in inf: | |
| #IR65/IR65_69_Contigs-against-EC958-complete.fas | |
| new = f.replace("-complete", "") | |
| os.system("fab bio_util.fasta_to_uppercase:"+f+","+new) | |
| #new = f.replace("ordered-", '') |
mscook
/ extract_Prokka.py
Created
March 17, 2014 07:01
Given a set order, extract out statistics from a Prokka run
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| import glob | |
| order = open("order.dat").readlines() | |
| #organism: Escherichia coli HVM1147 | |
| #contigs: 93 | |
| #bases: 5131204 | |
| #rRNA: 4 |
mscook
/ extract_SeqFindR_hits.py
Created
March 18, 2014 07:12
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| from Bio.Blast import NCBIXML | |
| input = 'CFT073.B2_comp.fa_blast.xml' | |
| for record in NCBIXML.parse(open('CFT073.B2_comp.fa_blast.xml')): | |
| for align in record.alignments: | |
| for idx, hsp in enumerate(align.hsps): | |
| if idx == 0: | |
| print ">"+input.split("_")[0]+"_"+record.query.split(',')[1].strip() | |
| print hsp.sbjct |
mscook
/ SeqFindR frequency plot
Created
March 27, 2014 04:42
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| import matplotlib | |
| matplotlib.use('Agg') | |
| import sys | |
| import collections | |
| import pylab as plt | |
| from matplotlib import rcParams | |
| rcParams.update({'figure.subplot.bottom': 0.25}) |
mscook
/ validate_SeqFindR.py
Created
April 3, 2014 23:56
Takes a SeqFindR database and does some simple validation
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| # Takes a SeqFindR database and does some simple validation | |
| # | |
| # usage: | |
| # | |
| # python validate_SeqFindR.py $input.fa | |
| import sys | |
| stored = [] |
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