小生这厢有礼了(BioFaceBook Personal Blog)

记录生物信息学点滴足迹（NGS,Genome,Meta,Linux)

how-to-extract-convert-gff3-cds-sequences-to-multifasta

https://bioinformatics.stackexchange.com/questions/2341/how-to-extract-convert-gff3-cds-sequences-to-multifasta

Using python and this GFF parser that mimics Biopython’s SeqIO parsers:

from BCBio import GFF

# Read the gff
for seq in GFF.parse('my_file.gff'):
    # only focus on the CDSs
    for feat in filter(lambda x: x.type == 'CDS',
                       seq.features):
        # extract the locus tag
        locus_tag = feat.qualifiers.get('locus_tag',
                                        ['unspecified'])[0]
        # extract the sequence
        dna_seq = seq[......]

python and PBS script

#!/bin/bash
#PBS -l walltime=48:00:00,nodes=8:ppn=4
#PBS -N bbmap_batch
#PBS -l walltime=48:00:00
#megahit -1 /disk/rdisk09/zhiyshen/combined_HKG_1.fastq.gz -2 /disk/rdisk09/zhiyshen/combined_HKG_2.fastq.gz -m 0.9 -o /disk/rdisk09/zhiyshen/HKG_coassembly_out –min-contig-len 2000 -t 28
source activate bbmap
cd /home/zhiyshen/zhiyshen/viral_bioaerosol/bbmap/HKG/test/
python2.7 /home/zhiyshen/zhiyshen/viral_bioaerosol/bbmap/HKG/test/batch_run_bbmap.py

#!/usr/bin/env python
import os,re,sys,string,commands,getopt,subprocess,glob
from os import path

#SL310935_adapter_remov[……]

data<-read.table("fastani_matrix.txt", header=TRUE )

(base) zyshen@wyq-P310:~/work/deltaBS/fastaANI$ more fastani_matrix.txt

B1147 E4385 E4742 E4930 EC5350 ROAR019

B1147 100 94.681488 94.696358 94.648102 99.785301 94.803284

E4385 94.681488 100 96.50248 97.408295 94.496964 95.691849

E4742 94.696358 96.50248 100 96.831787 94.59523 95.332825

E4930 94.648102 97.408295 96.831787 100 94.446297 95.715088

EC5350 99.785301 94.496964 94.59523 94.446297 100 94.630646

ROAR019 94.803284 95.691849 95.332825 95.715088 94.630646 100

> data
            B1147     E4385     E4742[......]

Metagenomics Tutorial (HUMAnN2)

https://github.com/LangilleLab/microbiome_helper/wiki/Metagenomics-Tutorial-(Humann2)

This tutorial is set-up to walk you through the process of determining the taxonomic and functional composition of several metagenomic samples. It covers the use of Metaphlan2 (for taxonomic classification), HUMAnN2 (for functional classification), and STAMP (for visualization and statistical evaluation).

Throughout the tutorial, there are several questions to ensure that you are understanding the process (and not just copy and pasting). You can check the answer sheet after you have answered them yourself[……]

Metagenomics standard operating procedure v2

http://www.360doc.com/content/20/0823/10/71250389_931761136.shtml

https://github.com/LangilleLab/microbiome_helper/wiki/Metagenomics-standard-operating-procedure-v2

Note that this workflow is continually being updated. If you want to use the below commands be sure to keep track of them locally.

Last updated: 9 Oct 2018 (see revisions above for earlier minor versions and Metagenomics SOPs on the SOP for earlier major versions)

Important points to keep in mind:

The below options are not necessarily best for your data; it is important to explore different options, especially at the r[……]

肠型分析学习

肠型，Enterotype，是2011年在这篇文章中提出的，即将过去的2018年又有20多们肠道微生物的大佬对肠型的概念进行了回顾和确认。一直比较好奇怎样来用代码分析肠型，今天找到了这个教程，放在这：

这是那篇原始的文章：Arumugam, M., Raes, J., et al. (2011) Enterotypes of the human gut microbiome, Nature,doi://10.1038/nature09944 在谷歌上一搜，作者竟然做了个分析肠型的教程在这，学习一下：http://enterotyping.embl.de/enterotypes.html 这是2018年大佬们的共识文章：这是国人翻译的这篇文章，http://blog.sciencenet.cn/blog-3334560-1096828.html 当然，如果你只需要获得自己的结果或者自己课题的结果，不需要跑代码的，有最新的网页版分型，更好用，网址也放在这，同样也是上面翻译的那篇文章里提到的网址：http://enterotypes.org/ 只需要把菌属的含量比例文件上就能很快得到结果。

下面我就边学习边做来尝试着来个分析，并把代码放在这里备忘。其实作者已经整理好了代码，我学习一下，争取实现对手上的数据进行分析。

首先下载测试数据，

wget http://enterotypi[......]

Making a pairwise distance matrix in pandas

This is a somewhat specialized problem that forms part of a lot of data science and clustering workflows. It starts with a relatively straightforward question: if we have a bunch of measurements for two different things, how do we come up with a single number that represents the difference between the two things?

An example will make the question clearer. Let’s load our olympic medal dataset:

import pandas as pd
pd.options.display.max_rows = 10
pd.options.display.max_columns = 6
data = pd.read_csv("https://raw.githubusercontent.com/mojones/binders/master/olympics.csv", sep="\t")
data

[……]

pandas isnull函数检查数据是否有缺失

pandas isnull sum with column headers

for col in main_df:
    print(sum(pd.isnull(data[col])))

I get a list of the null count for each column:

0
1
100

What I’m trying to do is create a new dataframe which has the column header alongside the null count, e.g.

col1 | 0
col2 | 1
col3 | 100

#print every column using:

nulls = df.isnull().sum().to_frame()
for index, row in nulls.iterrows():
    print(index, row[0])

for col in df:
    print(df[col].unique())

pandas.get_dummies 的用法 (One-Hot Encoding)

[……]

conda 报错　Solving environment: failed

现在说说我的解决思路：
1.根据错误内容，安装失败的原因应该是这个网址 https://repo.anaconda.com/pkgs/main/noarch/repodata.json.bz2 请求失败。
2.所以我尝试用

wget https://repo.anaconda.com/pkgs/main/noarch/repodata.json.bz2
1
手动下载这个包，结果出现以下错误。

-2018-12-12 18:29:18– https://repo.anaconda.com/pkgs/main/noarch/repodata.json.bz2
Connecting to 127.0.0.1:33473… failed: Connection refused.

1
2
3
那么应该寻找失败的原因，127.0.0.1表示的是本机，应该不会有什么问题，那么会不会是因为端口33473被占用的原因。
3.用netstat -ntpl查看本地端口的使用情况

netstat -ntpl
(Not all processes could be identified, non-owned process info
will not be shown, you would have to be root to see it all.)[……]

DBS model training

phenotype gproNOG.annotations bitscores

This is the complete workflow used to generate a random forest model using output data from an hmmsearch of your protein coding genes against eggNOG gamma proteobacterial protein HMMs. Before running this notebook, run the parse_hmmsearch.pl script to get a tab-delimited file containing bitscores for all isolates.

“`{r, read in data}
# library(gplots)
library(caret)
library(randomForest)
set.seed(1)
# set the directory you are working from
directory <- “/home/shenzy/UNISED/CII_ECOR_update_final_164genes”
# Reading in the eggNOG model sco[……]

小生这厢有礼了(BioFaceBook Personal Blog)

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链接表

how-to-extract-convert-gff3-cds-sequences-to-multifasta

python and PBS script

Ｒ heatmap for ANI

Metagenomics Tutorial (HUMAnN2)

Metagenomics standard operating procedure v2

肠型分析学习

首先下载测试数据，

Making a pairwise distance matrix in pandas

Pandas and Sklearn

pandas isnull函数检查数据是否有缺失

pandas isnull sum with column headers

pandas.get_dummies 的用法 (One-Hot Encoding)

conda 报错　Solving environment: failed

DBS model training

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Recent Comments

链接表

首先下载测试数据，

pandas isnull函数检查数据是否有缺失

pandas.get_dummies 的用法 (One-Hot Encoding)

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