faops-tutorial

My notes and tests for faops usage

faops 使用说明书 (with the latest version)

faops 是一个用于处理 FASTA 格式序列文件的轻量级工具，由 Wang-Q 开发。

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Usage

rc : reverse complement (DNA sequence)

I have a fasta called ufasta.fa, now I want to get the reverse complement version of it:

faops rc ufasta.fa RC_ufasta.fa  
# I input the ufasta.fa then output the RC_ufasta.fa, the output file, which call it whatever u want

the names in the RC_ufasta.fa have RC_ in front of the original name

extract :

• one/some (order) => extract one/some/in order fa record from ufasta.fa, I have some names of seqs in the list3.file

 faops one ufasta.fa read0 read0.fa
 #extract one seq called read0 from ufasta.fa

faops some ufasta.fa list3.file read_3.fa
#extract some seqs according to list3.file from ufasta.fa

faops order ufasta.fa list3.file read_3order.fa
#extract some seqs according to list3.file from ufasta.fa, in order!!!

• when using stdin and stdout, same as above

cat ufasta.fa | faops one stdin read0 stdout
cat ufasta.fa | faops some stdin list3.file stdout
cat ufasta.fa | faops order stdin list3.file stdout
# cat ufasta.fa把`ufasta.fa`的内容写到标准输出（stdout）。
# |（管道）把左侧命令的 stdout 作为右侧命令的标准输入（stdin）。
# faops one stdin read0 stdout调用 faops 的 one 子命令，从 stdin 读取 FASTA，提取 单个 ID 为 read0 的记录，并把结果写到 stdout（屏幕/下一步管道）。

sort:

• when u wanna sort by header ID:

faops order read_3.fa \
  <(cat read_3.fa | grep '>' | sed 's/>//' | sort) \
  header_read_3.fa

<( … ) is a process substitution, 把括号里的命令输出，伪装成一个“只读文件”的路径传给程序，they only read ufasta.fa here.

grep '>' means that they only grep the line with '>'

sed 's/>//' in it, sed is Stream EDitor, s means substitude, the 1st / is a mode matching for the latter; the 2nd / is the text u wanna substitude, which is empty here; after the 3rd / u can add modifiers.

• here's u wanna sort by lengths:

faops order read_3.fa \
  <(faops size read_3.fa | sort -n -r -k2,2 | cut -f 1)\
  lengths_read_3.fa

-n means they treat the number as a value/math, not a word/text

-r means reverse, from the bigger to the smaller

-k2,2 --- -k<start>,<end>, 2 is the column 2

cut is taking the text, -f1 pick the first field, here is the ID column

tidy:

• unify the length of the line:

here u wanna have 80 bases in a line (-l)

faops filter -l 80 read_3.fa sameline_read_3.fa

u also can use -l 0 for all content written on one line

if u wanna uppercase (-u) or lowercase (-l), add the choice:

faops filter -u -l 80 read_3.fa big_sameline_read_3.fa

• change format: when u use filter, the contact in the in/out file is different, the format can be change

compute:

n50 is an abstract command

• N50:

only show the number:

faops n50 -H ufasta.fa   # -H means hide header

or show the header

faops n50 ufasta.fa

• N75:

faops n50 -N 75 ufasta.fa

• N90：

 faops n50 -N 90 -S -A -g 10000 ufasta.fa

-S => sum

-A => average

-g 10000 =>设定估计基因组大小为 10,000 bp