1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
|
.. _adjust_seq_orientation:
.. index:: adjust_seq_orientation.py
*adjust_seq_orientation.py* -- Get the reverse complement of all sequences
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
Write the reverse complement of all seqs in seqs.fasta (-i) to seqs_rc.fasta (default, change output_fp with -o). Each sequence description line will have ' RC' appended to the end of it (default,
leave sequence description lines untouched by passing -r):
**Usage:** :file:`adjust_seq_orientation.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_fasta_fp
Path to the input fasta file
**[OPTIONAL]**
-o, `-`-output_fp
The output filepath
-r, `-`-retain_seq_id
Leave seq description lines untouched [default: append " RC" to seq description lines]
**Output:**
**Example:**
Reverse complement all sequences in seqs.fna and write result to seqs_rc.fna
::
adjust_seq_orientation.py -i seqs.fna
|
