# seq_tools
[](http://badge.fury.io/py/rna_seq_tools)
[](https://github.com/PyCQA/pylint)
[](https://github.com/psf/black)
a short python tool for working with sequences in dataframes
## how to install
```shell
pip install rna_seq_tools
```
## how to use
`seq_tools` is a python package that contains a few functions for working with sequences in
dataframes. If there is a single sequence results are printed. If input is a csv then a new csv is
created with the results. Default output is "output.csv" but can be changed with the `-o` flag.
```shell
$ seq_tools --help
Usage: seq_tools [OPTIONS] COMMAND [ARGS]...
a set scripts to manipulate sequences in csv files
Options:
--help Show this message and exit.
Commands:
add add a sequence to 5' and/or 3'
ec calculate the extinction coefficient for each sequence
edit-distance calculate the edit distance of a library
fold fold rna sequences
mw calculate the molecular weight for each sequence
rc calculate reverse complement for each sequence
to-dna convert rna sequence(s) to dna
to-dna-template convert rna sequence(s) to dna template, includes T7...
to-fasta generate fasta file from csv
to-opool generate oligo pool file from csv
to-rna convert rna sequence(s) to dna
transcribe convert dna sequence(s) to rna
trim trim 5'/3' ends of sequences
```
### add
Adds a sequence to the 5' and/or 3' end of a sequence.
```shell
$ seq_tools add -p5 "AAAA" "GGGGUUUUCCCC"
SEQ_TOOLS.get_input_dataframe - INFO - reading sequence GGGGUUUUCCCC
SEQ_TOOLS.handle_output - INFO - output->
name seq
sequence AAAAGGGGUUUUCCCC
Name: 0, dtype: object
```
### ec
Calculate the extinction coefficient for each sequence.
```shell
$ seq-tools ec "GGGGUUUUCCCC"
SEQ_TOOLS.get_input_dataframe - INFO - reading sequence GGGGUUUUCCCC
SEQ_TOOLS.handle_ntype - INFO - determining nucleic acid type: RNA
SEQ_TOOLS.handle_output - INFO - output->
name seq
sequence GGGGUUUUCCCC
extinction_coeff 109500
Name: 0, dtype: object
```
### edit-distance
Calculate the edit distance of a library. On average how different each sequence
is from the rest of the library.
```shell
seq-tools edit-distance test/resources/test.csv
SEQ_TOOLS.edit_distance - INFO - edit distance: 17.666666666666668
```
### fold
Fold rna sequences.
```shell
$ seq-tools fold "GGGGUUUUCCCC"
SEQ_TOOLS.get_input_dataframe - INFO - reading sequence GGGGUUUUCCCC
SEQ_TOOLS.handle_output - INFO - output->
name seq
sequence GGGGUUUUCCCC
structure ((((....))))
mfe -5.9
ens_defect 0.38
Name: 0, dtype: object
```
### to-dna
Convert all sequences to DNA i.e. replace T with U.
```shell
$ seq_tools to-dna "GGGGUUUUCCCC"
SEQ_TOOLS.get_input_dataframe - INFO - reading sequence GGGGUUUUCCCC
SEQ_TOOLS.to_dna - INFO - converted sequence: GGGGTTTTCCCC
```
### other non commandline
#### structure representation
```python
from seq_tools import SequenceStructure
struct = SequenceStructure("GGGGUUUUCCCC", "((((....))))")
```
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