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seq_tools

PYPI package linting: pylint formatting: black

a short python tool for working with sequences in dataframes

how to install

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.

$ 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.

$ 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.

$ 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.

seq-tools edit-distance test/resources/test.csv
SEQ_TOOLS.edit_distance - INFO - edit distance: 17.666666666666668

fold

Fold rna sequences.

$ 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.

$ 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

from seq_tools import SequenceStructure
struct = SequenceStructure("GGGGUUUUCCCC", "((((....))))")