Sequence Processor and Translator:

seqs_processor_and_translator_bin_V118_AGCT.py

script usage:

cos_soybean.fasta - example input file

$python  seqs_processor_and_translator_bin_V118_AGCT.py  cos_soybean.fasta  cos_soybean.xout  DNA  6  1  BIN  24

where:

1 argument: cos_soybean.fasta - input file

2 argument: cos_soybean.xout  - output file

3 argument: DNA (input file represented by DNA sequences)

4 argument: 6 (translate in six frames)

5 argument: 1 (standard genetic code)

6 argument: BIN (binary 0100101100111 file will be generated)

7 argument: 24 (ignore all sequences shorter than 24 nt)

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RUN SCRIPT WITH "BIN" OPTION ONLY IF YOU NEED IT
       OTHERWISE USE "NOBIN" OPTION
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if you run script without arguments, you will see primitive help:

bash-2.03$ python seqs_processor_and_translator_bin_V118_AGCT.py cos_soybean.fasta cos_soybean.xout               

  Program usage: 
  input_file  output_file  DNA/prot  trans_frame[0 1 3 6]  genetic_code[1 2 3]  BIN/NOBIN  seqs_min_len
  Script counts "ATGC" content in FASTA file
  and translate DNA sequence into protein
  0 - no translation; 1 - first frame
  3 - three frames; 6 - all six frame
  Genetic Code: 1 - Standard; 2 - Vertebrate Mitochondrial; 3 - Yeast Mitochondrial
  BIN option - to generate 0100111010101001100 style DNA file 

  use argument "help" - for help

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output files:

01  cos_soybean.xout.01BIN

02  cos_soybean.xout.01DNA

03  cos_soybean.xout.01TAB

04  cos_soybean.xout.02BIN

05  cos_soybean.xout.02DNA

06  cos_soybean.xout.fasta

07  cos_soybean.xout.forwrd

08  cos_soybean.xout.revcom

09  cos_soybean.xout.stat

10  cos_soybean.xout.tab

11  cos_soybean.xout.tab_frw

12  cos_soybean.xout.tab_rev

13  cos_soybean.xout.tr_frame1

14  cos_soybean.xout.tr_frame2

15  cos_soybean.xout.tr_frame3

16  cos_soybean.xout.tr_frame4

17  cos_soybean.xout.tr_frame5

18  cos_soybean.xout.tr_frame6

19  cos_soybean.xout.tr_longest_frame

20  cos_soybean.xout.tr_single_frame

21  cos_soybean.xout.x0_log

22  cos_soybean.xout.x1_log

23  cos_soybean.xout.x2_log

24  cos_soybean.xout.x3_log

25  cos_soybean.xout.x4_log

26  cos_soybean.xout.x5_log

27  cos_soybean.xout.x6_log

28  cos_soybean.xout.xx_log

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