• Intro

  • step_01
  • step_02
  • step_03
  • step_04
  • step_05
  • step_06
  • step_07
  • step_08
  • step_09
  • step_10
  • step_11
  • step_12
  • step_13
  • step_14
  • step_15
  • step_16
  • step_17
  • step_18
  • step_19
  • step_20
  • step_21
  • step_22
  • step_23
  • step_24

  • Credits

    UC Davis

    Step 19: Generation of tab-delimited file with consensus sequences

    seqs_processor_007.py Python scripts takes as an input EST or contig sequences in fasta file format and generates three output files:

    1. file with sequences in fasta format where every sequence formatted as a single line (this type of output is useful for pattern search using UNIX grep)
    2. file with info about "GC" content for every sequence
    3. tab-delimited file with sequences where first column - sequence ID, second column - sequence length and third column - sequence by itself.

    For contig_target_May_01_2003.pl Perl script and Primer3 program we need a third tab-delimited file only.

    In UNIX shell execute:

    $ python seqs_processor_007.py tomato_ABC.fasta.cap.contigs tomato_ABC.fasta.cap.contigs.one_line DNA

    tomato_ABC.fasta.cap.contigs.one_line.tab will be generated which can be used as an input for contig_target_May_01_2003.pl and Primer3 pipeline.