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
CGPDB
UC Davis
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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.
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