DSLab: Data Science Laboratory

One line command to pre-process the files
A.) Awk command to split a large multi-fasta file in to small files.

1. awk 'BEGIN {n_seq=0;} /^>/ {if(n_seq%200==0){file=sprintf("myseq%d.fa",n_seq);} print >> file; n_seq++; next;} { print >> file; }' < input_file
myseq = output file name. input_file = Name of multi-fasta input file. 200 = maximum no. of sequence in each output fasta file

B.) Perl command to replace/substitute the desire word into other word from a file.

2. perl -pi -e 's/query/result/g' file_name
query = the word to be replace. result = the new word to be placed. file_name = name of the input file

3. Convert xls to csv file command line
ssconvert file.xls file.csv

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