original FASTA file (there is an assumption that sequence string in one single line):
bash-2.03$ less fastassy_original.fa
>3SEQS_D L:60
AAATCCTGTCAAAATGGAAATTTTATATTTAAGAAAAGTAACAAAATGATAATTTTATAT
>1SEQS_E L:60
ATCTATACGACAAAATTGCAGTTTTTTTTGTCCTATACAAAAAGGCGGGACAAAGAATCT
>2SEQS_B L:60
CTTTGTGAATCCGCTATATTTTCTTTCTTTGCCCATTTCGGCGCATATGATTTCTAGAAG
>1SEQS_A L:60
GGTTGTTGGTTTTTTGGTGTTTTTGCATACAAGTTTTAGAAGGTGTTGTATCATTCTCAG
trim 10 nt from the right side (3') - one step approach:
(original sequences are 60 nt long)
bash-2.03$ cut -c1-50 fastassy_original.fa > fastassy_trim_right.fa
bash-2.03$ less fastassy_trim_right.fa
>3SEQS_D L:60
AAATCCTGTCAAAATGGAAATTTTATATTTAAGAAAAGTAACAAAATGAT
>1SEQS_E L:60
ATCTATACGACAAAATTGCAGTTTTTTTTGTCCTATACAAAAAGGCGGGA
>2SEQS_B L:60
CTTTGTGAATCCGCTATATTTTCTTTCTTTGCCCATTTCGGCGCATATGA
>1SEQS_A L:60
GGTTGTTGGTTTTTTGGTGTTTTTGCATACAAGTTTTAGAAGGTGTTGTA
trim 10 nt from the left side (5') - two step approach:
bash-2.03$ cp -i fastassy_original.fa fastassy_temporary.fa
bash-2.03$ perl -p -i -e 's/^\>/XXXXXXXXXX\>/' fastassy_temporary.fa
(step 1 - to modify FASTA header only)
bash-2.03$ less fastassy_temporary.fa
XXXXXXXXXX>3SEQS_D L:60
AAATCCTGTCAAAATGGAAATTTTATATTTAAGAAAAGTAACAAAATGATAATTTTATAT
XXXXXXXXXX>1SEQS_E L:60
ATCTATACGACAAAATTGCAGTTTTTTTTGTCCTATACAAAAAGGCGGGACAAAGAATCT
XXXXXXXXXX>2SEQS_B L:60
CTTTGTGAATCCGCTATATTTTCTTTCTTTGCCCATTTCGGCGCATATGATTTCTAGAAG
XXXXXXXXXX>1SEQS_A L:60
GGTTGTTGGTTTTTTGGTGTTTTTGCATACAAGTTTTAGAAGGTGTTGTATCATTCTCAG
bash-2.03$
bash-2.03$ cut -c11-60 fastassy_temporary.fa > fastassy_trim_left.fa
(step 2 - to cut first 10 characters)
bash-2.03$
bash-2.03$ less fastassy_trim_left.fa
>3SEQS_D L:60
AAAATGGAAATTTTATATTTAAGAAAAGTAACAAAATGATAATTTTATAT
>1SEQS_E L:60
CAAAATTGCAGTTTTTTTTGTCCTATACAAAAAGGCGGGACAAAGAATCT
>2SEQS_B L:60
CCGCTATATTTTCTTTCTTTGCCCATTTCGGCGCATATGATTTCTAGAAG
>1SEQS_A L:60
TTTTTGGTGTTTTTGCATACAAGTTTTAGAAGGTGTTGTATCATTCTCAG
(bio)-informatics, data processing and visualization
Sunday, December 20, 2009
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