1.2.2 sequence conversion J. R. Knight format fmtseq fmtseq perl "fmtseq -p -all " 0 seq Sequence File perl " < $value" 10 readseq_ok_alig perl 1 outfile perl "" "fmtseq.out" seqsfile perl $outformat !~ /2./ outformat Output Sequence Format perl " -f$value" 9 1 1 1. Raw 2 2. Plain 3 3. EMBL 4 4. Swiss-Prot 5 5. GenBank 6 6. PIR (codata) 7 7. ASN.1 8 8. FASTA (Pearson) 9 9. FASTA 12 12. NBRF 13 13. NBRF-old 14 14. IG/Stanford 15 15. IG-old 16 16. GCG 17 17. MSF 18 18. PHYLIP 19 19. PHYLIP-Interleaved 20 20. PHYLIP-Sequential 21 21. Clustalw 22 22. Pretty input Input parameters 1 gapin Set the gap symbol for the input (-gapin) perl ($value)? " -gapin=$value" : "" 1 . '.' - '-' informat Input sequence format (-inf[ormat]) perl ($value)? " -informat=$value" : "" 1 1 1. Raw 2 2. Plain 3 3. EMBL 4 4. Swiss-Prot 5 5. GenBank 6 6. PIR (codata) 7 7. ASN.1 9 9. FASTA 10 10. FASTA-output 11 11. BLAST-output 12 12. NBRF 13 13. NBRF-old 14 14. IG/Stanford 15 15. IG-old 16 16. GCG 17 17. MSF 18 18. PHYLIP 19 19. PHYLIP-Interleaved 20 20. PHYLIP-Sequential 21 21. Clustalw output Output parameters 1 caselower convert to lowercase (-c) perl ($value)? " -c":"" 1 CASEUPPER convert to upper case (-C) perl ($value)? " -C":"" 1 degap Remove gaps from sequences (-degap) perl ($value)? " -degap":"" 1 gapout Set the gap symbol for the output (-gapout) perl ($value)? " -gapout=$value":"" 1 . '.' - '-' list Only list sequence information (-li) perl ($value)? " -li":"" 1 long Long form conversion (input header included as comment) (-long) perl ($value)? " -long":"" 1 raw Gaps in sequences (-raw) perl ($value)? " -$value":"" 1 raw leave gaps noraw do not leave gaps reverse Reverse-complement each sequence (-re) perl ($value)? " -re":"" 1 prettyoptions Pretty-print options 2 interleave Output interleaved sequences (-interleave) perl ($value)? " -$value":"" 2 interleave interleave nointerleave nointerleave width Sequence line width (-width) perl (defined $value)?" -width=$value":"" 2 tab Indent sequence (-tab) perl (defined $value)?" -tab=$value":"" 2 colspace Add space columms in sequence lines (-colspace) perl (defined $value)?" -colspace=$value":"" 2 gapcount Count gap chars in sequence numbers (-gapcount) perl (defined $value)? " -$value" : "" 2 gapcount gap count nogapcount no gap count nameleft Name on left side (-nameleft) perl ($value) ? " -nameleft=$value" : "" 2 nameright Name on left side (-nameright) perl ($value) ? " -nameright=$value" : "" 2 nametop Name at top (-nametop) perl ($value)? " -nametop" : "" 0 3 numleft Sequence index on left/right side perl ($value)? " -num$value" : "" 2 left left right right numtop Index on top/bottom perl ($value)? " -num$value" : "" 2 top top bot bottom match Replace matches to first sequence with . (-match) perl ($value)? " -match=." : "" 0 2 interline How many blank line(s) between sequence blocks (-interline) perl (defined $value)?" -interline=$value":"" 2 skipempty Do not output lines with only gap characters (-skipempty) perl ($value)? " -skipempty" : "" 0 2 bigalign Convert FASTA program output to big alignment (-bigalign) perl ($value)? " -bigalign" : "" 1