Hi all, Using Emboss codcopy to format codon-usage tables generated with cusp I get an error when trying to read from stdin with the '-filter' option:
>codcopy cds.cusp -auto #works well >cat cds.cusp | codcopy -filter Error: Codon file is required Died: codcopy terminated: Bad value for '-infile' with -auto defined I am including here the "cds.cusp" and the "-debug" file. Your help will be appreciated. Best regards, Riccardo Percudani >cat codcopy.dbg Debug file codcopy.dbg buffered:No ajAcdInitPV pgm 'codcopy' package '' version '6.3.1' system 'Linux ajFileNewInNameS '/usr/share/EMBOSS/acd/ codcopy.acd' EOF ajFileGetsL file /usr/share/EMBOSS/acd/codcopy.acd ajFileNewInNameS '/usr/share/EMBOSS/acd/codes.english' EOF ajFileGetsL file /usr/share/EMBOSS/acd/codes.english ajFileNewInNameS '/usr/share/EMBOSS/acd/knowntypes.standard' EOF ajFileGetsL file /usr/share/EMBOSS/acd/knowntypes.standard >cat cds.cusp #CdsCount: 19259 #Coding GC 39.57% #1st letter GC 42.40% #2nd letter GC 36.84% #3rd letter GC 39.46% #Codon AA Fraction Frequency Number GCA A 0.192 12.100 6085 GCC A 0.192 12.087 6078 GCG A 0.263 16.547 8321 GCT A 0.354 22.274 11201 TGC C 0.548 10.187 5123 TGT C 0.452 8.420 4234 GAC D 0.255 9.756 4906 GAT D 0.745 28.510 14337 GAA E 0.700 36.550 18380 GAG E 0.300 15.664 7877 TTC F 0.202 12.647 6360 TTT F 0.798 49.822 25054 GGA G 0.177 9.987 5022 GGC G 0.299 16.839 8468 GGG G 0.331 18.635 9371 GGT G 0.193 10.850 5456 CAC H 0.361 9.324 4689 CAT H 0.639 16.521 8308 ATA I 0.171 10.289 5174 ATC I 0.323 19.371 9741 ATT I 0.506 30.354 15264 AAA K 0.730 62.376 31367 AAG K 0.270 23.073 11603 CTA L 0.102 10.158 5108 CTC L 0.087 8.664 4357 CTG L 0.040 4.031 2027 CTT L 0.188 18.808 9458 TTA L 0.347 34.711 17455 TTG L 0.237 23.658 11897 ATG M 1.000 18.197 9151 AAC N 0.409 20.616 10367 AAT N 0.591 29.773 14972 CCA P 0.255 9.060 4556 CCC P 0.284 10.090 5074 CCG P 0.101 3.577 1799 CCT P 0.360 12.759 6416 CAA Q 0.818 29.327 14748 CAG Q 0.182 6.544 3291 AGA R 0.323 20.087 10101 AGG R 0.188 11.703 5885 CGA R 0.108 6.684 3361 CGC R 0.206 12.824 6449 CGG R 0.063 3.892 1957 CGT R 0.112 6.948 3494 AGC S 0.352 24.082 12110 AGT S 0.153 10.502 5281 TCA S 0.160 10.957 5510 TCC S 0.085 5.834 2934 TCG S 0.061 4.194 2109 TCT S 0.188 12.896 6485 ACA T 0.237 9.283 4668 ACC T 0.276 10.818 5440 ACG T 0.218 8.547 4298 ACT T 0.269 10.535 5298 GTA V 0.127 5.725 2879 GTC V 0.124 5.562 2797 GTG V 0.400 18.026 9065 GTT V 0.349 15.698 7894 TGG W 1.000 12.116 6093 TAC Y 0.289 9.432 4743 TAT Y 0.711 23.203 11668 TAA * 0.449 17.193 8646 TAG * 0.210 8.050 4048 TGA * 0.341 13.055 6565 -- Prof. Riccardo Percudani <> Dipartimento di Bioscienze <> Unipr <> 0521-905140 perl -ple'$_=reverse'<<<moc.liamg@inducrep.odraccir Twitter @Percud _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss