[EMBOSS] Problem with codcopy -filter

[riccardo percudani]

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 at inducrep.odraccir
Twitter @Percud