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Revision 1.1 - (view) (download) (as text)
| 1 : | overbeek | 1.1 | $usage = "usage: check_sims_basic NR < sims > checked.sims 2> errors"; |
| 2 : | |||
| 3 : | ($nr = shift @ARGV) | ||
| 4 : | || die $usage; | ||
| 5 : | |||
| 6 : | open(NR,"<$nr") || die $usage; | ||
| 7 : | |||
| 8 : | $/ = "\n>"; | ||
| 9 : | while (defined($_ = <NR>)) | ||
| 10 : | { | ||
| 11 : | chomp; | ||
| 12 : | if ($_ =~ /^>?(\S+)[^\n]*\n(.*)/s) | ||
| 13 : | { | ||
| 14 : | $id = $1; | ||
| 15 : | $seq = $2; | ||
| 16 : | $seq =~ s/\s//gs; | ||
| 17 : | $ln{$id} = length($seq); | ||
| 18 : | } | ||
| 19 : | } | ||
| 20 : | $/ = "\n"; | ||
| 21 : | close(NR); | ||
| 22 : | |||
| 23 : | while (defined($_ = <STDIN>)) | ||
| 24 : | { | ||
| 25 : | chomp; # $/) | ||
| 26 : | if ($_ =~ m/^\S+\t\S+\t(\d+|\d+\.\d+)(\t\d+){7}\t(\d+(\.\d*)?e[-+]?\d+|\d+\.\d+)\t(\d\.\d*e[-+]?\d+|\d+\.\d+|\d+)/) | ||
| 27 : | { | ||
| 28 : | # print STDERR "$1\t$2\t$3\t$4\t$5\t$6\n"; | ||
| 29 : | ($id1,$id2,$iden,$ali_ln,$mis,$gaps,$b1,$e1,$b2,$e2,$psc,$bsc,$ln1,$ln2) = | ||
| 30 : | split(/\t/,$_); | ||
| 31 : | |||
| 32 : | if ($ln{$id1} && $ln{$id2} && ($ln{$id1} == $ln1) && ($ln{$id2} == $ln2)) | ||
| 33 : | { | ||
| 34 : | print "$_\n"; | ||
| 35 : | } | ||
| 36 : | else | ||
| 37 : | { | ||
| 38 : | if ($ln{$id1}) | ||
| 39 : | { | ||
| 40 : | if ($ln{$id1} != $ln1) { print STDERR "badlen1\t$id1\t$ln{$id1}\t$ln1\t$_\n"; } | ||
| 41 : | } | ||
| 42 : | else | ||
| 43 : | { | ||
| 44 : | print STDERR "undef1\t$id1\t\t\t$_\n"; | ||
| 45 : | } | ||
| 46 : | |||
| 47 : | if ($ln{$id2}) | ||
| 48 : | { | ||
| 49 : | if ($ln{$id2} != $ln2) { print STDERR "badlen2\t$id2\t$ln{$id2}\t$ln2\t$_\n"; } | ||
| 50 : | } | ||
| 51 : | else | ||
| 52 : | { | ||
| 53 : | print STDERR "undef2\t$id2\t\t\t$_\n"; | ||
| 54 : | } | ||
| 55 : | } | ||
| 56 : | } | ||
| 57 : | else | ||
| 58 : | { | ||
| 59 : | print STDERR "INVALID FORMAT: $_\n"; | ||
| 60 : | } | ||
| 61 : | } |
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