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}
#"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
# When the sec. str is not defined in DSSP, I delete the position of
# @stringDSSP to gap(ie. make it blank to exclude error rate calc)
#"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
for($i=0; $i < @stringDSSP; $i++){
if($stringDSSP[$i] =~ /\W/){ $seq_positionSTR[$i]= $gap_char;}
}
}
}elsif( $comm_col =~ /C/i){
print __LINE__, " Replacing position with \gap_char \"$gap_char\"\n" if $debug2 eq 1;
$ss_opt = 'ss'; # whether it was set or not, make it 'ss'
for($i=0; $i < @stringDSSP_common; $i++){
if($stringDSSP_common[$i] =~ /\W/){ $seq_positionSTR[$i]= $gap_char;}
}
}
if($debug2 eq 1){
print __LINE__,
print " \@seq_positionSTR is @seq_positionSTR\n";
}
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Opening input FILE!
#_______________________________________________
else{
print "\n# open_sso_files : processing @file \n\n";
for($i=0; $i< @file; $i++){
if($file[$i]=~/\S+\.msp *$/){ $big_msp_out_file=$file[$i]; splice (@file, $i, 1); $i--;
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Opening zipped file
#_______________________________________________
}elsif($file[$i]=~/\S+\.\gz$/ or -B $file[$i]){ ## if file has xxxx.gz extension
my (@sso);
@sso=`gunzip -c $file[$i]`;
if(@sso < 30){ @sso=`zcat $file[$i]`; } # if zcat fails to produce output use gunzip -c
if(@sso > 3000){ # if @sso is very big, I remove the useless contents
print "\n# open_sso_files: size of \@sso for $file[$i] exceeds 3000 lines, ", scalar(@sso), " !!! \n";
}
push(@OUT, &read_sso_lines(\@sso, $create_sso,
"u=$upper_expect_limit",
"l=$lower_expect_limit",
$attach_range_in_names,
}
#"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
# When the sec. str is not defined in DSSP, I delete the position of
# @stringDSSP to gap(ie. make it blank to exclude error rate calc)
#"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
for($i=0; $i < @stringDSSP; $i++){
if($stringDSSP[$i] =~ /\W/){ $seq_positionSTR[$i]= $gap_char;}
}
}
}elsif( $comm_col =~ /C/i){
print __LINE__, " Replacing position with \gap_char \"$gap_char\"\n" if $debug2 eq 1;
$ss_opt = 'ss'; # whether it was set or not, make it 'ss'
for($i=0; $i < @stringDSSP_common; $i++){
if($stringDSSP_common[$i] =~ /\W/){ $seq_positionSTR[$i]= $gap_char;}
}
}
if($debug2 eq 1){
print __LINE__,
print " \@seq_positionSTR is @seq_positionSTR\n";
}
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Opening input FILE!
#_______________________________________________
else{
print "\n# open_sso_files : processing @file \n\n";
for($i=0; $i< @file; $i++){
if($file[$i]=~/\S+\.msp *$/){ $big_msp_out_file=$file[$i]; splice (@file, $i, 1); $i--;
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Opening zipped file
#_______________________________________________
}elsif($file[$i]=~/\S+\.\gz$/ or -B $file[$i]){ ## if file has xxxx.gz extension
my (@sso);
@sso=`gunzip -c $file[$i]`;
if(@sso < 30){ @sso=`zcat $file[$i]`; } # if zcat fails to produce output use gunzip -c
if(@sso > 3000){ # if @sso is very big, I remove the useless contents
print "\n# open_sso_files: size of \@sso for $file[$i] exceeds 3000 lines, ", scalar(@sso), " !!! \n";
}
push(@OUT, &read_sso_lines(\@sso, $create_sso,
"u=$upper_expect_limit",
"l=$lower_expect_limit",
$attach_range_in_names,
( run in 0.272 second using v1.01-cache-2.11-cpan-87723dcf8b7 )