Earlier this year
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-
r14
(major revision of substring extraction based on quality scor...) committed by akozik
- major revision of substring extraction based on quality scores
major revision of substring extraction based on quality scores
-
Older
-
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Illumina_Quality_Scores
Wiki page added by akozik
- Revision r9 Created wiki page through web user interface.
Revision r9 Created wiki page through web user interface.
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-
-
-
r8
(add new script to the project:
tcl_solexa_qseq_parser_2009_...) committed by akozik
- add new script to the project:
tcl_solexa_qseq_parser_2009_07_16_Beta.tcl
to parse Illumina 'qseq' files
add new script to the project:
tcl_solexa_qseq_parser_2009_07_16_Beta.tcl
to parse Illumina 'qseq' files
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r7
(set upper_cut 180 (it was 200)
fixed bug with quality score...) committed by akozik
- set upper_cut 180 (it was 200)
fixed bug with quality scores - integer versus float
(should be float)
print info progress message every 1,000 lines instead of each line
set upper_cut 180 (it was 200)
fixed bug with quality scores - integer versus float
(should be float)
print info progress message every 1,000 lines instead of each line
-
r6
(submission of new script illupa_rectificator to the project) committed by akozik
- submission of new script illupa_rectificator to the project
submission of new script illupa_rectificator to the project
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r5
(June 09 2009:
comments, explanations
replacement of fixed ...) committed by akozik
- June 09 2009:
comments, explanations
replacement of fixed cutoff values with variables
June 09 2009:
comments, explanations
replacement of fixed cutoff values with variables
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r4
(June 08 2009:
1. modified criteria of so called 'good' and ...) committed by akozik
- June 08 2009:
1. modified criteria of so called 'good' and 'bad' files
2. introduction of two new parameters: first_cycle and last_cycle
3. optional trimming by adaptor sequence
June 08 2009:
1. modified criteria of so called 'good' and 'bad' files
2. introduction of two new parameters: first_cycle and last_cycle
3. optional trimming by adaptor sequence
-
r3
(#!/usr/bin/tcl
proc Sort_Table {argv} {
# set exp_id "...) committed by akozik
- #!/usr/bin/tcl
proc Sort_Table {argv} {
# set exp_id "SAAA_"
# set upper_cut 600
# set upper_cut 400
# set upper_dif 200
# set upper_dif 100
set upper_cut 200
set upper_dif 60
set good_diff 100
set number_of_runs 100
set quality_upper_limit 1000
set good_length 24
set gc_upper 0.8
set gc_lower 0.2
set f_in1 [open [lindex $argv 0] "r"]
set f_out [open [lindex $argv 1] "w"]
set f_out_qual [open [lindex $argv 1].qual "w"]
set f_out_clean [open [lindex $argv 1].trim.fasta "w"]
set f_out_clean_qual [open [lindex $argv 1].trim.qual "w"]
set f_out_fastq [open [lindex $argv 1].trim.fastq "w"]
set f_bad [open [lindex $argv 2] "w"]
set f_bcl [open [lindex $argv 3] "w"]
set exp_id [lindex $argv 4]
####### READ ID LIST TO EXTRACT #######
set k 1
while {[gets $f_in1 current_line] >= 0} {
set data_str [split $current_line "\t"]
set data_len [llength $data_str]
set line_id [lindex $data_str 0]
set cell_id [lindex $data_str 1]
set coord_x [lindex $data_str 2]
set coord_y [lindex $data_str 3]
# set num_str [lindex $data_str 4]
# set num_str [string trim $num_str]
puts "line: $k\tlength: $data_len"
if { $k <= 10000 } {
puts $f_bcl "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y COUNT: $k"
}
set dna_list ""
set qual_list ""
set fastq_list ""
set n 4
# set first_x 0
set first_x $number_of_runs
set x_found "FALSE"
while { $n <= [expr $data_len - 1] } {
set num_str [lindex $data_str $n]
set num_str [string trim $num_str]
# four times
regsub -all { } $num_str " " num_str
regsub -all { } $num_str " " num_str
regsub -all { } $num_str " " num_str
regsub -all { } $num_str " " num_str
regsub -all { } $num_str "\t" num_str
set val_pos [expr $n - 3]
# ACGT values
set val_A [lindex $num_str 0]
set val_C [lindex $num_str 1]
set val_G [lindex $num_str 2]
set val_T [lindex $num_str 3]
###
# puts $num_str
set num_sorted [lsort -real $num_str]
# puts $num_sorted
set value_max1 [lindex $num_sorted 3]
set value_max2 [lindex $num_sorted 2]
set value_max_diff [expr $value_max1 - $value_max2]
### QUALITY SCORES ### 2008 March 25
set current_quality "X"
set fastq_quality "!"
set value_ratio "X.XXXXXXXX"
if { $value_max1 != 0 } {
set value_ratio [expr $value_max2/$value_max1]
if { $value_ratio <= 0.2 } {
set current_quality "A"
set fastq_quality "I"
}
if { $value_ratio <= 0.4 && $value_ratio > 0.2 } {
set current_quality "B"
set fastq_quality "9"
}
if { $value_ratio <= 0.6 && $value_ratio > 0.4 } {
set current_quality "C"
set fastq_quality "5"
}
if { $value_ratio <= 0.8 && $value_ratio > 0.6 } {
set current_quality "D"
set fastq_quality "0"
}
if { $value_ratio > 0.8 } {
set current_quality "F"
set fastq_quality "+"
}
if { $value_ratio > 0.9 } {
set fastq_quality "#"
}
}
if { $value_max1 >= $quality_upper_limit } {
set current_quality [string toupper $current_quality]
}
if { $value_max1 < $quality_upper_limit } {
set current_quality [string tolower $current_quality]
}
if { $value_max1 < $upper_cut } {
set current_quality "x"
}
###
set value_status "NONE"
set base_call "N"
# set first_x 0
# set x_found "FALSE"
if { $val_A >= $upper_cut || $val_C >= $upper_cut || $val_G >= $upper_cut || $val_T
>= $upper_cut } {
set value_status "HOPE"
set base_call "X"
if { $val_A >= [expr $val_C + $upper_dif] && $val_A >= [expr $val_G +
$upper_dif] && $val_A >= [expr $val_T + $upper_dif] } {
set base_call "A"
set value_status "GOOD"
}
if { $val_C >= [expr $val_A + $upper_dif] && $val_C >= [expr $val_G +
$upper_dif] && $val_C >= [expr $val_T + $upper_dif] } {
set base_call "C"
set value_status "GOOD"
}
if { $val_G >= [expr $val_A + $upper_dif] && $val_G >= [expr $val_C +
$upper_dif] && $val_G >= [expr $val_T + $upper_dif] } {
set base_call "G"
set value_status "GOOD"
}
if { $val_T >= [expr $val_A + $upper_dif] && $val_T >= [expr $val_C +
$upper_dif] && $val_T >= [expr $val_G + $upper_dif] } {
set base_call "T"
set value_status "GOOD"
}
}
if { $value_max_diff < $good_diff } {
set base_call [string tolower $base_call]
}
if { $val_A == 0.0 && $val_C == 0.0 && $val_G == 0.0 && $val_T == 0.0 } {
set value_status "CRAP"
set base_call "*"
}
if { $base_call == "*" && $x_found == "FALSE" } {
set first_x [expr $n - 3]
set x_found "TRUE"
}
### PUT ALL TOGETHER ###
set dna_list [ lappend dna_list $base_call ]
set qual_list [ lappend qual_list $current_quality ]
set fastq_list [ lappend fastq_list $fastq_quality ]
if { $first_x == $number_of_runs } {
set cut_q "--"
}
if { $first_x != $number_of_runs } {
set cut_q $first_x
}
if { $k <= 10000 } {
puts $f_bcl
"$val_pos\:\tA:$val_A\tC:$val_C\tG:$val_G\tT:$val_T\t$value_status\tBASE_CALL:->
$base_call\tFIRST_FAIL: $cut_q MAX_DIFF: $value_max_diff RATIO: $value_ratio QUALITY:
$current_quality"
}
incr n
}
# puts $f_out "$num_str"
set dna_string [join $dna_list ""]
set qual_string [join $qual_list ""]
set fastq_string [join $fastq_list ""]
set dna_clean $dna_string
set string_quality [string range $dna_string 0 [expr $good_length-1]]
regsub -all {n} $string_quality "" string_quality
regsub -all {N} $string_quality "" string_quality
regsub -all {x} $string_quality "" string_quality
regsub -all {X} $string_quality "" string_quality
regsub -all {\*} $string_quality "" string_quality
regsub -all {n.*} $dna_clean "" dna_clean
regsub -all {N.*} $dna_clean "" dna_clean
regsub -all {x.*} $dna_clean "" dna_clean
regsub -all {X.*} $dna_clean "" dna_clean
regsub -all {\*.*} $dna_clean "" dna_clean
set clean_length [string length $dna_clean]
set clean_upper [string toupper $dna_clean]
regsub -all {A} $clean_upper "" clean_upper
regsub -all {T} $clean_upper "" clean_upper
set gc_length [string length $clean_upper]
set gc_ratio -1
set gc_status "UNDEFINED"
if { $clean_length != 0 } {
set gc_ratio [expr $gc_length*1.00/$clean_length]
}
set gc_status "UNKNOWN"
if { $gc_ratio >= $gc_upper && $clean_length != 0 } {
set gc_status "UPPER_GC"
}
if { $gc_ratio <= $gc_lower && $clean_length != 0 } {
set gc_status "LOWER_GC"
}
if { $gc_ratio > $gc_lower && $gc_ratio < $gc_upper && $clean_length != 0 } {
set gc_status "___GC___"
}
# puts $string_quality
set string_quality_len [string length $string_quality]
set string_qual "UNKNOWN"
if { $string_quality_len >= $good_length } {
set string_qual "LONG__Q: $string_quality_len"
}
if { $string_quality_len < $good_length } {
set string_qual "SHORT_Q $string_quality_len"
}
set fail_str $first_x
if { $fail_str == 100 } {
set fail_str "--"
}
if { $clean_length >= $good_length } {
### set super_quality "QUAL_ABCD"
### set find_me_F [string first "F" [string range $qual_string 0 [expr $clean_length
- 1]]]
### set find_me_f [string first "f" [string range $qual_string 0 [expr $clean_length
- 1]]]
### set find_me_D [string first "D" [string range $qual_string 0 [expr $clean_length
- 1]]]
### set find_me_d [string first "d" [string range $qual_string 0 [expr $clean_length
- 1]]]
### if { $find_me_F != -1 || $find_me_f != -1 } {}
### set super_quality "QUAL_FLOW"
### {}
set clean_quality_string [string range $qual_string 0 [expr $clean_length - 1]]
set fastq_string_clean [string range $fastq_string 0 [expr $clean_length - 1]]
set fffff_quality_string $clean_quality_string
regsub -all {f} $fffff_quality_string "" fffff_quality_string
regsub -all {F} $fffff_quality_string "" fffff_quality_string
set abcd_qual_length [string length $fffff_quality_string]
set ffff_qual_length [expr $clean_length - $abcd_qual_length]
set abcd_qual_fract [expr ($abcd_qual_length*1.00/$clean_length)*100]
set abcd_qual_fract [expr ceil($abcd_qual_fract)]
set abcd_qual_fract [expr int($abcd_qual_fract)]
### puts $f_out_clean "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k
\[ LENGTH: $clean_length \] \( $gc_status: $gc_length\/$clean_length \) $super_quality "
puts $f_out_clean "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k \[
LENGTH: $clean_length \] \( $gc_status: $gc_length\/$clean_length \) \[ ABCD_Q:$abcd_qual_length
F_QUAL:$ffff_qual_length \] \[ Q_FRACT:$abcd_qual_fract \] "
puts $f_out_clean "$dna_clean"
puts $f_out_clean ""
puts $f_out_clean_qual "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | \(
$gc_status: $gc_length\/$clean_length \) \[ ABCD_Q:$abcd_qual_length F_QUAL:$ffff_qual_length \]
\[ Q_FRACT:$abcd_qual_fract \] "
puts $f_out_clean_qual $clean_quality_string
puts $f_out_clean_qual ""
if { $gc_status == "___GC___" } {
puts $f_out_fastq "\@$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y"
puts $f_out_fastq $dna_clean
puts $f_out_fastq "\+"
puts $f_out_fastq $fastq_string_clean
puts $f_out_fastq ""
}
}
if { $first_x >= [expr $good_length+1] } {
# COUNT ABCD and F QUALITY #
set qall_length [string length $qual_string]
set qfff_string $qual_string
regsub -all {f} $qfff_string "" qfff_string
regsub -all {F} $qfff_string "" qfff_string
regsub -all {x} $qfff_string "" qfff_string
regsub -all {X} $qfff_string "" qfff_string
set abcd_length [string length $qfff_string]
set qfx_length [expr $qall_length - $abcd_length]
set abcd_fract [expr ($abcd_length*1.00/$qall_length)*100]
set abcd_fract [expr ceil($abcd_fract)]
set abcd_fract [expr int($abcd_fract)]
puts $f_out "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k \[ FAIL:
$fail_str \] :: $string_qual :: CLEAN_LENGTH: $clean_length \[ ABCD_Q:$abcd_length
F_QUAL:$qfx_length \] \[ Q_FRACT:$abcd_fract \] "
puts $f_out "$dna_string"
puts $f_out ""
puts $f_out_qual "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y \[
ABCD_Q:$abcd_length F_QUAL:$qfx_length \] \[ Q_FRACT:$abcd_fract \] "
puts $f_out_qual "$qual_string"
puts $f_out_qual ""
}
if { $first_x < [expr $good_length+1] } {
puts $f_bad "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k \[ FAIL:
$fail_str \] :: $string_qual :: CLEAN_LENGTH: $clean_length "
puts $f_bad "$dna_string"
puts $f_bad ""
}
# puts $f_out ""
# puts $f_bad ""
if { $k <= 10000 } {
puts $f_bcl ""
}
incr k
}
close $f_in1
close $f_out
close $f_out_qual
close $f_out_clean
close $f_out_clean_qual
close $f_out_fastq
close $f_bad
close $f_bcl
puts ""
puts "DONE"
}
if {$argc != 5} {
puts "Program usage:"
puts "Table_to_Process, output_file_good, output_file_bad, output_file_base_call, id_prefix"
} else {
Sort_Table $argv
}
#!/usr/bin/tcl
proc Sort_Table {argv} {
# set exp_id "SAAA_"
# set upper_cut 600
# set upper_cut 400
# set upper_dif 200
# set upper_dif 100
set upper_cut 200
set upper_dif 60
set good_diff 100
set number_of_runs 100
set quality_upper_limit 1000
set good_length 24
set gc_upper 0.8
set gc_lower 0.2
set f_in1 [open [lindex $argv 0] "r"]
set f_out [open [lindex $argv 1] "w"]
set f_out_qual [open [lindex $argv 1].qual "w"]
set f_out_clean [open [lindex $argv 1].trim.fasta "w"]
set f_out_clean_qual [open [lindex $argv 1].trim.qual "w"]
set f_out_fastq [open [lindex $argv 1].trim.fastq "w"]
set f_bad [open [lindex $argv 2] "w"]
set f_bcl [open [lindex $argv 3] "w"]
set exp_id [lindex $argv 4]
####### READ ID LIST TO EXTRACT #######
set k 1
while {[gets $f_in1 current_line] >= 0} {
set data_str [split $current_line "\t"]
set data_len [llength $data_str]
set line_id [lindex $data_str 0]
set cell_id [lindex $data_str 1]
set coord_x [lindex $data_str 2]
set coord_y [lindex $data_str 3]
# set num_str [lindex $data_str 4]
# set num_str [string trim $num_str]
puts "line: $k\tlength: $data_len"
if { $k <= 10000 } {
puts $f_bcl "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y COUNT: $k"
}
set dna_list ""
set qual_list ""
set fastq_list ""
set n 4
# set first_x 0
set first_x $number_of_runs
set x_found "FALSE"
while { $n <= [expr $data_len - 1] } {
set num_str [lindex $data_str $n]
set num_str [string trim $num_str]
# four times
regsub -all { } $num_str " " num_str
regsub -all { } $num_str " " num_str
regsub -all { } $num_str " " num_str
regsub -all { } $num_str " " num_str
regsub -all { } $num_str "\t" num_str
set val_pos [expr $n - 3]
# ACGT values
set val_A [lindex $num_str 0]
set val_C [lindex $num_str 1]
set val_G [lindex $num_str 2]
set val_T [lindex $num_str 3]
###
# puts $num_str
set num_sorted [lsort -real $num_str]
# puts $num_sorted
set value_max1 [lindex $num_sorted 3]
set value_max2 [lindex $num_sorted 2]
set value_max_diff [expr $value_max1 - $value_max2]
### QUALITY SCORES ### 2008 March 25
set current_quality "X"
set fastq_quality "!"
set value_ratio "X.XXXXXXXX"
if { $value_max1 != 0 } {
set value_ratio [expr $value_max2/$value_max1]
if { $value_ratio <= 0.2 } {
set current_quality "A"
set fastq_quality "I"
}
if { $value_ratio <= 0.4 && $value_ratio > 0.2 } {
set current_quality "B"
set fastq_quality "9"
}
if { $value_ratio <= 0.6 && $value_ratio > 0.4 } {
set current_quality "C"
set fastq_quality "5"
}
if { $value_ratio <= 0.8 && $value_ratio > 0.6 } {
set current_quality "D"
set fastq_quality "0"
}
if { $value_ratio > 0.8 } {
set current_quality "F"
set fastq_quality "+"
}
if { $value_ratio > 0.9 } {
set fastq_quality "#"
}
}
if { $value_max1 >= $quality_upper_limit } {
set current_quality [string toupper $current_quality]
}
if { $value_max1 < $quality_upper_limit } {
set current_quality [string tolower $current_quality]
}
if { $value_max1 < $upper_cut } {
set current_quality "x"
}
###
set value_status "NONE"
set base_call "N"
# set first_x 0
# set x_found "FALSE"
if { $val_A >= $upper_cut || $val_C >= $upper_cut || $val_G >= $upper_cut || $val_T
>= $upper_cut } {
set value_status "HOPE"
set base_call "X"
if { $val_A >= [expr $val_C + $upper_dif] && $val_A >= [expr $val_G +
$upper_dif] && $val_A >= [expr $val_T + $upper_dif] } {
set base_call "A"
set value_status "GOOD"
}
if { $val_C >= [expr $val_A + $upper_dif] && $val_C >= [expr $val_G +
$upper_dif] && $val_C >= [expr $val_T + $upper_dif] } {
set base_call "C"
set value_status "GOOD"
}
if { $val_G >= [expr $val_A + $upper_dif] && $val_G >= [expr $val_C +
$upper_dif] && $val_G >= [expr $val_T + $upper_dif] } {
set base_call "G"
set value_status "GOOD"
}
if { $val_T >= [expr $val_A + $upper_dif] && $val_T >= [expr $val_C +
$upper_dif] && $val_T >= [expr $val_G + $upper_dif] } {
set base_call "T"
set value_status "GOOD"
}
}
if { $value_max_diff < $good_diff } {
set base_call [string tolower $base_call]
}
if { $val_A == 0.0 && $val_C == 0.0 && $val_G == 0.0 && $val_T == 0.0 } {
set value_status "CRAP"
set base_call "*"
}
if { $base_call == "*" && $x_found == "FALSE" } {
set first_x [expr $n - 3]
set x_found "TRUE"
}
### PUT ALL TOGETHER ###
set dna_list [ lappend dna_list $base_call ]
set qual_list [ lappend qual_list $current_quality ]
set fastq_list [ lappend fastq_list $fastq_quality ]
if { $first_x == $number_of_runs } {
set cut_q "--"
}
if { $first_x != $number_of_runs } {
set cut_q $first_x
}
if { $k <= 10000 } {
puts $f_bcl
"$val_pos\:\tA:$val_A\tC:$val_C\tG:$val_G\tT:$val_T\t$value_status\tBASE_CALL:->
$base_call\tFIRST_FAIL: $cut_q MAX_DIFF: $value_max_diff RATIO: $value_ratio QUALITY:
$current_quality"
}
incr n
}
# puts $f_out "$num_str"
set dna_string [join $dna_list ""]
set qual_string [join $qual_list ""]
set fastq_string [join $fastq_list ""]
set dna_clean $dna_string
set string_quality [string range $dna_string 0 [expr $good_length-1]]
regsub -all {n} $string_quality "" string_quality
regsub -all {N} $string_quality "" string_quality
regsub -all {x} $string_quality "" string_quality
regsub -all {X} $string_quality "" string_quality
regsub -all {\*} $string_quality "" string_quality
regsub -all {n.*} $dna_clean "" dna_clean
regsub -all {N.*} $dna_clean "" dna_clean
regsub -all {x.*} $dna_clean "" dna_clean
regsub -all {X.*} $dna_clean "" dna_clean
regsub -all {\*.*} $dna_clean "" dna_clean
set clean_length [string length $dna_clean]
set clean_upper [string toupper $dna_clean]
regsub -all {A} $clean_upper "" clean_upper
regsub -all {T} $clean_upper "" clean_upper
set gc_length [string length $clean_upper]
set gc_ratio -1
set gc_status "UNDEFINED"
if { $clean_length != 0 } {
set gc_ratio [expr $gc_length*1.00/$clean_length]
}
set gc_status "UNKNOWN"
if { $gc_ratio >= $gc_upper && $clean_length != 0 } {
set gc_status "UPPER_GC"
}
if { $gc_ratio <= $gc_lower && $clean_length != 0 } {
set gc_status "LOWER_GC"
}
if { $gc_ratio > $gc_lower && $gc_ratio < $gc_upper && $clean_length != 0 } {
set gc_status "___GC___"
}
# puts $string_quality
set string_quality_len [string length $string_quality]
set string_qual "UNKNOWN"
if { $string_quality_len >= $good_length } {
set string_qual "LONG__Q: $string_quality_len"
}
if { $string_quality_len < $good_length } {
set string_qual "SHORT_Q $string_quality_len"
}
set fail_str $first_x
if { $fail_str == 100 } {
set fail_str "--"
}
if { $clean_length >= $good_length } {
### set super_quality "QUAL_ABCD"
### set find_me_F [string first "F" [string range $qual_string 0 [expr $clean_length
- 1]]]
### set find_me_f [string first "f" [string range $qual_string 0 [expr $clean_length
- 1]]]
### set find_me_D [string first "D" [string range $qual_string 0 [expr $clean_length
- 1]]]
### set find_me_d [string first "d" [string range $qual_string 0 [expr $clean_length
- 1]]]
### if { $find_me_F != -1 || $find_me_f != -1 } {}
### set super_quality "QUAL_FLOW"
### {}
set clean_quality_string [string range $qual_string 0 [expr $clean_length - 1]]
set fastq_string_clean [string range $fastq_string 0 [expr $clean_length - 1]]
set fffff_quality_string $clean_quality_string
regsub -all {f} $fffff_quality_string "" fffff_quality_string
regsub -all {F} $fffff_quality_string "" fffff_quality_string
set abcd_qual_length [string length $fffff_quality_string]
set ffff_qual_length [expr $clean_length - $abcd_qual_length]
set abcd_qual_fract [expr ($abcd_qual_length*1.00/$clean_length)*100]
set abcd_qual_fract [expr ceil($abcd_qual_fract)]
set abcd_qual_fract [expr int($abcd_qual_fract)]
### puts $f_out_clean "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k
\[ LENGTH: $clean_length \] \( $gc_status: $gc_length\/$clean_length \) $super_quality "
puts $f_out_clean "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k \[
LENGTH: $clean_length \] \( $gc_status: $gc_length\/$clean_length \) \[ ABCD_Q:$abcd_qual_length
F_QUAL:$ffff_qual_length \] \[ Q_FRACT:$abcd_qual_fract \] "
puts $f_out_clean "$dna_clean"
puts $f_out_clean ""
puts $f_out_clean_qual "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | \(
$gc_status: $gc_length\/$clean_length \) \[ ABCD_Q:$abcd_qual_length F_QUAL:$ffff_qual_length \]
\[ Q_FRACT:$abcd_qual_fract \] "
puts $f_out_clean_qual $clean_quality_string
puts $f_out_clean_qual ""
if { $gc_status == "___GC___" } {
puts $f_out_fastq "\@$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y"
puts $f_out_fastq $dna_clean
puts $f_out_fastq "\+"
puts $f_out_fastq $fastq_string_clean
puts $f_out_fastq ""
}
}
if { $first_x >= [expr $good_length+1] } {
# COUNT ABCD and F QUALITY #
set qall_length [string length $qual_string]
set qfff_string $qual_string
regsub -all {f} $qfff_string "" qfff_string
regsub -all {F} $qfff_string "" qfff_string
regsub -all {x} $qfff_string "" qfff_string
regsub -all {X} $qfff_string "" qfff_string
set abcd_length [string length $qfff_string]
set qfx_length [expr $qall_length - $abcd_length]
set abcd_fract [expr ($abcd_length*1.00/$qall_length)*100]
set abcd_fract [expr ceil($abcd_fract)]
set abcd_fract [expr int($abcd_fract)]
puts $f_out "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k \[ FAIL:
$fail_str \] :: $string_qual :: CLEAN_LENGTH: $clean_length \[ ABCD_Q:$abcd_length
F_QUAL:$qfx_length \] \[ Q_FRACT:$abcd_fract \] "
puts $f_out "$dna_string"
puts $f_out ""
puts $f_out_qual "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y \[
ABCD_Q:$abcd_length F_QUAL:$qfx_length \] \[ Q_FRACT:$abcd_fract \] "
puts $f_out_qual "$qual_string"
puts $f_out_qual ""
}
if { $first_x < [expr $good_length+1] } {
puts $f_bad "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k \[ FAIL:
$fail_str \] :: $string_qual :: CLEAN_LENGTH: $clean_length "
puts $f_bad "$dna_string"
puts $f_bad ""
}
# puts $f_out ""
# puts $f_bad ""
if { $k <= 10000 } {
puts $f_bcl ""
}
incr k
}
close $f_in1
close $f_out
close $f_out_qual
close $f_out_clean
close $f_out_clean_qual
close $f_out_fastq
close $f_bad
close $f_bcl
puts ""
puts "DONE"
}
if {$argc != 5} {
puts "Program usage:"
puts "Table_to_Process, output_file_good, output_file_bad, output_file_base_call, id_prefix"
} else {
Sort_Table $argv
}
-
r2
(#!/usr/bin/tcl
proc Sort_Table {argv} {
# set exp_id "...) committed by akozik
- #!/usr/bin/tcl
proc Sort_Table {argv} {
# set exp_id "SAAA_"
# set upper_cut 600
# set upper_cut 400
# set upper_dif 200
# set upper_dif 100
set upper_cut 200
set upper_dif 60
set good_diff 100
set number_of_runs 100
set quality_upper_limit 1000
set good_length 24
set gc_upper 0.8
set gc_lower 0.2
set f_in1 [open [lindex $argv 0] "r"]
set f_out [open [lindex $argv 1] "w"]
set f_out_qual [open [lindex $argv 1].qual "w"]
set f_out_clean [open [lindex $argv 1].trim.fasta "w"]
set f_out_clean_qual [open [lindex $argv 1].trim.qual "w"]
set f_bad [open [lindex $argv 2] "w"]
set f_bcl [open [lindex $argv 3] "w"]
set exp_id [lindex $argv 4]
####### READ ID LIST TO EXTRACT #######
set k 1
while {[gets $f_in1 current_line] >= 0} {
set data_str [split $current_line "\t"]
set data_len [llength $data_str]
set line_id [lindex $data_str 0]
set cell_id [lindex $data_str 1]
set coord_x [lindex $data_str 2]
set coord_y [lindex $data_str 3]
# set num_str [lindex $data_str 4]
# set num_str [string trim $num_str]
puts "line: $k\tlength: $data_len"
if { $k <= 10000 } {
puts $f_bcl "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y COUNT: $k"
}
set dna_list ""
set qual_list ""
set n 4
# set first_x 0
set first_x $number_of_runs
set x_found "FALSE"
while { $n <= [expr $data_len - 1] } {
set num_str [lindex $data_str $n]
set num_str [string trim $num_str]
# four times
regsub -all { } $num_str " " num_str
regsub -all { } $num_str " " num_str
regsub -all { } $num_str " " num_str
regsub -all { } $num_str " " num_str
regsub -all { } $num_str "\t" num_str
set val_pos [expr $n - 3]
# ACGT values
set val_A [lindex $num_str 0]
set val_C [lindex $num_str 1]
set val_G [lindex $num_str 2]
set val_T [lindex $num_str 3]
###
# puts $num_str
set num_sorted [lsort -real $num_str]
# puts $num_sorted
set value_max1 [lindex $num_sorted 3]
set value_max2 [lindex $num_sorted 2]
set value_max_diff [expr $value_max1 - $value_max2]
### QUALITY SCORES ### 2008 March 25
set current_quality "X"
set value_ratio "X.XXXXXXXX"
if { $value_max1 != 0 } {
set value_ratio [expr $value_max2/$value_max1]
if { $value_ratio <= 0.2 } {
set current_quality "A"
}
if { $value_ratio <= 0.4 && $value_ratio > 0.2 } {
set current_quality "B"
}
if { $value_ratio <= 0.6 && $value_ratio > 0.4 } {
set current_quality "C"
}
if { $value_ratio <= 0.8 && $value_ratio > 0.6 } {
set current_quality "D"
}
if { $value_ratio > 0.8 } {
set current_quality "F"
}
}
if { $value_max1 >= $quality_upper_limit } {
set current_quality [string toupper $current_quality]
}
if { $value_max1 < $quality_upper_limit } {
set current_quality [string tolower $current_quality]
}
if { $value_max1 < $upper_cut } {
set current_quality "x"
}
###
set value_status "NONE"
set base_call "N"
# set first_x 0
# set x_found "FALSE"
if { $val_A >= $upper_cut || $val_C >= $upper_cut || $val_G >= $upper_cut || $val_T
>= $upper_cut } {
set value_status "HOPE"
set base_call "X"
if { $val_A >= [expr $val_C + $upper_dif] && $val_A >= [expr $val_G +
$upper_dif] && $val_A >= [expr $val_T + $upper_dif] } {
set base_call "A"
set value_status "GOOD"
}
if { $val_C >= [expr $val_A + $upper_dif] && $val_C >= [expr $val_G +
$upper_dif] && $val_C >= [expr $val_T + $upper_dif] } {
set base_call "C"
set value_status "GOOD"
}
if { $val_G >= [expr $val_A + $upper_dif] && $val_G >= [expr $val_C +
$upper_dif] && $val_G >= [expr $val_T + $upper_dif] } {
set base_call "G"
set value_status "GOOD"
}
if { $val_T >= [expr $val_A + $upper_dif] && $val_T >= [expr $val_C +
$upper_dif] && $val_T >= [expr $val_G + $upper_dif] } {
set base_call "T"
set value_status "GOOD"
}
}
if { $value_max_diff < $good_diff } {
set base_call [string tolower $base_call]
}
if { $val_A == 0.0 && $val_C == 0.0 && $val_G == 0.0 && $val_T == 0.0 } {
set value_status "CRAP"
set base_call "*"
}
if { $base_call == "*" && $x_found == "FALSE" } {
set first_x [expr $n - 3]
set x_found "TRUE"
}
### PUT ALL TOGETHER ###
set dna_list [ lappend dna_list $base_call ]
set qual_list [ lappend qual_list $current_quality ]
if { $first_x == $number_of_runs } {
set cut_q "--"
}
if { $first_x != $number_of_runs } {
set cut_q $first_x
}
if { $k <= 10000 } {
puts $f_bcl
"$val_pos\:\tA:$val_A\tC:$val_C\tG:$val_G\tT:$val_T\t$value_status\tBASE_CALL:->
$base_call\tFIRST_FAIL: $cut_q MAX_DIFF: $value_max_diff RATIO: $value_ratio QUALITY:
$current_quality"
}
incr n
}
# puts $f_out "$num_str"
set dna_string [join $dna_list ""]
set qual_string [join $qual_list ""]
set dna_clean $dna_string
set string_quality [string range $dna_string 0 [expr $good_length-1]]
regsub -all {n} $string_quality "" string_quality
regsub -all {N} $string_quality "" string_quality
regsub -all {x} $string_quality "" string_quality
regsub -all {X} $string_quality "" string_quality
regsub -all {\*} $string_quality "" string_quality
regsub -all {n.*} $dna_clean "" dna_clean
regsub -all {N.*} $dna_clean "" dna_clean
regsub -all {x.*} $dna_clean "" dna_clean
regsub -all {X.*} $dna_clean "" dna_clean
regsub -all {\*.*} $dna_clean "" dna_clean
set clean_length [string length $dna_clean]
set clean_upper [string toupper $dna_clean]
regsub -all {A} $clean_upper "" clean_upper
regsub -all {T} $clean_upper "" clean_upper
set gc_length [string length $clean_upper]
set gc_ratio -1
set gc_status "UNDEFINED"
if { $clean_length != 0 } {
set gc_ratio [expr $gc_length*1.00/$clean_length]
}
set gc_status "UNKNOWN"
if { $gc_ratio >= $gc_upper && $clean_length != 0 } {
set gc_status "UPPER_GC"
}
if { $gc_ratio <= $gc_lower && $clean_length != 0 } {
set gc_status "LOWER_GC"
}
if { $gc_ratio > $gc_lower && $gc_ratio < $gc_upper && $clean_length != 0 } {
set gc_status "___GC___"
}
# puts $string_quality
set string_quality_len [string length $string_quality]
set string_qual "UNKNOWN"
if { $string_quality_len >= $good_length } {
set string_qual "LONG__Q: $string_quality_len"
}
if { $string_quality_len < $good_length } {
set string_qual "SHORT_Q $string_quality_len"
}
set fail_str $first_x
if { $fail_str == 100 } {
set fail_str "--"
}
if { $clean_length >= $good_length } {
### set super_quality "QUAL_ABCD"
### set find_me_F [string first "F" [string range $qual_string 0 [expr $clean_length
- 1]]]
### set find_me_f [string first "f" [string range $qual_string 0 [expr $clean_length
- 1]]]
### set find_me_D [string first "D" [string range $qual_string 0 [expr $clean_length
- 1]]]
### set find_me_d [string first "d" [string range $qual_string 0 [expr $clean_length
- 1]]]
### if { $find_me_F != -1 || $find_me_f != -1 } {}
### set super_quality "QUAL_FLOW"
### {}
set clean_quality_string [string range $qual_string 0 [expr $clean_length - 1]]
set fffff_quality_string $clean_quality_string
regsub -all {f} $fffff_quality_string "" fffff_quality_string
regsub -all {F} $fffff_quality_string "" fffff_quality_string
set abcd_qual_length [string length $fffff_quality_string]
set ffff_qual_length [expr $clean_length - $abcd_qual_length]
set abcd_qual_fract [expr ($abcd_qual_length*1.00/$clean_length)*100]
set abcd_qual_fract [expr ceil($abcd_qual_fract)]
set abcd_qual_fract [expr int($abcd_qual_fract)]
### puts $f_out_clean "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k
\[ LENGTH: $clean_length \] \( $gc_status: $gc_length\/$clean_length \) $super_quality "
puts $f_out_clean "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k \[
LENGTH: $clean_length \] \( $gc_status: $gc_length\/$clean_length \) \[ ABCD_Q:$abcd_qual_length
F_QUAL:$ffff_qual_length \] \[ Q_FRACT:$abcd_qual_fract \] "
puts $f_out_clean "$dna_clean"
puts $f_out_clean ""
puts $f_out_clean_qual "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | \(
$gc_status: $gc_length\/$clean_length \) \[ ABCD_Q:$abcd_qual_length F_QUAL:$ffff_qual_length \]
\[ Q_FRACT:$abcd_qual_fract \] "
puts $f_out_clean_qual $clean_quality_string
puts $f_out_clean_qual ""
}
if { $first_x >= [expr $good_length+1] } {
# COUNT ABCD and F QUALITY #
set qall_length [string length $qual_string]
set qfff_string $qual_string
regsub -all {f} $qfff_string "" qfff_string
regsub -all {F} $qfff_string "" qfff_string
regsub -all {x} $qfff_string "" qfff_string
regsub -all {X} $qfff_string "" qfff_string
set abcd_length [string length $qfff_string]
set qfx_length [expr $qall_length - $abcd_length]
set abcd_fract [expr ($abcd_length*1.00/$qall_length)*100]
set abcd_fract [expr ceil($abcd_fract)]
set abcd_fract [expr int($abcd_fract)]
puts $f_out "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k \[ FAIL:
$fail_str \] :: $string_qual :: CLEAN_LENGTH: $clean_length \[ ABCD_Q:$abcd_length
F_QUAL:$qfx_length \] \[ Q_FRACT:$abcd_fract \] "
puts $f_out "$dna_string"
puts $f_out ""
puts $f_out_qual "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y \[
ABCD_Q:$abcd_length F_QUAL:$qfx_length \] \[ Q_FRACT:$abcd_fract \] "
puts $f_out_qual "$qual_string"
puts $f_out_qual ""
}
if { $first_x < [expr $good_length+1] } {
puts $f_bad "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k \[ FAIL:
$fail_str \] :: $string_qual :: CLEAN_LENGTH: $clean_length "
puts $f_bad "$dna_string"
puts $f_bad ""
}
# puts $f_out ""
# puts $f_bad ""
if { $k <= 10000 } {
puts $f_bcl ""
}
incr k
}
close $f_in1
close $f_out
close $f_out_qual
close $f_out_clean
close $f_out_clean_qual
close $f_bad
close $f_bcl
puts ""
puts "DONE"
}
if {$argc != 5} {
puts "Program usage:"
puts "Table_to_Process, output_file_good, output_file_bad, output_file_base_call, id_prefix"
} else {
Sort_Table $argv
}
#!/usr/bin/tcl
proc Sort_Table {argv} {
# set exp_id "SAAA_"
# set upper_cut 600
# set upper_cut 400
# set upper_dif 200
# set upper_dif 100
set upper_cut 200
set upper_dif 60
set good_diff 100
set number_of_runs 100
set quality_upper_limit 1000
set good_length 24
set gc_upper 0.8
set gc_lower 0.2
set f_in1 [open [lindex $argv 0] "r"]
set f_out [open [lindex $argv 1] "w"]
set f_out_qual [open [lindex $argv 1].qual "w"]
set f_out_clean [open [lindex $argv 1].trim.fasta "w"]
set f_out_clean_qual [open [lindex $argv 1].trim.qual "w"]
set f_bad [open [lindex $argv 2] "w"]
set f_bcl [open [lindex $argv 3] "w"]
set exp_id [lindex $argv 4]
####### READ ID LIST TO EXTRACT #######
set k 1
while {[gets $f_in1 current_line] >= 0} {
set data_str [split $current_line "\t"]
set data_len [llength $data_str]
set line_id [lindex $data_str 0]
set cell_id [lindex $data_str 1]
set coord_x [lindex $data_str 2]
set coord_y [lindex $data_str 3]
# set num_str [lindex $data_str 4]
# set num_str [string trim $num_str]
puts "line: $k\tlength: $data_len"
if { $k <= 10000 } {
puts $f_bcl "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y COUNT: $k"
}
set dna_list ""
set qual_list ""
set n 4
# set first_x 0
set first_x $number_of_runs
set x_found "FALSE"
while { $n <= [expr $data_len - 1] } {
set num_str [lindex $data_str $n]
set num_str [string trim $num_str]
# four times
regsub -all { } $num_str " " num_str
regsub -all { } $num_str " " num_str
regsub -all { } $num_str " " num_str
regsub -all { } $num_str " " num_str
regsub -all { } $num_str "\t" num_str
set val_pos [expr $n - 3]
# ACGT values
set val_A [lindex $num_str 0]
set val_C [lindex $num_str 1]
set val_G [lindex $num_str 2]
set val_T [lindex $num_str 3]
###
# puts $num_str
set num_sorted [lsort -real $num_str]
# puts $num_sorted
set value_max1 [lindex $num_sorted 3]
set value_max2 [lindex $num_sorted 2]
set value_max_diff [expr $value_max1 - $value_max2]
### QUALITY SCORES ### 2008 March 25
set current_quality "X"
set value_ratio "X.XXXXXXXX"
if { $value_max1 != 0 } {
set value_ratio [expr $value_max2/$value_max1]
if { $value_ratio <= 0.2 } {
set current_quality "A"
}
if { $value_ratio <= 0.4 && $value_ratio > 0.2 } {
set current_quality "B"
}
if { $value_ratio <= 0.6 && $value_ratio > 0.4 } {
set current_quality "C"
}
if { $value_ratio <= 0.8 && $value_ratio > 0.6 } {
set current_quality "D"
}
if { $value_ratio > 0.8 } {
set current_quality "F"
}
}
if { $value_max1 >= $quality_upper_limit } {
set current_quality [string toupper $current_quality]
}
if { $value_max1 < $quality_upper_limit } {
set current_quality [string tolower $current_quality]
}
if { $value_max1 < $upper_cut } {
set current_quality "x"
}
###
set value_status "NONE"
set base_call "N"
# set first_x 0
# set x_found "FALSE"
if { $val_A >= $upper_cut || $val_C >= $upper_cut || $val_G >= $upper_cut || $val_T
>= $upper_cut } {
set value_status "HOPE"
set base_call "X"
if { $val_A >= [expr $val_C + $upper_dif] && $val_A >= [expr $val_G +
$upper_dif] && $val_A >= [expr $val_T + $upper_dif] } {
set base_call "A"
set value_status "GOOD"
}
if { $val_C >= [expr $val_A + $upper_dif] && $val_C >= [expr $val_G +
$upper_dif] && $val_C >= [expr $val_T + $upper_dif] } {
set base_call "C"
set value_status "GOOD"
}
if { $val_G >= [expr $val_A + $upper_dif] && $val_G >= [expr $val_C +
$upper_dif] && $val_G >= [expr $val_T + $upper_dif] } {
set base_call "G"
set value_status "GOOD"
}
if { $val_T >= [expr $val_A + $upper_dif] && $val_T >= [expr $val_C +
$upper_dif] && $val_T >= [expr $val_G + $upper_dif] } {
set base_call "T"
set value_status "GOOD"
}
}
if { $value_max_diff < $good_diff } {
set base_call [string tolower $base_call]
}
if { $val_A == 0.0 && $val_C == 0.0 && $val_G == 0.0 && $val_T == 0.0 } {
set value_status "CRAP"
set base_call "*"
}
if { $base_call == "*" && $x_found == "FALSE" } {
set first_x [expr $n - 3]
set x_found "TRUE"
}
### PUT ALL TOGETHER ###
set dna_list [ lappend dna_list $base_call ]
set qual_list [ lappend qual_list $current_quality ]
if { $first_x == $number_of_runs } {
set cut_q "--"
}
if { $first_x != $number_of_runs } {
set cut_q $first_x
}
if { $k <= 10000 } {
puts $f_bcl
"$val_pos\:\tA:$val_A\tC:$val_C\tG:$val_G\tT:$val_T\t$value_status\tBASE_CALL:->
$base_call\tFIRST_FAIL: $cut_q MAX_DIFF: $value_max_diff RATIO: $value_ratio QUALITY:
$current_quality"
}
incr n
}
# puts $f_out "$num_str"
set dna_string [join $dna_list ""]
set qual_string [join $qual_list ""]
set dna_clean $dna_string
set string_quality [string range $dna_string 0 [expr $good_length-1]]
regsub -all {n} $string_quality "" string_quality
regsub -all {N} $string_quality "" string_quality
regsub -all {x} $string_quality "" string_quality
regsub -all {X} $string_quality "" string_quality
regsub -all {\*} $string_quality "" string_quality
regsub -all {n.*} $dna_clean "" dna_clean
regsub -all {N.*} $dna_clean "" dna_clean
regsub -all {x.*} $dna_clean "" dna_clean
regsub -all {X.*} $dna_clean "" dna_clean
regsub -all {\*.*} $dna_clean "" dna_clean
set clean_length [string length $dna_clean]
set clean_upper [string toupper $dna_clean]
regsub -all {A} $clean_upper "" clean_upper
regsub -all {T} $clean_upper "" clean_upper
set gc_length [string length $clean_upper]
set gc_ratio -1
set gc_status "UNDEFINED"
if { $clean_length != 0 } {
set gc_ratio [expr $gc_length*1.00/$clean_length]
}
set gc_status "UNKNOWN"
if { $gc_ratio >= $gc_upper && $clean_length != 0 } {
set gc_status "UPPER_GC"
}
if { $gc_ratio <= $gc_lower && $clean_length != 0 } {
set gc_status "LOWER_GC"
}
if { $gc_ratio > $gc_lower && $gc_ratio < $gc_upper && $clean_length != 0 } {
set gc_status "___GC___"
}
# puts $string_quality
set string_quality_len [string length $string_quality]
set string_qual "UNKNOWN"
if { $string_quality_len >= $good_length } {
set string_qual "LONG__Q: $string_quality_len"
}
if { $string_quality_len < $good_length } {
set string_qual "SHORT_Q $string_quality_len"
}
set fail_str $first_x
if { $fail_str == 100 } {
set fail_str "--"
}
if { $clean_length >= $good_length } {
### set super_quality "QUAL_ABCD"
### set find_me_F [string first "F" [string range $qual_string 0 [expr $clean_length
- 1]]]
### set find_me_f [string first "f" [string range $qual_string 0 [expr $clean_length
- 1]]]
### set find_me_D [string first "D" [string range $qual_string 0 [expr $clean_length
- 1]]]
### set find_me_d [string first "d" [string range $qual_string 0 [expr $clean_length
- 1]]]
### if { $find_me_F != -1 || $find_me_f != -1 } {}
### set super_quality "QUAL_FLOW"
### {}
set clean_quality_string [string range $qual_string 0 [expr $clean_length - 1]]
set fffff_quality_string $clean_quality_string
regsub -all {f} $fffff_quality_string "" fffff_quality_string
regsub -all {F} $fffff_quality_string "" fffff_quality_string
set abcd_qual_length [string length $fffff_quality_string]
set ffff_qual_length [expr $clean_length - $abcd_qual_length]
set abcd_qual_fract [expr ($abcd_qual_length*1.00/$clean_length)*100]
set abcd_qual_fract [expr ceil($abcd_qual_fract)]
set abcd_qual_fract [expr int($abcd_qual_fract)]
### puts $f_out_clean "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k
\[ LENGTH: $clean_length \] \( $gc_status: $gc_length\/$clean_length \) $super_quality "
puts $f_out_clean "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k \[
LENGTH: $clean_length \] \( $gc_status: $gc_length\/$clean_length \) \[ ABCD_Q:$abcd_qual_length
F_QUAL:$ffff_qual_length \] \[ Q_FRACT:$abcd_qual_fract \] "
puts $f_out_clean "$dna_clean"
puts $f_out_clean ""
puts $f_out_clean_qual "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | \(
$gc_status: $gc_length\/$clean_length \) \[ ABCD_Q:$abcd_qual_length F_QUAL:$ffff_qual_length \]
\[ Q_FRACT:$abcd_qual_fract \] "
puts $f_out_clean_qual $clean_quality_string
puts $f_out_clean_qual ""
}
if { $first_x >= [expr $good_length+1] } {
# COUNT ABCD and F QUALITY #
set qall_length [string length $qual_string]
set qfff_string $qual_string
regsub -all {f} $qfff_string "" qfff_string
regsub -all {F} $qfff_string "" qfff_string
regsub -all {x} $qfff_string "" qfff_string
regsub -all {X} $qfff_string "" qfff_string
set abcd_length [string length $qfff_string]
set qfx_length [expr $qall_length - $abcd_length]
set abcd_fract [expr ($abcd_length*1.00/$qall_length)*100]
set abcd_fract [expr ceil($abcd_fract)]
set abcd_fract [expr int($abcd_fract)]
puts $f_out "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k \[ FAIL:
$fail_str \] :: $string_qual :: CLEAN_LENGTH: $clean_length \[ ABCD_Q:$abcd_length
F_QUAL:$qfx_length \] \[ Q_FRACT:$abcd_fract \] "
puts $f_out "$dna_string"
puts $f_out ""
puts $f_out_qual "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y \[
ABCD_Q:$abcd_length F_QUAL:$qfx_length \] \[ Q_FRACT:$abcd_fract \] "
puts $f_out_qual "$qual_string"
puts $f_out_qual ""
}
if { $first_x < [expr $good_length+1] } {
puts $f_bad "\>$exp_id$line_id\_$cell_id\_$coord_x\_$coord_y | LINE: $k \[ FAIL:
$fail_str \] :: $string_qual :: CLEAN_LENGTH: $clean_length "
puts $f_bad "$dna_string"
puts $f_bad ""
}
# puts $f_out ""
# puts $f_bad ""
if { $k <= 10000 } {
puts $f_bcl ""
}
incr k
}
close $f_in1
close $f_out
close $f_out_qual
close $f_out_clean
close $f_out_clean_qual
close $f_bad
close $f_bcl
puts ""
puts "DONE"
}
if {$argc != 5} {
puts "Program usage:"
puts "Table_to_Process, output_file_good, output_file_bad, output_file_base_call, id_prefix"
} else {
Sort_Table $argv
}
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Project atgc-illumina
created by akozik
- tools to process and manipulate Illumina sequences
tools to process and manipulate Illumina sequences
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