polish of QA_Illumina_report.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1995 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_scripts/QA_Illumina_report.rb b/bp_scripts/QA_Illumina_report.rb
index 7b54e4df88ac875912e37bd15ca8434c786dbce7..d82c0cf4b1793c1091dc46844ca129639ef3e2ee 100755 (executable)
--- a/bp_scripts/QA_Illumina_report.rb
+++ b/bp_scripts/QA_Illumina_report.rb
@@ -74,8 +74,8 @@ system(
    plot_distribution -k SEQ_LEN -T 'Sequence length distribution' -X 'Sequence length' -t png -o #{lendist_file} |
    plot_scores -c -t png -o #{scores_file} |
    plot_nucleotide_distribution -t png -o #{nucdist_file} |
-   bin_vals -k SEQ_LEN -b 50 |
-   plot_distribution -T '50 bases bin sequence length distribution' -X 'Sequence length' -k SEQ_LEN_BIN -t png -o #{lendist_bin_file} |
+   bin_vals -k SEQ_LEN -b 25 |
+   plot_distribution -T '25 bases bin sequence length distribution' -X 'Sequence length' -k SEQ_LEN_BIN -t png -o #{lendist_bin_file} |
    mean_scores |
    bin_vals -k SCORES_MEAN -b 5 |
    plot_distribution -k SCORES_MEAN_BIN -T '5 bin mean score distribution' -X 'Mean scores' -t png -o #{scores_bin_file} -x"

diff --git a/bp_scripts/QA_Solexa_report.sh b/bp_scripts/QA_Solexa_report.sh
deleted file mode 100755 (executable)
index e76e1d9..0000000
--- a/bp_scripts/QA_Solexa_report.sh
+++ /dev/null
@@ -1,167 +0,0 @@
-#!/bin/bash
-
-# Copyright (C) 2010 Martin A. Hansen (mail@maasha.dk).
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-fastq_files=$@
-
-if [ ! $1 ]; then
-    echo
-    echo "QA_Solexa_report.sh generates a quality assurance report for"
-    echo "each of a given number of Solexa/Illumina FASTQ files."
-    echo
-    echo "Usage: `basename $0` <FASTQ file(s)>"
-    echo
-    exit
-fi
-
-function puts
-{
-    msg=$1
-
-    echo $msg >> $out_file
-}
-
-function pcat
-{
-    file=$1
-
-    cat $file >> $out_file
-}
-
-for fastq_file in $fastq_files; do
-    base=`basename $fastq_file`
-    date=`date | sed 's/[ :]/_/g' | sed 's/__/_/g'`
-    tmp_dir="$HOME/QA_Solexa_report_$date"
-    out_file="$tmp_dir/QA_Solexa_report_$date.txt"
-    plot_scores="$tmp_dir/plot_scores.txt"
-    plot_lendist="$tmp_dir/plot_lendist.txt"
-    freq_table="$tmp_dir/freq_table.txt"
-    read_count="$tmp_dir/read_count.txt"
-    read_length="$tmp_dir/read_length.txt"
-    top30_reads="$tmp_dir/top30_reads.txt"
-
-    if [ ! -d $tmp_dir ]; then
-        mkdir $tmp_dir
-    fi
-
-    read_fastq -n 1 -i $fastq_file |
-    write_tab -k SEQ_LEN -o $read_length -x
-
-    echo "" && echo "Plotting scores and length distributions ... "
-    read_fastq -i $fastq_file |
-    progress_meter -c 10000 |
-    count_records -o $read_count |
-    plot_scores -o $plot_scores -Y "Mean score" -X "Sequence length" |
-    trim_seq |
-    bin_vals -k SEQ_LEN |
-    plot_lendist -k SEQ_LEN_BIN -o $plot_lendist -Y "Count" -X "Sequence Length (5nt bins)" -x
-
-    echo "" && echo "Running composition analysis on sequences ... "
-    read_fastq -i $fastq_file |
-    progress_meter -c 10000 |
-    create_weight_matrix -p |
-    flip_tab |
-    write_tab -o $freq_table -x
-
-    echo "" && echo "Locating top 30 unique reads ... "
-    read_fastq -i $fastq_file |
-    progress_meter -c 10000 |
-    uniq_seq -c |
-    sort_records -rk SEQ_COUNTn |
-    head_records -n 30 |
-    write_tab -ck SEQ_COUNT,SEQ -o $top30_reads -x
-
-    echo "" && echo -n "Generating report ... "
-    puts ""
-    puts ""
-    puts ""
-    puts "QA Solexa Report"
-    puts "============="
-    puts ""
-    puts ""
-    puts ""
-    puts "Date: `date`"
-    puts ""
-    puts "File: `pwd`/$fastq_file"
-    puts ""
-    puts ""
-    puts "Sequence analysis"
-    puts "-----------------"
-    puts ""
-    puts ""
-    puts "Read length:"
-    puts ""
-    pcat $read_length
-    puts ""
-    puts "Read count:"
-    puts ""
-    pcat $read_count
-    puts ""
-    puts ""
-    puts "Quality score means"
-    puts "-------------------"
-    puts ""
-    puts ""
-    puts "The mean scores of the untrimmed sequences:"
-    puts ""
-    pcat $plot_scores
-    puts ""
-    puts ""
-    puts "Sequence length distribution"
-    puts "----------------------------"
-    puts ""
-    puts ""
-    puts "The length distribution of trimmed reads where the lengths are binned in buckets of size 5:"
-    puts ""
-    pcat $plot_lendist
-    puts ""
-    puts ""
-    puts "Residue frequency analysis"
-    puts "--------------------------"
-    puts ""
-    puts ""
-    puts "The below table contains the residue frequency (in percent) of all base positions:"
-    puts ""
-    pcat $freq_table
-    puts ""
-    puts ""
-    puts "Top 30 reads"
-    puts "--------------------------"
-    puts ""
-    puts ""
-    pcat $top30_reads
-    puts ""
-    puts ""
-    puts "end."
-
-    rm $plot_scores
-    rm $plot_lendist
-    rm $freq_table
-    rm $read_count
-    rm $read_length
-    rm $top30_reads
-
-    echo "done."
-
-    echo ""
-    echo "Report located here: $out_file"
-    echo ""
-done
-
-echo "All done."