--- /dev/null
+#!/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
+
+sff_files=$@
+
+if [ ! $1 ]; then
+ echo
+ echo "QA_454_report.sh generates a quality assurance report for"
+ echo "each of a given number of Roche/FLX 454 .sff files."
+ echo
+ echo "Usage: `basename $0` <sff file(s)>"
+ echo
+ exit
+fi
+
+function puts
+{
+ msg=$1
+
+ echo $msg >> $out_file
+}
+
+function pcat
+{
+ file=$1
+
+ cat $file >> $out_file
+}
+
+for sff_file in $sff_files; do
+ base=`basename $sff_file .sff`
+
+ tmp_dir="$HOME/QA_454_report_$base"
+
+ if [ ! -d $tmp_dir ]; then
+ mkdir $tmp_dir
+ fi
+
+ fq_file="$tmp_dir/$base.fq"
+ xml_file="$tmp_dir/$base.xml"
+ out_file="$tmp_dir/QA_454_report_$base.txt"
+
+ if [ -f $out_file ]; then
+ mv $out_file "$out_file.bak"
+ fi
+
+ analysis_vals="$tmp_dir/analysis_vals.txt"
+ analysis_seqs="$tmp_dir/analysis_seqs.txt"
+ plot_lendist_unclipped="$tmp_dir/plot_lendist_unclipped.txt"
+ plot_lendist_clipped="$tmp_dir/plot_lendist_clipped.txt"
+ plot_scores_unclipped="$tmp_dir/plot_scores_unclipped.txt"
+ plot_scores_clipped="$tmp_dir/plot_scores_clipped.txt"
+ plot_mean_scores="$tmp_dir/plot_mean_scores.txt"
+ count_score_mean="$tmp_dir/count_score_mean.txt"
+ table_mid="$tmp_dir/table_mid.tab"
+ table_mid_len="$tmp_dir/table_mid_len.tab"
+ table_mid_len_score="$tmp_dir/table_mid_len_score.tab"
+ table_mid_join="$tmp_dir/table_mid_join.tab"
+ table_freq="$tmp_dir/table_freq.tab"
+
+ # sff_extract is a 3rd party tool from the MIRA package.
+ # http://sourceforge.net/projects/mira-assembler/files/
+ echo -n "Converting sff file $sff_file to FASTQ format ... "
+ sff_extract --fastq $sff_file --seq_file $fq_file --xml_file $xml_file > /dev/null 2>&1
+ echo "done."
+
+ # Using Biopieces -> www.biopieces.org
+
+ echo "" && echo "Running composition analysis on sequences ... "
+ read_fastq -i $fq_file |
+ progress_meter |
+ analyze_vals -k SEQ -o $analysis_vals |
+ analyze_seq |
+ mean_vals -k 'GC%,HARD_MASK%,SOFT_MASK%' |
+ grab -e 'REC_TYPE eq MEAN' |
+ write_tab -ck 'GC%_MEAN,HARD_MASK%_MEAN,SOFT_MASK%_MEAN' -o $analysis_seqs -x
+
+ echo "" && echo "Plotting length distributions and scores before and after clipping ..."
+ read_fastq -i $fq_file |
+ progress_meter |
+ bin_vals -k SEQ_LEN -b 50 |
+ plot_lendist -k SEQ_LEN_BIN -T "Length Distribution - unclipped" -X "50 nucleotide bins" -Y "Count" -o $plot_lendist_unclipped |
+ plot_scores -o $plot_scores_unclipped -X "Sequence length" -Y "Score" |
+ clip_seq |
+ bin_vals -k SEQ_LEN -b 50 |
+ plot_lendist -k SEQ_LEN_BIN -T "Length Distribution - clipped" -X "50 nucleotide bins" -Y "Count" -o $plot_lendist_clipped |
+ plot_scores -o $plot_scores_clipped -X "Sequence length" -Y "Score" -x
+
+ echo "" && echo "Plotting mean score bins and counting mean scores greater than 20 ... "
+ read_fastq -i $fq_file |
+ progress_meter |
+ mean_scores |
+ bin_vals -k SCORES_MEAN -b 5 |
+ plot_histogram -s num -k SCORES_MEAN_BIN -T "Mean score bins" -X "Bins (size 5)" -Y "Count" -o $plot_mean_scores |
+ grab -e 'SCORES_MEAN >= 20' |
+ count_records -o $count_score_mean -x
+
+ echo "" && echo "Locating and counting MID tags ... "
+ read_fastq -i $fq_file |
+ progress_meter |
+ find_mids |
+ write_tab -o $table_mid -c -k MID_NUM,MID_SEQ,MID_COUNT -x
+
+ echo "" && echo "Locating and counting MID tags for sequences longer than 250 ... "
+ read_fastq -i $fq_file |
+ progress_meter |
+ grab -e 'SEQ_LEN >= 250' |
+ find_mids |
+ write_tab -o $table_mid_len -c -k MID_NUM,MID_SEQ,MID_COUNT -x
+
+ echo "" && echo "Locating and counting MID tags for sequences longer than 250 and mean score above 20 ... "
+ read_fastq -i $fq_file |
+ progress_meter |
+ grab -e 'SEQ_LEN >= 250' |
+ mean_scores |
+ grab -e 'SCORES_MEAN >= 20' |
+ find_mids |
+ write_tab -o $table_mid_len_score -c -k MID_NUM,MID_SEQ,MID_COUNT -x
+
+ echo "" && echo -n "Joining MID tables ... "
+ read_tab -i $table_mid |
+ rename_keys -k MID_NUM,A |
+ rename_keys -k MID_COUNT,TOTAL |
+ read_tab -i $table_mid_len |
+ rename_keys -k MID_NUM,B |
+ rename_keys -k MID_COUNT,L250 |
+ merge_records -k A,B |
+ read_tab -i $table_mid_len_score |
+ rename_keys -k MID_NUM,C |
+ rename_keys -k MID_COUNT,L250_S20 |
+ merge_records -k A,C |
+ rename_keys -k A,MID_NUM |
+ sort_records -k MID_NUMn |
+ write_tab -o $table_mid_join -c -k MID_NUM,MID_SEQ,TOTAL,L250,L250_S20 -x
+ echo "done."
+
+ echo "" && echo "Creating residue frequency table ... "
+ read_fastq -i $fq_file |
+ progress_meter |
+ extract_seq -l 50 |
+ uppercase_seq |
+ create_weight_matrix -p |
+ flip_tab |
+ write_tab -o $table_freq -x
+
+ echo "" && echo -n "Generating report ... "
+ puts ""
+ puts ""
+ puts ""
+ puts "QA 454 Report"
+ puts "============="
+ puts ""
+ puts ""
+ puts ""
+ puts "Date: `date`"
+ puts ""
+ puts "File: `pwd`/$sff_file"
+ puts ""
+ puts ""
+ puts "Sequence analysis"
+ puts "-----------------"
+ puts ""
+ puts ""
+ puts "The below table contains some basic info:"
+ puts ""
+ puts " COUNT is the number of sequences in the file."
+ puts " MIN is the minimum sequence length found."
+ puts " MAX is the maximum sequence length found."
+ puts " MEAN is the mean sequence length found."
+ puts " SUM is the total number of bases in the file."
+ puts ""
+ pcat $analysis_vals
+ puts ""
+ puts ""
+ puts "Sequence composition"
+ puts "--------------------"
+ puts ""
+ puts ""
+ puts "The below table contains composition analysis of the sequences:"
+ puts ""
+ puts " GC%_MEAN is the mean GC content."
+ puts " HARD_MASK%_MEAN is the mean of hard masked sequence (i.e. % of N's)."
+ puts " SOFT_MASK%_MEAN is the mean of soft masked sequence (i.e. lowercase residues = clipped sequence)."
+ puts ""
+ pcat $analysis_seqs
+ puts ""
+ puts ""
+ puts "Sequence length distribution"
+ puts "----------------------------"
+ puts ""
+ puts ""
+ puts "The length distribution of unclipped reads where the lengths are binned in buckets of size 50:"
+ puts ""
+ pcat $plot_lendist_unclipped
+ puts ""
+ puts "The length distribution of clipped reads where the lengths are binned in buckets of size 50:"
+ puts ""
+ pcat $plot_lendist_clipped
+ puts ""
+ puts ""
+ puts "Quality score means"
+ puts "-------------------"
+ puts ""
+ puts ""
+ puts "The mean scores of the unclipped sequences:"
+ puts ""
+ pcat $plot_scores_unclipped
+ puts ""
+ puts "The mean scores of the clipped sequences:"
+ puts ""
+ pcat $plot_scores_clipped
+ puts ""
+ puts "Histogram of bins with mean quality scores:"
+ puts ""
+ pcat $plot_mean_scores
+ puts ""
+ puts "Number of sequences with a mean score >= 20:"
+ puts ""
+ pcat $count_score_mean
+ puts ""
+ puts ""
+ puts "MID tag analysis"
+ puts "----------------"
+ puts ""
+ puts ""
+ puts "The below table contains the identified MID tags and the number of times they were found:"
+ puts ""
+ puts " MID_NUM is the MID tag identifier."
+ puts " MID_SEQ is the sequence of the MID tag."
+ puts " TOTAL is the number of times this MID tag was found."
+ puts " L250 is the a subset count of TOTAL af sequences longer than 250 bases"
+ puts " L250_S20 is a subset count of L250 af sequences with a mean score above 20"
+ puts ""
+ pcat $table_mid_join
+ puts ""
+ puts ""
+ puts "Residue frequency analysis"
+ puts "--------------------------"
+ puts ""
+ puts ""
+ puts "The below table contains the residue frequency (in percent) of the first 50 bases:"
+ puts ""
+ pcat $table_freq
+ puts ""
+ puts "end."
+
+ rm $fq_file
+ rm $xml_file
+ rm $analysis_vals
+ rm $analysis_seqs
+ rm $plot_lendist_unclipped
+ rm $plot_lendist_clipped
+ rm $plot_scores_unclipped
+ rm $plot_scores_clipped
+ rm $plot_mean_scores
+ rm $count_score_mean
+ rm $table_mid
+ rm $table_mid_len
+ rm $table_mid_len_score
+ rm $table_mid_join
+ rm $table_freq
+
+ echo "done."
+
+ echo ""
+ echo "Report located here: $out_file"
+ echo ""
+done
+
+echo "All done."
projects / biopieces.git / commitdiff