Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 55:6cd12c71c3d3 draft

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Uploaded
author davidvanzessen
date Wed, 14 Jun 2017 11:14:00 -0400
parents f5fe63533c58
children ee807645b224
comparison
equal deleted inserted replaced
54:ba3220f921af 55:6cd12c71c3d3
553 553
554 cd $outdir/change_o 554 cd $outdir/change_o
555 555
556 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt 556 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
557 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt 557 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt
558 558 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-db-defined_first_clones.txt 2>&1
559
560 mkdir $outdir/new_IMGT_changeo
561 cp $outdir/new_IMGT/* $outdir/new_IMGT_changeo
562
563 Rscript $dir/new_imgt.r $outdir/new_IMGT_changeo $outdir/change_o/change-o-db-defined_first_clones.txt "-" 2>&1
564
565 cd $outdir/new_IMGT_changeo
566 tar -cJf ../new_IMGT_first_seq_of_clone.txz *
567 cd $outdir/change_o
568
569 rm -rf $outdir/new_IMGT_changeo
570
559 Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1 571 Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1
560
561 echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1" 572 echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1"
562 573
563 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then 574 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
564 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt 575 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
565 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGA.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-defined_clones-summary-IGA.txt 576 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGA.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-defined_clones-summary-IGA.txt
577 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-db-defined_first_clones-IGA.txt 2>&1
578
579 mkdir $outdir/new_IMGT_IGA_changeo
580 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA_changeo
581
582 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA_changeo $outdir/change_o/change-o-db-defined_first_clones-IGA.txt "-" 2>&1
583
584 cd $outdir/new_IMGT_IGA_changeo
585 tar -cJf ../new_IMGT_IGA_first_seq_of_clone.txz *
586
587 rm -rf $outdir/new_IMGT_IGA_changeo
588
589 cd $outdir/change_o
566 else 590 else
567 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt" 591 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
568 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt" 592 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
569 fi 593 fi
570 594
571 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then 595 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
572 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt 596 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
573 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGG.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-defined_clones-summary-IGG.txt 597 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGG.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-defined_clones-summary-IGG.txt
598 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-db-defined_first_clones-IGG.txt 2>&1
599
600 mkdir $outdir/new_IMGT_IGG_changeo
601 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG_changeo
602
603 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG_changeo $outdir/change_o/change-o-db-defined_first_clones-IGG.txt "-" 2>&1
604
605 cd $outdir/new_IMGT_IGG_changeo
606 tar -cJf ../new_IMGT_IGG_first_seq_of_clone.txz *
607 rm -rf $outdir/new_IMGT_IGG_changeo
608
609 cd $outdir/change_o
574 else 610 else
575 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt" 611 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
576 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt" 612 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
577 fi 613 fi
578 614
579 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then 615 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
580 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt 616 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
581 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGM.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-defined_clones-summary-IGM.txt 617 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGM.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-defined_clones-summary-IGM.txt
618 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-db-defined_first_clones-IGM.txt 2>&1
619
620 mkdir $outdir/new_IMGT_IGM_changeo
621 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM_changeo
622
623 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM_changeo $outdir/change_o/change-o-db-defined_first_clones-IGM.txt "-" 2>&1
624
625 cd $outdir/new_IMGT_IGM_changeo
626 tar -cJf ../new_IMGT_IGM_first_seq_of_clone.txz *
627
628 rm -rf $outdir/new_IMGT_IGM_changeo
629
630 cd $outdir/change_o
582 else 631 else
583 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt" 632 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
584 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt" 633 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
585 fi 634 fi
586 635
587 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then 636 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
588 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt 637 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
589 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGE.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-defined_clones-summary-IGE.txt 638 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGE.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-defined_clones-summary-IGE.txt
639 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-db-defined_first_clones-IGE.txt 2>&1
640
641 mkdir $outdir/new_IMGT_IGE_changeo
642 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE_changeo
643
644 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE_changeo $outdir/change_o/change-o-db-defined_first_clones-IGE.txt "-" 2>&1
645
646 cd $outdir/new_IMGT_IGE_changeo
647 tar -cJf ../new_IMGT_IGE_first_seq_of_clone.txz *
648
649 rm -rf $outdir/new_IMGT_IGE_changeo
650
651 cd $outdir/change_o
590 else 652 else
591 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt" 653 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
592 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt" 654 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
593 fi 655 fi
594 656
595 PWD="$tmp" 657 cd "$tmp"
658
659 rm -rf $outdir/new_IMGT
660 rm -rf $outdir/new_IMGT_IGA/
661 rm -rf $outdir/new_IMGT_IGA1/
662 rm -rf $outdir/new_IMGT_IGA2/
663 rm -rf $outdir/new_IMGT_IGG/
664 rm -rf $outdir/new_IMGT_IGG1/
665 rm -rf $outdir/new_IMGT_IGG2/
666 rm -rf $outdir/new_IMGT_IGG3/
667 rm -rf $outdir/new_IMGT_IGG4/
668 rm -rf $outdir/new_IMGT_IGM/
669 rm -rf $outdir/new_IMGT_IGE/
596 670
597 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab 671 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
598 672
599 function clonality_table { 673 function clonality_table {
600 local infile=$1 674 local infile=$1
710 784
711 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output 785 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
712 echo "<tr><td>The data for the IGA subclass distribution plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output 786 echo "<tr><td>The data for the IGA subclass distribution plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
713 echo "<tr><td>The data for the IGG subclass distribution plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output 787 echo "<tr><td>The data for the IGG subclass distribution plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output
714 788
789
715 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output 790 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
716 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output 791 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
717 echo "<tr><td>The Change-O DB file with defined clones and subclass annotation</td><td><a href='change_o/change-o-db-defined_clones.txt' download='change_o/change-o-db-defined_clones.txt' >Download</a></td></tr>" >> $output 792 echo "<tr><td>The Change-O DB file with defined clones and subclass annotation</td><td><a href='change_o/change-o-db-defined_clones.txt' download='change_o/change-o-db-defined_clones.txt' >Download</a></td></tr>" >> $output
718 echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt' download='change_o/change-o-defined_clones-summary.txt' >Download</a></td></tr>" >> $output 793 echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt' download='change_o/change-o-defined_clones-summary.txt' >Download</a></td></tr>" >> $output
794 echo "<tr><td>An IMGT archive with just just the first sequence of a clone</td><td><a href='new_IMGT_first_seq_of_clone.txz' download='new_IMGT_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
795
719 echo "<tr><td>The Change-O DB file with defined clones of IGA</td><td><a href='change_o/change-o-db-defined_clones-IGA.txt' download='change_o/change-o-db-defined_clones-IGA.txt' >Download</a></td></tr>" >> $output 796 echo "<tr><td>The Change-O DB file with defined clones of IGA</td><td><a href='change_o/change-o-db-defined_clones-IGA.txt' download='change_o/change-o-db-defined_clones-IGA.txt' >Download</a></td></tr>" >> $output
720 echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href='change_o/change-o-defined_clones-summary-IGA.txt' download='change_o/change-o-defined_clones-summary-IGA.txt' >Download</a></td></tr>" >> $output 797 echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href='change_o/change-o-defined_clones-summary-IGA.txt' download='change_o/change-o-defined_clones-summary-IGA.txt' >Download</a></td></tr>" >> $output
798 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGA)</td><td><a href='new_IMGT_IGA_first_seq_of_clone.txz' download='new_IMGT_IGA_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
799
721 echo "<tr><td>The Change-O DB file with defined clones of IGG</td><td><a href='change_o/change-o-db-defined_clones-IGG.txt' download='change_o/change-o-db-defined_clones-IGG.txt' >Download</a></td></tr>" >> $output 800 echo "<tr><td>The Change-O DB file with defined clones of IGG</td><td><a href='change_o/change-o-db-defined_clones-IGG.txt' download='change_o/change-o-db-defined_clones-IGG.txt' >Download</a></td></tr>" >> $output
722 echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href='change_o/change-o-defined_clones-summary-IGG.txt' download='change_o/change-o-defined_clones-summary-IGG.txt' >Download</a></td></tr>" >> $output 801 echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href='change_o/change-o-defined_clones-summary-IGG.txt' download='change_o/change-o-defined_clones-summary-IGG.txt' >Download</a></td></tr>" >> $output
802 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGG)</td><td><a href='new_IMGT_IGG_first_seq_of_clone.txz' download='new_IMGT_IGG_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
803
723 echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href='change_o/change-o-db-defined_clones-IGM.txt' download='change_o/change-o-db-defined_clones-IGM.txt' >Download</a></td></tr>" >> $output 804 echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href='change_o/change-o-db-defined_clones-IGM.txt' download='change_o/change-o-db-defined_clones-IGM.txt' >Download</a></td></tr>" >> $output
724 echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output 805 echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output
806 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGM)</td><td><a href='new_IMGT_IGM_first_seq_of_clone.txz' download='new_IMGT_IGM_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
807
725 echo "<tr><td>The Change-O DB file with defined clones of IGE</td><td><a href='change_o/change-o-db-defined_clones-IGE.txt' download='change_o/change-o-db-defined_clones-IGE.txt' >Download</a></td></tr>" >> $output 808 echo "<tr><td>The Change-O DB file with defined clones of IGE</td><td><a href='change_o/change-o-db-defined_clones-IGE.txt' download='change_o/change-o-db-defined_clones-IGE.txt' >Download</a></td></tr>" >> $output
726 echo "<tr><td>The Change-O DB defined clones summary file of IGE</td><td><a href='change_o/change-o-defined_clones-summary-IGE.txt' download='change_o/change-o-defined_clones-summary-IGE.txt' >Download</a></td></tr>" >> $output 809 echo "<tr><td>The Change-O DB defined clones summary file of IGE</td><td><a href='change_o/change-o-defined_clones-summary-IGE.txt' download='change_o/change-o-defined_clones-summary-IGE.txt' >Download</a></td></tr>" >> $output
810 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGE)</td><td><a href='new_IMGT_IGE_first_seq_of_clone.txz' download='new_IMGT_IGE_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
727 811
728 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output 812 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
729 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz' download='new_IMGT.txz' >Download</a></td></tr>" >> $output 813 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz' download='new_IMGT.txz' >Download</a></td></tr>" >> $output
730 echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='new_IMGT_IGA.txz' download='new_IMGT_IGA.txz' >Download</a></td></tr>" >> $output 814 echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='new_IMGT_IGA.txz' download='new_IMGT_IGA.txz' >Download</a></td></tr>" >> $output
731 echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='new_IMGT_IGA1.txz' download='new_IMGT_IGA1.txz' >Download</a></td></tr>" >> $output 815 echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='new_IMGT_IGA1.txz' download='new_IMGT_IGA1.txz' >Download</a></td></tr>" >> $output