Mercurial > repos > stef > falco
changeset 74:00f63511d177 draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 27 Feb 2015 09:45:42 -0500 |
| parents | 78f10251a484 |
| children | 3515b026d78b |
| files | falco-filter-report.sh falco-filter-report.xml falco/lib/perl/filter.pl |
| diffstat | 3 files changed, 25 insertions(+), 16 deletions(-) [+] |
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--- a/falco-filter-report.sh Fri Feb 27 09:33:15 2015 -0500 +++ b/falco-filter-report.sh Fri Feb 27 09:45:42 2015 -0500 @@ -20,12 +20,19 @@ ## ---------- ## set params ## ---------- -# if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default is "None" for some reason -# then -# FILTER_PARAM=" --filter "$filter_file -# else -# FILTER_PARAM="" -# fi +if [[ $canonicals_file != 'None' && $canonicals_file != '' ]] # Galaxy default is "None" for some reason +then + CANONICALS_PARAM=" --canonicals "$canonicals_file +else + CANONICALS_PARAM="" +fi + +if [[ $vcf2_file != 'None' && $vcf2_file != '' ]] # Galaxy default is "None" for some reason +then + VCF2_PARAM=" --vcfOther "$vcf2_file +else + VCF2_PARAM="" +fi # if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None" for some reason # then @@ -66,7 +73,7 @@ ## running analysis ## ---------- echo "[INFO] Starting FALCO reporting" -CMD_STRING="$TOOLDIR/falco/bin/falco-filter-report --vcf $vcf_file --output $vcf_base --qc_ann_qual_txt $qc_ann_qual_file --qc2_ann_txt $qc2_ann_txt_file --qc_targets_txt $qc_targets_txt_file" +CMD_STRING="$TOOLDIR/falco/bin/falco-filter-report --vcf $vcf_file --output $vcf_base --qc_ann_qual_txt $qc_ann_qual_file --qc2_ann_txt $qc2_ann_txt_file --qc_targets_txt $qc_targets_txt_file $VCF2_PARAM $CANONICALS_PARAM" echo "[INFO] "$CMD_STRING perl $CMD_STRING echo "[INFO] done with FALCO reporting"
--- a/falco-filter-report.xml Fri Feb 27 09:33:15 2015 -0500 +++ b/falco-filter-report.xml Fri Feb 27 09:45:42 2015 -0500 @@ -50,6 +50,7 @@ <param format="tsv" name="qc_ann_qual" optional="false" type="data" label="qc_ann_qual file" help=""/> <param format="tsv" name="qc2_ann_txt" optional="false" type="data" label="qc2_ann_txt file" help=""/> <param format="tsv" name="qc_targets_txt" optional="false" type="data" label="qc_targets_txt file" help=""/> + <param format="tsv" name="canonicals" optional="true" type="data" label="canonicals file" help=""/> <!-- ==================== --> <!-- Option to use your own bin annotations --> @@ -65,6 +66,7 @@ vcf_file=$vcf vcf_file2=$vcf2 + canonicals_file=$canonicals qc_ann_qual_file=$qc_ann_qual qc2_ann_txt_file=$qc2_ann_txt
--- a/falco/lib/perl/filter.pl Fri Feb 27 09:33:15 2015 -0500 +++ b/falco/lib/perl/filter.pl Fri Feb 27 09:45:42 2015 -0500 @@ -81,15 +81,15 @@ $trans =~ s/\..*$//; ## impossible to switch off these two transcript filters - ## so commented out for now - # if (not exists($nm{$trans})) { - # print STDERR "Unknown transcript: $row[$col{Gene_Name}] $trans\n"; - # next; - # } - # elsif ($nm{$trans} != 0) { - # print STDERR "Non cannonical: $row[$col{Gene_Name}] $trans\n"; - # next; - # } + ## so comment these out if no other way provided + if (not exists($nm{$trans})) { + print STDERR "Unknown transcript: $row[$col{Gene_Name}] $trans\n"; + next; + } + elsif ($nm{$trans} != 0) { + print STDERR "Non cannonical: $row[$col{Gene_Name}] $trans\n"; + next; + } # Annotate clinincal variants and cosmic mutations