Mercurial > repos > fubar > htseq_bams_to_count_matrix
changeset 15:9b2f58a260e9 draft
Uploaded
| author | fubar |
|---|---|
| date | Fri, 07 Jun 2013 02:46:09 -0400 |
| parents | b227f5edbe52 |
| children | 63eaa64904be |
| files | htseq_bams_to_count_matrix/generatetest.sh htseq_bams_to_count_matrix/htseqsams2mx.py htseq_bams_to_count_matrix/htseqsams2mx.xml htseq_bams_to_count_matrix/test-data/htseqsams2mx_test1_out.xls |
| diffstat | 4 files changed, 16 insertions(+), 12 deletions(-) [+] |
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--- a/htseq_bams_to_count_matrix/generatetest.sh Fri Jun 07 01:50:53 2013 -0400 +++ b/htseq_bams_to_count_matrix/generatetest.sh Fri Jun 07 02:46:09 2013 -0400 @@ -1,1 +1,2 @@ -python ../htseqsams2mx.py -g rn4_chr20_100k.gtf -o test.xls --samf "'rn4chr20test1.bam','col1'" --samf "'rn4chr20test2.bam','col2'" +#python ../htseqsams2mx.py -g rn4_chr20_100k.gtf -o test.xls --samf "'rn4chr20test1.bam','col1'" --samf "'rn4chr20test2.bam','col2'" +python ../htseqsams2mx.py -g rn4_chr20_100k.gtf -o htseqsams2mx_test1_out.xls --samf "'rn4chr20test1.bam',''" --samf "'rn4chr20test2.bam',''"
--- a/htseq_bams_to_count_matrix/htseqsams2mx.py Fri Jun 07 01:50:53 2013 -0400 +++ b/htseq_bams_to_count_matrix/htseqsams2mx.py Fri Jun 07 02:46:09 2013 -0400 @@ -306,6 +306,8 @@ assert os.path.isfile(b),'## Supplied input sam file "%s" not found' % b sam_filenames.append(b) sampName = scolnames[i] # better be unique + if sampName == "": + sampName = b # for test sampName = sampName.replace('#','') # for R sampName = sampName.replace('(','') # for R sampName = sampName.replace(')','') # for R
--- a/htseq_bams_to_count_matrix/htseqsams2mx.xml Fri Jun 07 01:50:53 2013 -0400 +++ b/htseq_bams_to_count_matrix/htseqsams2mx.xml Fri Jun 07 02:46:09 2013 -0400 @@ -13,17 +13,19 @@ <command interpreter="python"> htseqsams2mx.py -g "$gfffile" -o "$outfile" -m "$model" --id_attribute "$id_attr" --feature_type "$feature_type" --samf "'$firstsamf','${firstsamf.name}'" - #if secondsamfile: + #if $secondsamf: --samf "'$secondsamf','${secondsamf.name}'" #end if - #if thirdsamfile: + #if $thirdsamf: --samf "'$thirdsamf','${thirdsamf.name}'" #end if - #if fourthsamfile: + #if $fourthsamf: --samf "'$fourthsamf','${fourthsamf.name}'" #end if #for $s in $samfiles: - --samf "'${s.samf}','${s.samf.name}'" + #if $s.samf.name: + --samf "'${s.samf}','${s.samf.name}'" + #end if #end for </command> <inputs> @@ -72,16 +74,15 @@ <tests> <test> <param name="feature_type" value="exon" /> + <param name="gfffile" value="rn4_chr20_100k.gtf" /> <param name="firstsamf" dbkey='rn4' ftype="bam" value="rn4chr20test1.bam" /> - <param name="firstsamf.name" value="rn4chr20test1.bam" /> <param name="id_attr" value="gene_id" /> <param name="model" value="union" /> <param name="stranded" value="no" /> - <param name="title" value="htseq test" /> - <param name="mapqmin" value="0" /> - <param name="secondsamfile" value="rn4chr20test2.bam" ftype="bam" dbkey="rn4" /> - <param name="secondsamfile.name" value="rn4chr20test2.bam" /> - <output name="outfile" file="htseqsams2mx_test1_out.xls" ftype="tabular" lines_diff="30"/> + <param name="title" value="htseqtest" /> + <param name="mapqMin" value="0" /> + <param name="secondsamf" value="rn4chr20test2.bam" ftype="bam" dbkey="rn4" /> + <output name="outfile" file="htseqsams2mx_test1_out.xls" ftype="tabular" lines_diff="1"/> </test> </tests> <help>
--- a/htseq_bams_to_count_matrix/test-data/htseqsams2mx_test1_out.xls Fri Jun 07 01:50:53 2013 -0400 +++ b/htseq_bams_to_count_matrix/test-data/htseqsams2mx_test1_out.xls Fri Jun 07 02:46:09 2013 -0400 @@ -1,4 +1,4 @@ -Contig col1 col2 +Contig rn4chr20test1.bam rn4chr20test2.bam Clic2 494 944 F1M7K0_RAT 3 2 Tmlhe 164 172