Mercurial > repos > fubar > htseq_bams_to_count_matrix

changeset 50:0edc994d4021 draft

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Uploaded
author iuc
date Wed, 18 Feb 2015 11:37:05 -0500
parents c57e63d1a9d2
children d641738a7b3a
files generatetest.sh htseqsams2mx.py test-data/generatetest.sh test-data/rn4chr20test1.bam.bai test-data/rn4chr20test2.bam.bai tool_dependencies.xml
diffstat 6 files changed, 5 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/generatetest.sh	Fri Jan 02 03:32:39 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-python ../htseqsams2mx.py -g rn4_chr20_100k.gtf -o test.xls --samf "'rn4chr20test1.bam','col1'" --samf "'rn4chr20test2.bam','col2'"
--- a/htseqsams2mx.py	Fri Jan 02 03:32:39 2015 -0500
+++ b/htseqsams2mx.py	Wed Feb 18 11:37:05 2015 -0500
@@ -130,8 +130,8 @@
            hasbai = sam_bais[sami] > ''
            if hasbai:
                tempname = os.path.splitext(os.path.basename(sam_filename))[0]
-               tempbam = '%s.bam' % tempname
-               tempbai = '%s.bai' % tempname
+               tempbam = '%s_TEMP.bam' % tempname
+               tempbai = '%s_TEMP.bai' % tempname
                os.link(sam_filename,tempbam)
                os.link(sam_bais[sami],tempbai)
            try:
--- a/test-data/generatetest.sh	Fri Jan 02 03:32:39 2015 -0500
+++ b/test-data/generatetest.sh	Wed Feb 18 11:37:05 2015 -0500
@@ -1,3 +1,1 @@
-#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','test1','bam','rn4chr20test1.bai'" --samf "'rn4chr20test2.bam','test2','bam','rn4chr20test2.bai'"
-
+python ../htseqsams2mx.py -g rn4_chr20_100k.gtf -o test.xls --samf "'rn4chr20test1.bam','rn4chr20test1.bam','bam','rn4chr20test1.bam.bai'" --samf "'rn4chr20test2.bam','rn4chr20test2.bam','bam','rn4chr20test2.bam.bai'"
Binary file test-data/rn4chr20test1.bam.bai has changed
Binary file test-data/rn4chr20test2.bam.bai has changed
--- a/tool_dependencies.xml	Fri Jan 02 03:32:39 2015 -0500
+++ b/tool_dependencies.xml	Wed Feb 18 11:37:05 2015 -0500
@@ -4,7 +4,7 @@
         <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="de9c362fb3f2" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="b08a9f0f28ec" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="htseq" version="0.5.4p3">
         <install version="1.0">
@@ -14,7 +14,7 @@
                         <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="pysam" version="0.7.6" />
                         </repository>
-                        <repository changeset_revision="de9c362fb3f2" name="package_matplotlib_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="b08a9f0f28ec" name="package_matplotlib_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="matplotlib" version="1.2.1" />
                         </repository>
                 </action>