[mira_talk] Parsing SSAHA output with Mira 2.9.35x1

Hi Bastien:

I'm trying to screen out some midi and fusion primers (primer B) out of 454
fasta files using SSAHA ver 3.2. I'm using the commands  -wl 6 -da 0 -pf
with SSAHA to create a file  sal_BM_ssahavectorscreen_in.txt to parse.

The input files to mira are:


sal_BM_traceinfo_in.454.xml
sal_BM_in.454.fasta
sal_BM_in.454.fasta.qual
sal_BM_ssahavectorscreen_in.txt


My mira command is

 mira -job=denovo,est,accurate,454 -fasta -GE:kcim=yes:not=4:uti=no
-project=sal_BM  454_SETTINGS -LR:mxti=yes -CL::msvs=yes   &> log.txt


The sal_BM_ssahavectorscreen_in.txt looks like
======
FF      MID-1   1       12      FF3M6TC02IZ9WF  1       12      12
100.00
FF      MID-1   1       12      FF3M6TC02H6KM0  1       12      12
100.00
FF      MID-1   1       12      FF3M6TC02IWHHB  1       12      12
100.00
FF      MID-1   1       12      FF3M6TC02GIIEO  1       12      12
100.00
FF      MID-1   1       12      FF3M6TC02JUA9J  1       12      12
100.00
FF      MID-1   1       12      FF3M6TC02IHV0K  1       12      12
100.00
=======


But if I look in the sal_LB_d_log/sal_LB_int_clippings.0.txt file I get

======
load:  SSAHA clip left FF3M6TC02IZ9WF to: 0
load:  SSAHA clip left FF3M6TC02H6KM0 to: 0
load:  SSAHA clip left FF3M6TC02IWHHB to: 0
=======

Clipping info for FF3M6TC02IZ9WF, FF3M6TC02H6KM0 , FF3M6TC02IWHHB occur only
once in sal_LB_int_clippings.0.txt.

I conclude from the above that the clipping info in
sal_BM_ssahavectorscreen_in.txt  isn't getting into mira.

Am I missing something? Do you have any suggestions?


Thanks,
Greg


Gregory P. Harhay, PhD
Computational Biologist
Animal Health Research Unit
USDA-ARS-Roman L. Hruska  U.S. Meat Animal Research Center
Clay Center, NE 68933
v - 402.762.4250




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