bethany reads

GSM1462461,GSM1462462,GSM1462463,GSM1462464,GSM1462465,GSM1462466,GSM1462467,GSM1462468,GSM1462469,GSM1462470,GSM1589798,GSM1589799
BCL6_REP1_ChIPSeq,BCL6_REP1_INPUT,H3K4me1_REP1_ChIPSeq,H3K4me1_REP2_ChIPSeq,H3K4me3_REP1_ChIPSeq,H3K4me3_REP2_ChIPSeq,H3K27ac_REP1_ChIPSeq,H3K27ac_REP2_ChIPSeq,INPUT1_ChIPSeq,INPUT2_ChIPSeq,BCL6_REP2_ChIPSeq,BCL6_REP2_INPUT
200,200,200,200,200,200,200,200,200,200,200,200

[zfu@login-0-0 src]$ python mergeAllLowCoverageRegions.py Sample_9-1 ../02.Mapping/9-1_coverage_cutoff10_merged.tsv ../../Merge.LowCoverage.tsv ../../00.RawData/R6_Feature.bed
../../Merge.LowCoverage.tsv  do not exist!
Sample_9-1     2174     36149

[zfu@login-0-0 src]$
[zfu@login-0-0 src]$ python mergeAllGaps.py Sample_9-1 ../02.Mapping/9-1_sorted_0Coverage.bedGraph ../../Merged.Gaps.tsv ../../00.RawData/R6_Feature.bed
../../Merged.Gaps.tsv  do not exist!
Traceback (most recent call last):
  File "mergeAllGaps.py", line 61, in <module>
    if (start >= Feature_Hash[gene][0]) and (start <= Feature_Hash[gene][1]):
NameError: name 'start' is not defined
[zfu@login-0-0 src]$
[zfu@login-0-0 src]$ python mergeSNPs.py Sample_9-1 ../03.Freebayes/9-1_snpInfo.tsv ../../Merge.SNPs.tsv ../../00.RawData/R6_Feature.bed 'gi|15902044|ref|NC_003098.1|:'
../../Merge.SNPs.tsv  do not exist!
Sample_9-1     41857

[zfu@login-0-0 src]$
[zfu@login-0-0 src]$ python mergeSNPs.py Sample_9-1 ../03.Freebayes/9-1_snpInfo.filtered.tsv ../../Merge.SNPs.filtered.tsv ../../00.RawData/R6_Feature.bed 'gi|15902044|ref|NC_003098.1|:'
../../Merge.SNPs.filtered.tsv  do not exist!
Sample_9-1     11255

[zfu@login-0-0 src]$ python mergeAllGaps.py Sample_9-1 ../02.Mapping/9-1_sorted_0Coverage.bedGraph ../../Merged.Gaps.tsv ../../00.RawData/R6_Feature.bed
../../Merged.Gaps.tsv  do exist!
Sample_9-1     1004     177935