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Rephrased to answer the question I wanted to ask but hadn't made clear originally; included an awk command to make the conversion
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terdon ♦
terdon ♦
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this is the swift standard primer file. You are a bit off in your interpretation of the columns (seems like you missed one as there are 12 columns, not 11 which threw everything off):

  1. Chromosome

  2. Target Start

  3. Target Stop

  4. Target Name (change which affected everything downstream in counting)

  5. 5' Primer Start

  6. 5' Primer Stop

  7. 5' Primer Name

  8. 3' Primer Start

  9. 3' Primer Stop

  10. 3' Primer Name

  11. 5' Primer Sequence

  12. 3' Primer Sequence

To convert to a BEDPE describing the primer locations, you only will need the first 4 columns 1, 5, 6, 8, and the9 (and optionally 4). The last letter of the Region name for the denotes the strand orientation of the region. For example Region 1 has _F denoting forward or (+) strand for BEDPE usage, while region 2 has _R in name denoting reverse or (-) strand for BEDPE. Putting all this together, you can convert to BEDPE with:

$ awk -v OFS="\t" '{ 
            o="."; 
            if($4~/_F\//){
                o="+"
            }
            else if($4~/_R\//){
                o="-"
            } 
            print $1,$5,$6,$1,$8,$9,$4,".",o}' foo.masterfile
1   43814932    43814951    1   43815064    43815081    MPL_S505N-A519T_F/2 .   +
1   115256457   115256480   1   115256576   115256602   NRAS_G60-S65_new_R/1    .   -

this is the swift standard primer file. You are a bit off in your interpretation of the columns (seems like you missed one as there are 12 columns, not 11 which threw everything off):

  1. Chromosome

  2. Target Start

  3. Target Stop

  4. Target Name (change which affected everything downstream in counting)

  5. 5' Primer Start

  6. 5' Primer Stop

  7. 5' Primer Name

  8. 3' Primer Start

  9. 3' Primer Stop

  10. 3' Primer Name

  11. 5' Primer Sequence

  12. 3' Primer Sequence

To convert to BEDPE you only will need the first 4 columns, and the last letter of the Region name denotes the strand orientation of the region. For example Region 1 has _F denoting forward or (+) strand for BEDPE usage, while region 2 has _R in name denoting reverse or (-) strand for BEDPE.

this is the swift standard primer file. You are a bit off in your interpretation of the columns (seems like you missed one as there are 12 columns, not 11 which threw everything off):

  1. Chromosome

  2. Target Start

  3. Target Stop

  4. Target Name (change which affected everything downstream in counting)

  5. 5' Primer Start

  6. 5' Primer Stop

  7. 5' Primer Name

  8. 3' Primer Start

  9. 3' Primer Stop

  10. 3' Primer Name

  11. 5' Primer Sequence

  12. 3' Primer Sequence

To convert to a BEDPE describing the primer locations, you only will need columns 1, 5, 6, 8, and 9 (and optionally 4). The last letter of the Region name for the denotes the strand orientation of the region. For example Region 1 has _F denoting forward or (+) strand for BEDPE usage, while region 2 has _R in name denoting reverse or (-) strand for BEDPE. Putting all this together, you can convert to BEDPE with:

$ awk -v OFS="\t" '{ 
            o="."; 
            if($4~/_F\//){
                o="+"
            }
            else if($4~/_R\//){
                o="-"
            } 
            print $1,$5,$6,$1,$8,$9,$4,".",o}' foo.masterfile
1   43814932    43814951    1   43815064    43815081    MPL_S505N-A519T_F/2 .   +
1   115256457   115256480   1   115256576   115256602   NRAS_G60-S65_new_R/1    .   -
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d_kennetz
d_kennetz
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  • 18

this is the swift standard primer file. You are a bit off in your interpretation of the columns (seems like you missed one as there are 12 columns, not 11 which threw everything off):

  1. Chromosome

  2. Target Start

  3. Target Stop

  4. Target Name (change which affected everything downstream in counting)

  5. 5' Primer Start

  6. 5' Primer Stop

  7. 5' Primer Name

  8. 3' Primer Start

  9. 3' Primer Stop

  10. 3' Primer Name

  11. 5' Primer Sequence

  12. 3' Primer Sequence

To convert to BEDPE you only will need the first 4 columns, and the last letter of the Region name denotes the strand orientation of the region. For example Region 1 has _F denoting forward or (+) strand for BEDPE usage, while region 2 has _R in name denoting reverse or (-) strand for BEDPE.