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find and replace in first column

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# 1  
Old 04-30-2010
find and replace in first column
Dear All
I need help with find and replacing a string:..

In the following example of a file named say <filename.gff> with 9 columns
Code:
1       ensembl chromosome      1       300239041       .       .       .       ID=1;Name=chromosome:AGPv1:1:1:300239041:1
1       ensembl exon    3       104     .       +       .       Parent=GRMZM2G060082_T01;Name=GRMZM2G060082_E07
1       ensembl gene    3       3807    .       +       .       ID=GRMZM2G060082;Name=GRMZM2G060082;biotype=protein_coding
1       ensembl mRNA    3       3807    .       +       .       ID=GRMZM2G060082_T01;Parent=GRMZM2G060082;Name=GRMZM2G060082_T01;biotype=protein_coding
1       ensembl intron  105     199     .       +       .       Parent=GRMZM2G060082_T01
3       ensembl exon    200     313     .       +       .       Parent=GRMZM2G060082_T01;Name=GRMZM2G060082_E06
3       ensembl CDS     230     313     .       +       .       Parent=GRMZM2G060082_T01;Name=CDS.98360
3       ensembl intron  314     421     .       +       .       Parent=GRMZM2G060082_T01
3       ensembl CDS     422     604     .       +       0       Parent=GRMZM2G060082_T01;Name=CDS.98361
3       ensembl exon    422     604     .       +       .       Parent=GRMZM2G060082_T01;Name=GRMZM2G060082_E05



I need to convert all the "1" in column one to "chr1" and all the "3" in column one to "chr3"
I used the command
Code:
sed 's/1/chr1/' <filename.gff>

to change the first occurence of 1 to chr1, this worked dandy. The same command will not work for "3" since '3' occurs in line 2 in the 4th field and some other places too. How can I find and replace 3 with chr3 only in the first field (column)?

thanks much
Siva
# 2  
Old 04-30-2010
Code:
xxx@yyyy:~/test> cat filname.gff
1       ensembl chromosome      1       300239041       .       .       .       ID=1;Name=chromosome:AGPv1:1:1:300239041:1
1       ensembl exon    3       104     .       +       .       Parent=GRMZM2G060082_T01;Name=GRMZM2G060082_E07
1       ensembl gene    3       3807    .       +       .       ID=GRMZM2G060082;Name=GRMZM2G060082;biotype=protein_coding
1       ensembl mRNA    3       3807    .       +       .       ID=GRMZM2G060082_T01;Parent=GRMZM2G060082;Name=GRMZM2G060082_T01;biotype=protein_coding
1       ensembl intron  105     199     .       +       .       Parent=GRMZM2G060082_T01
3       ensembl exon    200     313     .       +       .       Parent=GRMZM2G060082_T01;Name=GRMZM2G060082_E06
3       ensembl CDS     230     313     .       +       .       Parent=GRMZM2G060082_T01;Name=CDS.98360
3       ensembl intron  314     421     .       +       .       Parent=GRMZM2G060082_T01
3       ensembl CDS     422     604     .       +       0       Parent=GRMZM2G060082_T01;Name=CDS.98361
3       ensembl exon    422     604     .       +       .       Parent=GRMZM2G060082_T01;Name=GRMZM2G060082_E05

if you just want to replace the first column try
Code:
xxx@yyyy:~/test> sed 's/^\([13]\)/chr\1/' filname.gff
chr1       ensembl chromosome      1       300239041       .       .       .       ID=1;Name=chromosome:AGPv1:1:1:300239041:1
chr1       ensembl exon    3       104     .       +       .       Parent=GRMZM2G060082_T01;Name=GRMZM2G060082_E07
chr1       ensembl gene    3       3807    .       +       .       ID=GRMZM2G060082;Name=GRMZM2G060082;biotype=protein_coding
chr1       ensembl mRNA    3       3807    .       +       .       ID=GRMZM2G060082_T01;Parent=GRMZM2G060082;Name=GRMZM2G060082_T01;biotype=protein_coding
chr1       ensembl intron  105     199     .       +       .       Parent=GRMZM2G060082_T01
chr3       ensembl exon    200     313     .       +       .       Parent=GRMZM2G060082_T01;Name=GRMZM2G060082_E06
chr3       ensembl CDS     230     313     .       +       .       Parent=GRMZM2G060082_T01;Name=CDS.98360
chr3       ensembl intron  314     421     .       +       .       Parent=GRMZM2G060082_T01
chr3       ensembl CDS     422     604     .       +       0       Parent=GRMZM2G060082_T01;Name=CDS.98361
chr3       ensembl exon    422     604     .       +       .       Parent=GRMZM2G060082_T01;Name=GRMZM2G060082_E05

Last edited by n.wawerek; 04-30-2010 at 06:29 AM.. Reason: failed to read correct the first time
# 3  
Old 05-01-2010
Hello
Thanks, I am reading up a bit on regular expressions and patterns. Hope to get better in this.

Siva
# 4  
Old 05-01-2010
Or:
Code:
sed 's/^[13]/chr&/'

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