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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| #!/usr/bin/env | ||
| ''' | ||
| Extract rRNA coordinates from GTF | ||
| ''' | ||
| import sys | ||
| import GTF | ||
| import numpy as np | ||
| import pandas as pd | ||
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| def main(GENCODE): | ||
| gc = GTF.dataframe(GENCODE) | ||
| gc.gene_id = gc.gene_id.replace(to_replace=r'\.[0-9]+', value='', regex=True) | ||
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| idx = (gc.feature == 'transcript') & gc.transcript_type.str.contains('rRNA') | ||
| rRNA = gc.ix[idx, ['seqname','start','end','transcript_id','gene_name', 'strand']] | ||
| rRNA.start = rRNA.start.astype(int) | ||
| rRNA.end = rRNA.end.astype(int) | ||
| rRNA.sort_values(by=['seqname','start','end'], inplace=True) | ||
| rRNA.to_csv('rRNA_transcripts.bed', sep='\t', header=False, index=False) | ||
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| idx = (gc.feature == 'gene') & gc.gene_type.str.contains('rRNA') | ||
| rRNA = gc.ix[idx, ['seqname','start','end','gene_id','gene_name', 'strand']] | ||
| rRNA.start = rRNA.start.astype(int) | ||
| rRNA.end = rRNA.end.astype(int) | ||
| rRNA.sort_values(by=['seqname','start','end'], inplace=True) | ||
| rRNA.to_csv('rRNA_genes.bed', sep='\t', header=False, index=False) | ||
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||
| if __name__ == '__main__': | ||
| main(sys.argv[1]) | ||
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| #!/usr/bin/env | ||
| ''' | ||
| Extract tRNA coordinates from GTF | ||
| ''' | ||
| import sys | ||
| import GTF | ||
| import numpy as np | ||
| import pandas as pd | ||
|
|
||
| def main(GENCODE): | ||
| gc = GTF.dataframe(GENCODE) | ||
| gc.gene_id = gc.gene_id.replace(to_replace=r'\.[0-9]+', value='', regex=True) | ||
|
|
||
| idx = (gc.feature == 'transcript') & gc.transcript_type.str.contains('tRNA') | ||
| tRNA = gc.ix[idx, ['seqname','start','end','transcript_id','gene_name', 'strand']] | ||
| tRNA.start = tRNA.start.astype(int) | ||
| tRNA.end = tRNA.end.astype(int) | ||
| tRNA.sort_values(by=['seqname','start','end'], inplace=True) | ||
| tRNA.to_csv('tRNA_transcripts.bed', sep='\t', header=False, index=False) | ||
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||
| idx = (gc.feature == 'gene') & gc.gene_type.str.contains('tRNA') | ||
| tRNA = gc.ix[idx, ['seqname','start','end','gene_id','gene_name', 'strand']] | ||
| tRNA.start = tRNA.start.astype(int) | ||
| tRNA.end = tRNA.end.astype(int) | ||
| tRNA.sort_values(by=['seqname','start','end'], inplace=True) | ||
| tRNA.to_csv('tRNA_genes.bed', sep='\t', header=False, index=False) | ||
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||
| if __name__ == '__main__': | ||
| main(sys.argv[1]) | ||
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