export_gff3_feature

This python script parses features within .gff and .gff3 annotation files and prints the feature type and sequence.

Use the following parameters to use this program.

--source_gff Enter the filepath of the file.

--type Enter the type of attribute

--attribute Provide the type of the value.

--value Provide the gene value or other feature to return.

Example input and output

$ python export_gff3_feature.py --source_gff=/home/jzuker1/final/Saccharomyces_cerevisiae_S288C.annotation.gff --type=gene --attribute=ID --value=YAL068W

gene:ID:YAL068W chrI CACTCACATCATTATGCACGGCACTTGCCTCAGCGG TCTATACCCTGTGCCATTTACCCATAACGCCCATCATTATCCACATTTTGATATCTATATCTCATTCGGCGGTCCCAAAT ATTGTATAACTGCCCTTAATACATACGTTATACCACTTTTGCACCATATACTTACCACTCCATTTATATACACTTATGTC AATATTACAGAAAAATCCCCACAAAAATCACCTAAACATAAAAATATTCTAC

$ python export_gff3_feature.py --source_gff=/home/jzuker1/final/Saccharomyces_cerevisiae_S288C.annotation.gff --type=gene --attribute=ID --value=YAL063C-A

gene:ID:YAL063C-A chrI TAGGTCGAAAATTTAAGGCCACATAAATCCAGAGCCCGCAACTTGGATAGGTATTTACTTGATTTTTAGTTTG CTTTCAATAGTGTCGTGAAATTATAAAGTACGCCGCATATATATCTTGATTAGTTAAAAATAGCAGTGTTCAATGATGAT TTGATAGGGTTCATAACTGGTACCAGCGTAGTACAATTACGATTATCCATGAACATAAAAGTGGTTTAAGTACTATATAT CAGTGAAGCTTCAAAGTAAGCAAACGAGATACCAAGATCTTGTAGGACCAC

$ python export_gff3_feature.py --source_gff=/home/jzuker1/final/Saccharomyces_cerevisiae_S288C.annotation.gff --type=gene --attribute=ID --value=YAL065C

gene:ID:YAL065C chrI GCCATTAACTAACAAGAGAATTAATAATGTTAAAACACAGATACCTCGAAACAAACTCTATGTAAACACTTATTTTATT GTGGTAATATTTTTTGATAACAACACATCTGAAACAAAATAATGCAAAGCCGAATAGTTAGGCTAAAAATGTACTCTTAG ACATTTAAAAAGGTTTATGAATCCTATGGTATTTAATATATTAAAGAACGAAGTAAATGGGAAAAAATGTGTAAACACTA TAAGCGTGATGATAGAATTATTAATATAAGATGATGCCGTGCGTTTACCATACGATTGCCAGCAATACGGTGGAAATAAA AACACTTATGCCATTATTGGTCAACAGACCATTGGCAATACCAACGTAGGTTGAGATTT

An example where the feature does not exist within the file

$ python export_gff3_feature.py --source_gff=/home/jzuker1/final/Saccharomyces_cerevisiae_S288C.annotation.gff --type=ARS --attribute=ID --value=ARS102FS

Sorry, no matches were found. ARS:ID:ARS102FS